jBio 0.8

Table of Contents

jBio

This manual is for jBio (version 0.8, 20 February 2009), which is `BioPerl in JavaScript'.

Copyright © 2008 László Kaján.

Permission is granted to copy, distribute and/or modify this document under the terms of the GNU Free Documentation License, Version 1.2 or any later version published by the Free Software Foundation; with no Invariant Sections, no Front-Cover Texts, and no Back-Cover Texts. A copy of the license is included in the section entitled “GNU Free Documentation License”.

1 Abstract

The last section to be filled.

2 Introduction

jBio is BioPerl (pmid12368254) in JavaScript.

3 Systems and methods

3.1 Requirements

jBio requires jQuery.

3.2 Namespaces

Namespaces are mostly implemented as empty functions. A class (i.e. prototype constructor) can also act as a namespace. 

var jBio = window.jBio = function(){ /* namespace */ };

3.2.1 jBio

— Namespace: jBio

jBio namespace.

All jBio code is found within this namespace.

Definition at line 18 of file jbio.js.

— Variable of jBio: Object _cache

Data cache.

— Function on jBio: jBio.Root.SeqIO SeqIO (Object __p)

Creates the appropriate sequence format adapter for the format requested.

Parameters:
__p
Parameter hash:
String format
File format.
String url
URL to open for reading.
String alphabet
Alphabet, one of ‘dna’, ‘rna’, or ‘protein’. If not given, the code tries to guess the alphabet.

Returns:
Sequence IO instance.
Definition at line 3369 of file jbio.js.

— Function on jBio: Object data (Object __subj, String __name, Object __data)

Stores into the global jBio data cache.

Parameters:
__subj
Object instance to store data for.
__name
Name of data slot. Optional.
__data
Payload data. Optional.

Returns:
Payload data for named slot of __name is given, UUID of __subj otherwise.
Use this to avoid circular references. Adapted from jQuery. Do not use for DOM elements, use jQuery.data() for that.

Definition at line 57 of file jbio.js.

— Function on jBio: void removeData (Object __subj, String __name)

Removes data from the global jBio data cache.

Parameters:
__subj
Object instance to remove stored data for.
__name
Name of data slot.
If the last data element is removed from the slot, the slot is removed as well.

Definition at line 97 of file jbio.js.

3.2.2 jBio.Annotation

— Namespace: jBio.Annotation

jBio.Annotation namespace.

Definition at line 2087 of file jbio.js.

3.2.3 jBio.Annotation.XML

— Namespace: jBio.Annotation.XML

jBio.Annotation.XML namespace.

Definition at line 2253 of file jbio.js.

3.2.4 jBio.Factory

— Namespace: jBio.Factory

jBio.Factory namespace.

Definition at line 927 of file jbio.js.

3.2.5 jBio.Graphics

— Namespace: jBio.Graphics

jBio.Graphics namespace.

Definition at line 18 of file jbio.graphics.js.

3.2.6 jBio.Graphics.DOM

— Namespace: jBio.Graphics.DOM

jBio.Graphics.DOM namespace.

Definition at line 140 of file jbio.graphics.dom.js.

— Variable of jBio.Graphics.DOM: String RESOURCEURL

URL to resources. Default: ‘/jbio/resources’.

3.2.7 jBio.Graphics.Exception

— Namespace: jBio.Graphics.Exception

jBio.Graphics.Exception namespace.

Definition at line 27 of file jbio.graphics.js.

3.2.8 jBio.Graphics.Glyph

— Namespace: jBio.Graphics.Glyph

jBio.Graphics.Glyph namespace.

Definition at line 17 of file jbio.graphics.glyph.js.

3.2.9 jBio.Location

— Namespace: jBio.Location

jBio.Location namespace.

Definition at line 658 of file jbio.js.

3.2.10 jBio.Location.Ppxml

— Namespace: jBio.Location.Ppxml

jBio.Location.Ppxml namespace.

Definition at line 1468 of file jbio.js.

3.2.11 jBio.Ontology

— Namespace: jBio.Ontology

jBio.Ontology namespace.

Definition at line 649 of file jbio.js.

3.2.12 jBio.SeqFeature

— Namespace: jBio.SeqFeature

jBio.SeqFeature namespace.

Definition at line 894 of file jbio.js.

3.2.13 jBio.SeqFeature.Alignment

— Namespace: jBio.SeqFeature.Alignment

jBio.SeqFeature.Alignment namespace.

Definition at line 1862 of file jbio.js.

3.2.14 jBio.SeqFeature.DisoReg

— Namespace: jBio.SeqFeature.DisoReg

jBio.SeqFeature.DisoReg namespace.

Definition at line 1776 of file jbio.js.

3.2.15 jBio.SeqFeature.SolvAcc

— Namespace: jBio.SeqFeature.SolvAcc

jBio.SeqFeature.SolvAcc namespace.

Definition at line 1819 of file jbio.js.

3.3 Classes

Classes are presented in a rough order of dependence, base classes listed first.

In this document class refers to a JavaScript constructor that is used to create a prototype, e.g. ‘jBio.Root’ or ‘jBio.Seq’. Constructors that create operational instances - such as ‘jBio.Seq_FAC()’ - are not considered classes and are referred to as constructors.

Base classes are given following a `:' after the class name. Class member names beginning with `_' are private or protected. Direct access to such members is not expected and is discouraged unless you know what you are doing. Private or protected members, apart of a few examples, are not listed in this document. Inherited methods are indicated in derived classes when (re-)implemented. Abstract member functions (member functions with no implementation) are indicated with `=0'.

Optional arguments are listed with the default value given after `='. Accessors take at most one argument. If a value is given, the property is updated. The resulting value of the property is returned.

3.3.1 jBio.Alphabet

— Class: jBio.Alphabet : jBio.Root

Alphabet.

This should follow Bio::Symbol::AlphabetI, but it does not.

Definition at line 1555 of file jbio.js.

— Variable of jBio.Alphabet: String classname
— Variable of jBio.Alphabet: Array of String parents
— Function on jBio.Alphabet: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.Alphabet: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.Alphabet: unknown toString ()

3.3.2 jBio.AnnotatableI

— Class: jBio.AnnotatableI : jBio.Root

Class with annotations.

Should be called AnnotatedI.

Definition at line 775 of file jbio.js.

— Variable of jBio.AnnotatableI: String classname
— Variable of jBio.AnnotatableI: Array of String parents
— Function on jBio.AnnotatableI: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.AnnotatableI: unknown annotation ()
— Function on jBio.AnnotatableI: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

3.3.3 jBio.Annotation.Collection

— Class: jBio.Annotation.Collection : jBio.Root, jBio.AnnotationCollectionI, jBio.AnnotationI

Set of annotations organised by `keys'.

Definition at line 2436 of file jbio.js.

— Variable of jBio.Annotation.Collection: String classname
— Variable of jBio.Annotation.Collection: Array of String parents
— Function on jBio.Annotation.Collection: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.Annotation.Collection: unknown _typemap ()
— Function on jBio.Annotation.Collection: unknown add_Annotation ()
— Function on jBio.Annotation.Collection: unknown as_text ()
— Function on jBio.Annotation.Collection: unknown flatten_Annotations ()
— Function on jBio.Annotation.Collection: unknown get_Annotations ()
— Function on jBio.Annotation.Collection: unknown get_all_Annotations ()
— Function on jBio.Annotation.Collection: unknown get_all_annotation_keys ()
— Function on jBio.Annotation.Collection: unknown get_num_of_annotations ()
— Function on jBio.Annotation.Collection: unknown hash_tree ()
— Function on jBio.Annotation.Collection: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.Annotation.Collection: unknown remove_Annotations ()
— Function on jBio.Annotation.Collection: unknown tagname ()

3.3.4 jBio.Annotation.Collection.Ppxml

— Class: jBio.Annotation.Collection.Ppxml : jBio.Root, jBio.AnnotationCollectionI, jBio.AnnotationI, jBio.XMLelementI

Annotation collection for features with reliability scores.

Base class for further specialisation.

Definition at line 2666 of file jbio.js.

— Variable of jBio.Annotation.Collection.Ppxml: String classname
— Variable of jBio.Annotation.Collection.Ppxml: Array of String parents
— Function on jBio.Annotation.Collection.Ppxml: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.Annotation.Collection.Ppxml: unknown add_Annotation ()
— Function on jBio.Annotation.Collection.Ppxml: unknown as_text ()
— Function on jBio.Annotation.Collection.Ppxml: unknown getElementsByTagNameAndAttr ()
— Function on jBio.Annotation.Collection.Ppxml: unknown get_Annotations ()
— Function on jBio.Annotation.Collection.Ppxml: unknown get_all_annotation_keys ()
— Function on jBio.Annotation.Collection.Ppxml: unknown get_num_of_annotations ()
— Function on jBio.Annotation.Collection.Ppxml: unknown hash_tree ()
— Function on jBio.Annotation.Collection.Ppxml: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.Annotation.Collection.Ppxml: unknown remove_Annotations ()
— Function on jBio.Annotation.Collection.Ppxml: unknown tagname ()
— Function on jBio.Annotation.Collection.Ppxml: unknown xml_instance ()

3.3.5 jBio.Annotation.Collection.Ppxml.Alignment

— Class: jBio.Annotation.Collection.Ppxml.Alignment : jBio.Root, jBio.Annotation.Collection.Ppxml

Annotation collection for a PredictProtein XML alignment.

Definition at line 2785 of file jbio.js.

— Variable of jBio.Annotation.Collection.Ppxml.Alignment: String classname
— Variable of jBio.Annotation.Collection.Ppxml.Alignment: Array of String parents
— Function on jBio.Annotation.Collection.Ppxml.Alignment: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.Annotation.Collection.Ppxml.Alignment: unknown add_Annotation ()
— Function on jBio.Annotation.Collection.Ppxml.Alignment: unknown as_text ()
— Function on jBio.Annotation.Collection.Ppxml.Alignment: unknown getElementsByTagNameAndAttr ()
— Function on jBio.Annotation.Collection.Ppxml.Alignment: unknown get_Annotations ()
— Function on jBio.Annotation.Collection.Ppxml.Alignment: unknown get_all_annotation_keys ()
— Function on jBio.Annotation.Collection.Ppxml.Alignment: unknown get_num_of_annotations ()
— Function on jBio.Annotation.Collection.Ppxml.Alignment: unknown hash_tree ()
— Function on jBio.Annotation.Collection.Ppxml.Alignment: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.Annotation.Collection.Ppxml.Alignment: unknown remove_Annotations ()
— Function on jBio.Annotation.Collection.Ppxml.Alignment: unknown tagname ()
— Function on jBio.Annotation.Collection.Ppxml.Alignment: unknown xml_instance ()

3.3.6 jBio.Annotation.Collection.Ppxml.DisoReg

— Class: jBio.Annotation.Collection.Ppxml.DisoReg : jBio.Root, jBio.Annotation.Collection.Ppxml.FeatWRel

Annotation collection for a disordered region feature.

Wrapper for the respective data structure in a PredictProtein XML document.

Definition at line 2723 of file jbio.js.

— Variable of jBio.Annotation.Collection.Ppxml.DisoReg: String classname
— Variable of jBio.Annotation.Collection.Ppxml.DisoReg: Array of String parents
— Function on jBio.Annotation.Collection.Ppxml.DisoReg: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.Annotation.Collection.Ppxml.DisoReg: unknown add_Annotation ()
— Function on jBio.Annotation.Collection.Ppxml.DisoReg: unknown as_text ()
— Function on jBio.Annotation.Collection.Ppxml.DisoReg: unknown getElementsByTagNameAndAttr ()
— Function on jBio.Annotation.Collection.Ppxml.DisoReg: unknown get_Annotations ()
— Function on jBio.Annotation.Collection.Ppxml.DisoReg: unknown get_all_annotation_keys ()
— Function on jBio.Annotation.Collection.Ppxml.DisoReg: unknown get_num_of_annotations ()
— Function on jBio.Annotation.Collection.Ppxml.DisoReg: unknown hash_tree ()
— Function on jBio.Annotation.Collection.Ppxml.DisoReg: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.Annotation.Collection.Ppxml.DisoReg: unknown remove_Annotations ()
— Function on jBio.Annotation.Collection.Ppxml.DisoReg: unknown tagname ()
— Function on jBio.Annotation.Collection.Ppxml.DisoReg: unknown xml_instance ()

3.3.7 jBio.Annotation.Collection.Ppxml.FeatWRel

— Class: jBio.Annotation.Collection.Ppxml.FeatWRel : jBio.Root, jBio.Annotation.Collection.Ppxml
— Variable of jBio.Annotation.Collection.Ppxml.FeatWRel: String classname
— Variable of jBio.Annotation.Collection.Ppxml.FeatWRel: Array of String parents
— Function on jBio.Annotation.Collection.Ppxml.FeatWRel: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.Annotation.Collection.Ppxml.FeatWRel: unknown add_Annotation ()
— Function on jBio.Annotation.Collection.Ppxml.FeatWRel: unknown as_text ()
— Function on jBio.Annotation.Collection.Ppxml.FeatWRel: unknown getElementsByTagNameAndAttr ()
— Function on jBio.Annotation.Collection.Ppxml.FeatWRel: unknown get_Annotations ()
— Function on jBio.Annotation.Collection.Ppxml.FeatWRel: unknown get_all_annotation_keys ()
— Function on jBio.Annotation.Collection.Ppxml.FeatWRel: unknown get_num_of_annotations ()
— Function on jBio.Annotation.Collection.Ppxml.FeatWRel: unknown hash_tree ()
— Function on jBio.Annotation.Collection.Ppxml.FeatWRel: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.Annotation.Collection.Ppxml.FeatWRel: unknown remove_Annotations ()
— Function on jBio.Annotation.Collection.Ppxml.FeatWRel: unknown tagname ()
— Function on jBio.Annotation.Collection.Ppxml.FeatWRel: unknown xml_instance ()

3.3.8 jBio.Annotation.Collection.Ppxml.SolvAcc

— Class: jBio.Annotation.Collection.Ppxml.SolvAcc : jBio.Root, jBio.Annotation.Collection.Ppxml.FeatWRel

Annotation collection for a solvent accessibility feature.

Wrapper for the respective data structure in a PredictProtein XML document.

Definition at line 2754 of file jbio.js.

— Variable of jBio.Annotation.Collection.Ppxml.SolvAcc: String classname
— Variable of jBio.Annotation.Collection.Ppxml.SolvAcc: Array of String parents
— Function on jBio.Annotation.Collection.Ppxml.SolvAcc: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.Annotation.Collection.Ppxml.SolvAcc: unknown add_Annotation ()
— Function on jBio.Annotation.Collection.Ppxml.SolvAcc: unknown as_text ()
— Function on jBio.Annotation.Collection.Ppxml.SolvAcc: unknown getElementsByTagNameAndAttr ()
— Function on jBio.Annotation.Collection.Ppxml.SolvAcc: unknown get_Annotations ()
— Function on jBio.Annotation.Collection.Ppxml.SolvAcc: unknown get_all_annotation_keys ()
— Function on jBio.Annotation.Collection.Ppxml.SolvAcc: unknown get_num_of_annotations ()
— Function on jBio.Annotation.Collection.Ppxml.SolvAcc: unknown hash_tree ()
— Function on jBio.Annotation.Collection.Ppxml.SolvAcc: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.Annotation.Collection.Ppxml.SolvAcc: unknown remove_Annotations ()
— Function on jBio.Annotation.Collection.Ppxml.SolvAcc: unknown tagname ()
— Function on jBio.Annotation.Collection.Ppxml.SolvAcc: unknown xml_instance ()

3.3.9 jBio.Annotation.Collection.UniProtKBXML

— Class: jBio.Annotation.Collection.UniProtKBXML : jBio.Root, jBio.AnnotationCollectionI, jBio.AnnotationI, jBio.XMLelementI

Annotation collection in a UniProtKB XML document.

Not implemented.

Definition at line 2592 of file jbio.js.

— Variable of jBio.Annotation.Collection.UniProtKBXML: String classname
— Variable of jBio.Annotation.Collection.UniProtKBXML: Array of String parents
— Function on jBio.Annotation.Collection.UniProtKBXML: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.Annotation.Collection.UniProtKBXML: unknown add_Annotation ()
— Function on jBio.Annotation.Collection.UniProtKBXML: unknown as_text ()
— Function on jBio.Annotation.Collection.UniProtKBXML: unknown getElementsByTagNameAndAttr ()
— Function on jBio.Annotation.Collection.UniProtKBXML: unknown get_Annotations ()
— Function on jBio.Annotation.Collection.UniProtKBXML: unknown get_all_annotation_keys ()
— Function on jBio.Annotation.Collection.UniProtKBXML: unknown get_num_of_annotations ()
— Function on jBio.Annotation.Collection.UniProtKBXML: unknown hash_tree ()
— Function on jBio.Annotation.Collection.UniProtKBXML: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.Annotation.Collection.UniProtKBXML: unknown remove_Annotations ()
— Function on jBio.Annotation.Collection.UniProtKBXML: unknown tagname ()
— Function on jBio.Annotation.Collection.UniProtKBXML: unknown xml_instance ()

3.3.10 jBio.Annotation.SimpleValue

— Class: jBio.Annotation.SimpleValue : jBio.Root, jBio.AnnotationI

Scalar annotation value.

Definition at line 2110 of file jbio.js.

— Variable of jBio.Annotation.SimpleValue: String classname
— Variable of jBio.Annotation.SimpleValue: Array of String parents
— Function on jBio.Annotation.SimpleValue: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.Annotation.SimpleValue: unknown as_text ()
— Function on jBio.Annotation.SimpleValue: unknown hash_tree ()
— Function on jBio.Annotation.SimpleValue: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.Annotation.SimpleValue: unknown tag_term ()
— Function on jBio.Annotation.SimpleValue: unknown tagname ()
— Function on jBio.Annotation.SimpleValue: unknown value ()

3.3.11 jBio.Annotation.StructuredValue

— Class: jBio.Annotation.StructuredValue : jBio.Root, jBio.Annotation.SimpleValue

Annotation in a multidimensional array structure.

Definition at line 2172 of file jbio.js.

— Variable of jBio.Annotation.StructuredValue: String classname
— Variable of jBio.Annotation.StructuredValue: Array of String parents
— Function on jBio.Annotation.StructuredValue: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.Annotation.StructuredValue: unknown _to_text ()
— Function on jBio.Annotation.StructuredValue: unknown add_value ()
— Function on jBio.Annotation.StructuredValue: unknown as_text ()
— Function on jBio.Annotation.StructuredValue: unknown get_all_values ()
— Function on jBio.Annotation.StructuredValue: unknown get_values ()
— Function on jBio.Annotation.StructuredValue: unknown hash_tree ()
— Function on jBio.Annotation.StructuredValue: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.Annotation.StructuredValue: unknown tag_term ()
— Function on jBio.Annotation.StructuredValue: unknown tagname ()
— Function on jBio.Annotation.StructuredValue: unknown value ()

3.3.12 jBio.Annotation.TypeManager

— Class: jBio.Annotation.TypeManager : jBio.Root

“Annotation collection type manager.”

Definition at line 2376 of file jbio.js.

— Variable of jBio.Annotation.TypeManager: String classname
— Variable of jBio.Annotation.TypeManager: Array of String parents
— Function on jBio.Annotation.TypeManager: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.Annotation.TypeManager: unknown _add_type_map ()
— Function on jBio.Annotation.TypeManager: unknown is_valid ()
— Function on jBio.Annotation.TypeManager: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.Annotation.TypeManager: unknown type_for_key ()

3.3.13 jBio.Annotation.XML.BaseSimpleAttrValue

— Class: jBio.Annotation.XML.BaseSimpleAttrValue : jBio.Root, jBio.Annotation.SimpleValue, jBio.XMLelementI

Scalar annotation in an XML document.

The value is stored as an attribute of the underlying xml element.

Definition at line 2311 of file jbio.js.

— Variable of jBio.Annotation.XML.BaseSimpleAttrValue: String _attribute

Name of the attribute that holds the annotation value.

— Variable of jBio.Annotation.XML.BaseSimpleAttrValue: String classname
— Variable of jBio.Annotation.XML.BaseSimpleAttrValue: Array of String parents
— Function on jBio.Annotation.XML.BaseSimpleAttrValue: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.Annotation.XML.BaseSimpleAttrValue: unknown as_text ()
— Function on jBio.Annotation.XML.BaseSimpleAttrValue: unknown getElementsByTagNameAndAttr ()
— Function on jBio.Annotation.XML.BaseSimpleAttrValue: unknown hash_tree ()
— Function on jBio.Annotation.XML.BaseSimpleAttrValue: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.Annotation.XML.BaseSimpleAttrValue: unknown tag_term ()
— Function on jBio.Annotation.XML.BaseSimpleAttrValue: unknown tagname ()
— Function on jBio.Annotation.XML.BaseSimpleAttrValue: unknown value ()
— Function on jBio.Annotation.XML.BaseSimpleAttrValue: unknown xml_instance ()

3.3.14 jBio.Annotation.XML.SimpleAttrValue

— Class: jBio.Annotation.XML.SimpleAttrValue : jBio.Root, jBio.Annotation.XML.BaseSimpleAttrValue

Scalar annotation in an XML document.

The value is stored in the ‘value’ attribute of the xml_instance.

Definition at line 2345 of file jbio.js.

— Variable of jBio.Annotation.XML.SimpleAttrValue: String _attribute

Name of the attribute that holds the annotation value.

— Variable of jBio.Annotation.XML.SimpleAttrValue: String classname
— Variable of jBio.Annotation.XML.SimpleAttrValue: Array of String parents
— Function on jBio.Annotation.XML.SimpleAttrValue: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.Annotation.XML.SimpleAttrValue: unknown as_text ()
— Function on jBio.Annotation.XML.SimpleAttrValue: unknown getElementsByTagNameAndAttr ()
— Function on jBio.Annotation.XML.SimpleAttrValue: unknown hash_tree ()
— Function on jBio.Annotation.XML.SimpleAttrValue: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.Annotation.XML.SimpleAttrValue: unknown tag_term ()
— Function on jBio.Annotation.XML.SimpleAttrValue: unknown tagname ()
— Function on jBio.Annotation.XML.SimpleAttrValue: unknown value ()
— Function on jBio.Annotation.XML.SimpleAttrValue: unknown xml_instance ()

3.3.15 jBio.Annotation.XML.SimpleValue

— Class: jBio.Annotation.XML.SimpleValue : jBio.Root, jBio.Annotation.SimpleValue, jBio.XMLelementI

Scalar annotation in an XML document.

The value is stored in the text node of the xml_instance.

Definition at line 2273 of file jbio.js.

— Variable of jBio.Annotation.XML.SimpleValue: String classname
— Variable of jBio.Annotation.XML.SimpleValue: Array of String parents
— Function on jBio.Annotation.XML.SimpleValue: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.Annotation.XML.SimpleValue: unknown as_text ()
— Function on jBio.Annotation.XML.SimpleValue: unknown getElementsByTagNameAndAttr ()
— Function on jBio.Annotation.XML.SimpleValue: unknown hash_tree ()
— Function on jBio.Annotation.XML.SimpleValue: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.Annotation.XML.SimpleValue: unknown tag_term ()
— Function on jBio.Annotation.XML.SimpleValue: unknown tagname ()
— Function on jBio.Annotation.XML.SimpleValue: unknown value ()
— Function on jBio.Annotation.XML.SimpleValue: unknown xml_instance ()

3.3.16 jBio.AnnotationCollectionI

— Class: jBio.AnnotationCollectionI : jBio.Root, jBio.AnnotationI

Set of annotations organised by `keys'.

This class defined the interface.

Definition at line 742 of file jbio.js.

— Variable of jBio.AnnotationCollectionI: String classname
— Variable of jBio.AnnotationCollectionI: Array of String parents
— Function on jBio.AnnotationCollectionI: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.AnnotationCollectionI: unknown add_Annotation ()
— Function on jBio.AnnotationCollectionI: unknown as_text ()
— Function on jBio.AnnotationCollectionI: unknown get_Annotations ()
— Function on jBio.AnnotationCollectionI: unknown get_all_annotation_keys ()
— Function on jBio.AnnotationCollectionI: unknown get_num_of_annotations ()
— Function on jBio.AnnotationCollectionI: unknown hash_tree ()
— Function on jBio.AnnotationCollectionI: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.AnnotationCollectionI: unknown prototype ()
— Function on jBio.AnnotationCollectionI: unknown remove_Annotations ()
— Function on jBio.AnnotationCollectionI: unknown tagname ()

3.3.17 jBio.AnnotationI

— Class: jBio.AnnotationI : jBio.Root

Annotation.

Definition at line 709 of file jbio.js.

— Variable of jBio.AnnotationI: String classname
— Variable of jBio.AnnotationI: Array of String parents
— Function on jBio.AnnotationI: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.AnnotationI: unknown as_text ()
— Function on jBio.AnnotationI: unknown hash_tree ()
— Function on jBio.AnnotationI: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.AnnotationI: unknown tagname ()

3.3.18 jBio.DescribableI

— Class: jBio.DescribableI : jBio.Root

Class with description.

Pure abstract class.

Definition at line 1066 of file jbio.js.

— Variable of jBio.DescribableI: String classname
— Variable of jBio.DescribableI: Array of String parents
— Function on jBio.DescribableI: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.DescribableI: unknown description ()
— Function on jBio.DescribableI: unknown display_name ()
— Function on jBio.DescribableI: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

3.3.19 jBio.Exception

— Class: jBio.Exception : jBio.Root

Generic jBio exception class and constructor.

Use this to throw jBio exceptions: 

     if( __start === undefined ) throw new jBio.Exception('start is undefined');

Definition at line 188 of file jbio.js.

— Variable of jBio.Exception: String classname
— Variable of jBio.Exception: Array of String parents
— Function on jBio.Exception: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.Exception: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

3.3.20 jBio.Exception.Deprecated

— Class: jBio.Exception.Deprecated : jBio.Root

‘Deprecated’ exception class and constructor.

Definition at line 282 of file jbio.js.

— Variable of jBio.Exception.Deprecated: String classname
— Variable of jBio.Exception.Deprecated: Array of String parents
— Function on jBio.Exception.Deprecated: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.Exception.Deprecated: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

3.3.21 jBio.Exception.NaN

— Class: jBio.Exception.NaN : jBio.Root

‘Not a Number’ exception class and constructor.

Message produced: ‘'__p' is not a number (by type) but <typeof(__p)>’.

Definition at line 314 of file jbio.js.

— Variable of jBio.Exception.NaN: String classname
— Variable of jBio.Exception.NaN: Array of String parents
— Function on jBio.Exception.NaN: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.Exception.NaN: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

3.3.22 jBio.Exception.NotImplemented

— Class: jBio.Exception.NotImplemented : jBio.Root

‘Not Implemented’ exception class and constructor.

Definition at line 220 of file jbio.js.

— Variable of jBio.Exception.NotImplemented: String classname
— Variable of jBio.Exception.NotImplemented: Array of String parents
— Function on jBio.Exception.NotImplemented: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.Exception.NotImplemented: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

3.3.23 jBio.Exception.ReadOnly

— Class: jBio.Exception.ReadOnly : jBio.Root

‘Read Only’ exception class and constructor.

Definition at line 251 of file jbio.js.

— Variable of jBio.Exception.ReadOnly: String classname
— Variable of jBio.Exception.ReadOnly: Array of String parents
— Function on jBio.Exception.ReadOnly: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.Exception.ReadOnly: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

3.3.24 jBio.Factory.ObjectFactoryI

— Class: jBio.Factory.ObjectFactoryI : jBio.Root

Object factory.

Pure abstract class.

Definition at line 979 of file jbio.js.

— Variable of jBio.Factory.ObjectFactoryI: String classname
— Variable of jBio.Factory.ObjectFactoryI: Array of String parents
— Function on jBio.Factory.ObjectFactoryI: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.Factory.ObjectFactoryI: unknown craete_object ()
— Function on jBio.Factory.ObjectFactoryI: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.Factory.ObjectFactoryI: unknown type ()

3.3.25 jBio.Factory.SequenceFactoryI

— Class: jBio.Factory.SequenceFactoryI : jBio.Root, jBio.Factory.ObjectFactoryI

Sequence factory.

Pure abstract class.

Definition at line 1007 of file jbio.js.

— Variable of jBio.Factory.SequenceFactoryI: String classname
— Variable of jBio.Factory.SequenceFactoryI: Array of String parents
— Function on jBio.Factory.SequenceFactoryI: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.Factory.SequenceFactoryI: unknown craete_object ()
— Function on jBio.Factory.SequenceFactoryI: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.Factory.SequenceFactoryI: unknown type ()

3.3.26 jBio.Factory.SequenceStreamI

— Class: jBio.Factory.SequenceStreamI : jBio.Root

Sequence stream.

Pure abstract class.

Definition at line 948 of file jbio.js.

— Variable of jBio.Factory.SequenceStreamI: String classname
— Variable of jBio.Factory.SequenceStreamI: Array of String parents
— Function on jBio.Factory.SequenceStreamI: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.Factory.SequenceStreamI: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.Factory.SequenceStreamI: unknown next_seq ()
— Function on jBio.Factory.SequenceStreamI: unknown sequence_factory ()
— Function on jBio.Factory.SequenceStreamI: unknown write_seq ()

3.3.27 jBio.FeatureHolderI

— Class: jBio.FeatureHolderI : jBio.Root

Class with features.

Definition at line 845 of file jbio.js.

— Variable of jBio.FeatureHolderI: String classname
— Variable of jBio.FeatureHolderI: Array of String parents
— Function on jBio.FeatureHolderI: unknown _add_flattened_SeqFeatures ()
— Function on jBio.FeatureHolderI: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.FeatureHolderI: unknown add_SeqFeature ()
— Function on jBio.FeatureHolderI: unknown feature_count ()
— Function on jBio.FeatureHolderI: unknown get_SeqFeatures ()
— Function on jBio.FeatureHolderI: unknown get_all_SeqFeatures ()
— Function on jBio.FeatureHolderI: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.FeatureHolderI: unknown remove_SeqFeatures ()

3.3.28 jBio.Graphics.CollisionControl

— Class: jBio.Graphics.CollisionControl : jBio.Root

Drawing space manager.

Keeps track of allocated segments of the drawing space and finds empty space for more drawing.

Definition at line 695 of file jbio.graphics.js.

— Variable of jBio.Graphics.CollisionControl: String classname
— Variable of jBio.Graphics.CollisionControl: Array of String parents
— Function on jBio.Graphics.CollisionControl: unknown _add_collision ()
— Function on jBio.Graphics.CollisionControl: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.Graphics.CollisionControl: unknown _collides ()
— Function on jBio.Graphics.CollisionControl: unknown _collision_keys ()
— Function on jBio.Graphics.CollisionControl: unknown add_collision ()
— Function on jBio.Graphics.CollisionControl: unknown collides ()
— Function on jBio.Graphics.CollisionControl: unknown grids ()
— Function on jBio.Graphics.CollisionControl: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.Graphics.CollisionControl: unknown reset_bins ()

3.3.29 jBio.Graphics.DOM.Box_zoomer

— Class: jBio.Graphics.DOM.Box_zoomer : jBio.Root, jBio.Graphics.DOM.Zoomer

Live element resizing (zooming) for boxes.

Definition at line 1906 of file jbio.graphics.dom.glyph.js.

— Variable of jBio.Graphics.DOM.Box_zoomer: String classname
— Variable of jBio.Graphics.DOM.Box_zoomer: Array of String parents
— Function on jBio.Graphics.DOM.Box_zoomer: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.Graphics.DOM.Box_zoomer: unknown _zoom_face ()
— Function on jBio.Graphics.DOM.Box_zoomer: unknown do_zoom ()
— Function on jBio.Graphics.DOM.Box_zoomer: unknown domElement ()
— Function on jBio.Graphics.DOM.Box_zoomer: unknown height ()
— Function on jBio.Graphics.DOM.Box_zoomer: unknown iheight ()
— Function on jBio.Graphics.DOM.Box_zoomer: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.Graphics.DOM.Box_zoomer: unknown iwidth ()
— Function on jBio.Graphics.DOM.Box_zoomer: unknown left ()
— Function on jBio.Graphics.DOM.Box_zoomer: unknown llw ()
— Function on jBio.Graphics.DOM.Box_zoomer: unknown tlw ()
— Function on jBio.Graphics.DOM.Box_zoomer: unknown top ()
— Function on jBio.Graphics.DOM.Box_zoomer: unknown width ()

3.3.30 jBio.Graphics.DOM.Disulf_zoomer

— Class: jBio.Graphics.DOM.Disulf_zoomer : jBio.Root, jBio.Graphics.DOM.Zoomer

Live element resizing (zooming) for jBio.Graphics.DOM.Glyph.Disulfide.

Definition at line 1981 of file jbio.graphics.dom.glyph.js.

— Variable of jBio.Graphics.DOM.Disulf_zoomer: String classname
— Variable of jBio.Graphics.DOM.Disulf_zoomer: Array of String parents
— Function on jBio.Graphics.DOM.Disulf_zoomer: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.Graphics.DOM.Disulf_zoomer: unknown _zoom_face ()
— Function on jBio.Graphics.DOM.Disulf_zoomer: unknown blw ()
— Function on jBio.Graphics.DOM.Disulf_zoomer: unknown do_zoom ()
— Function on jBio.Graphics.DOM.Disulf_zoomer: unknown domElement ()
— Function on jBio.Graphics.DOM.Disulf_zoomer: unknown height ()
— Function on jBio.Graphics.DOM.Disulf_zoomer: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.Graphics.DOM.Disulf_zoomer: unknown left ()
— Function on jBio.Graphics.DOM.Disulf_zoomer: unknown llw ()
— Function on jBio.Graphics.DOM.Disulf_zoomer: unknown rlw ()
— Function on jBio.Graphics.DOM.Disulf_zoomer: unknown top ()
— Function on jBio.Graphics.DOM.Disulf_zoomer: unknown vlheight ()
— Function on jBio.Graphics.DOM.Disulf_zoomer: unknown vltop ()
— Function on jBio.Graphics.DOM.Disulf_zoomer: unknown width ()

3.3.31 jBio.Graphics.DOM.Faceted_zoomer

— Class: jBio.Graphics.DOM.Faceted_zoomer : jBio.Root, jBio.Graphics.DOM.Zoomer

Live element resizing (zooming) for faceted glyphs.

Definition at line 2060 of file jbio.graphics.dom.glyph.js.

— Variable of jBio.Graphics.DOM.Faceted_zoomer: String classname
— Variable of jBio.Graphics.DOM.Faceted_zoomer: Array of String parents
— Function on jBio.Graphics.DOM.Faceted_zoomer: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.Graphics.DOM.Faceted_zoomer: unknown _zoom_face ()
— Function on jBio.Graphics.DOM.Faceted_zoomer: unknown do_zoom ()
— Function on jBio.Graphics.DOM.Faceted_zoomer: unknown domElement ()
— Function on jBio.Graphics.DOM.Faceted_zoomer: unknown facet_data ()
— Function on jBio.Graphics.DOM.Faceted_zoomer: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.Graphics.DOM.Faceted_zoomer: unknown left ()
— Function on jBio.Graphics.DOM.Faceted_zoomer: unknown top ()

3.3.32 jBio.Graphics.DOM.Glyph

— Class: jBio.Graphics.DOM.Glyph : jBio.Root, jBio.Graphics.DOMbase, jBio.Graphics.DOMevents_binderI, jBio.Graphics.GlyphI

Base class for glyphs that are rendered through the document object model (DOM).

Definition at line 31 of file jbio.graphics.dom.glyph.js.

— Variable of jBio.Graphics.DOM.Glyph: String classname
— Variable of jBio.Graphics.DOM.Glyph: Array of String parents
— Function on jBio.Graphics.DOM.Glyph: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.Graphics.DOM.Glyph: unknown _evtgt_bind_from_hash ()
— Function on jBio.Graphics.DOM.Glyph: unknown _subfeat ()
— Function on jBio.Graphics.DOM.Glyph: unknown bgElement ()
— Function on jBio.Graphics.DOM.Glyph: unknown bgcolor ()
— Function on jBio.Graphics.DOM.Glyph: unknown bump ()
— Function on jBio.Graphics.DOM.Glyph: unknown collision_controller ()
— Function on jBio.Graphics.DOM.Glyph: unknown connector ()
— Function on jBio.Graphics.DOM.Glyph: unknown do_layout ()
— Function on jBio.Graphics.DOM.Glyph: unknown draw ()
— Function on jBio.Graphics.DOM.Glyph: unknown draw_box ()
— Function on jBio.Graphics.DOM.Glyph: unknown draw_component ()
— Function on jBio.Graphics.DOM.Glyph: unknown draw_track_key ()
— Function on jBio.Graphics.DOM.Glyph: unknown end ()
— Function on jBio.Graphics.DOM.Glyph: unknown escapeHTML ()
— Function on jBio.Graphics.DOM.Glyph: unknown evtgt_bind ()
— Function on jBio.Graphics.DOM.Glyph: unknown evtgt_innervate ()
— Function on jBio.Graphics.DOM.Glyph: unknown exceeds_depth ()
— Function on jBio.Graphics.DOM.Glyph: unknown factory ()
— Function on jBio.Graphics.DOM.Glyph: unknown feature ()
— Function on jBio.Graphics.DOM.Glyph: unknown feature_has_subparts ()
— Function on jBio.Graphics.DOM.Glyph: unknown fgcolor ()
— Function on jBio.Graphics.DOM.Glyph: unknown get_not_ignored_subparts ()
— Function on jBio.Graphics.DOM.Glyph: unknown get_visible_parts ()
— Function on jBio.Graphics.DOM.Glyph: unknown get_zoomer ()
— Function on jBio.Graphics.DOM.Glyph: unknown hbumppad ()
— Function on jBio.Graphics.DOM.Glyph: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.Graphics.DOM.Glyph: unknown layout_sort ()
— Function on jBio.Graphics.DOM.Glyph: unknown level ()
— Function on jBio.Graphics.DOM.Glyph: unknown llength ()
— Function on jBio.Graphics.DOM.Glyph: unknown make_key_name ()
— Function on jBio.Graphics.DOM.Glyph: unknown maxdepth ()
— Function on jBio.Graphics.DOM.Glyph: unknown no_subparts ()
— Function on jBio.Graphics.DOM.Glyph: unknown not_ignored_subparts ()
— Function on jBio.Graphics.DOM.Glyph: unknown overbumped ()
— Function on jBio.Graphics.DOM.Glyph: unknown pad_bottom ()
— Function on jBio.Graphics.DOM.Glyph: unknown pad_left ()
— Function on jBio.Graphics.DOM.Glyph: unknown pad_right ()
— Function on jBio.Graphics.DOM.Glyph: unknown pad_top ()
— Function on jBio.Graphics.DOM.Glyph: unknown panel ()
— Function on jBio.Graphics.DOM.Glyph: unknown partno ()
— Function on jBio.Graphics.DOM.Glyph: unknown parts ()
— Function on jBio.Graphics.DOM.Glyph: unknown point ()
— Function on jBio.Graphics.DOM.Glyph: unknown property ()
— Function on jBio.Graphics.DOM.Glyph: unknown start ()
— Function on jBio.Graphics.DOM.Glyph: unknown stop ()
— Function on jBio.Graphics.DOM.Glyph: unknown subfeat ()
— Function on jBio.Graphics.DOM.Glyph: unknown ticks ()
— Function on jBio.Graphics.DOM.Glyph: unknown tkcolor ()
— Function on jBio.Graphics.DOM.Glyph: unknown total_parts ()
— Function on jBio.Graphics.DOM.Glyph: unknown track2key ()
— Function on jBio.Graphics.DOM.Glyph: unknown track_index ()

3.3.33 jBio.Graphics.DOM.Glyph.Alignment

— Class: jBio.Graphics.DOM.Glyph.Alignment : jBio.Root, jBio.Graphics.DOM.Glyph.Generic

Glyph for alignments.

Definition at line 1578 of file jbio.graphics.dom.glyph.js.

— Variable of jBio.Graphics.DOM.Glyph.Alignment: String classname
— Variable of jBio.Graphics.DOM.Glyph.Alignment: Array of String parents
— Function on jBio.Graphics.DOM.Glyph.Alignment: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.Graphics.DOM.Glyph.Alignment: unknown _evtgt_bind_from_hash ()
— Function on jBio.Graphics.DOM.Glyph.Alignment: unknown _label ()
— Function on jBio.Graphics.DOM.Glyph.Alignment: unknown _subfeat ()
— Function on jBio.Graphics.DOM.Glyph.Alignment: unknown bgElement ()
— Function on jBio.Graphics.DOM.Glyph.Alignment: unknown bgcolor ()
— Function on jBio.Graphics.DOM.Glyph.Alignment: unknown bump ()
— Function on jBio.Graphics.DOM.Glyph.Alignment: unknown collision_controller ()
— Function on jBio.Graphics.DOM.Glyph.Alignment: unknown connector ()
— Function on jBio.Graphics.DOM.Glyph.Alignment: unknown do_layout ()
— Function on jBio.Graphics.DOM.Glyph.Alignment: unknown draw ()
— Function on jBio.Graphics.DOM.Glyph.Alignment: unknown draw_box ()
— Function on jBio.Graphics.DOM.Glyph.Alignment: unknown draw_component ()
— Function on jBio.Graphics.DOM.Glyph.Alignment: unknown draw_label ()
— Function on jBio.Graphics.DOM.Glyph.Alignment: unknown draw_track_key ()
— Function on jBio.Graphics.DOM.Glyph.Alignment: unknown end ()
— Function on jBio.Graphics.DOM.Glyph.Alignment: unknown escapeHTML ()
— Function on jBio.Graphics.DOM.Glyph.Alignment: unknown evtgt_bind ()
— Function on jBio.Graphics.DOM.Glyph.Alignment: unknown evtgt_innervate ()
— Function on jBio.Graphics.DOM.Glyph.Alignment: unknown exceeds_depth ()
— Function on jBio.Graphics.DOM.Glyph.Alignment: unknown factory ()
— Function on jBio.Graphics.DOM.Glyph.Alignment: unknown feature ()
— Function on jBio.Graphics.DOM.Glyph.Alignment: unknown feature_has_subparts ()
— Function on jBio.Graphics.DOM.Glyph.Alignment: unknown fgcolor ()
— Function on jBio.Graphics.DOM.Glyph.Alignment: unknown get_not_ignored_subparts ()
— Function on jBio.Graphics.DOM.Glyph.Alignment: unknown get_visible_parts ()
— Function on jBio.Graphics.DOM.Glyph.Alignment: unknown get_zoomer ()
— Function on jBio.Graphics.DOM.Glyph.Alignment: unknown hbumppad ()
— Function on jBio.Graphics.DOM.Glyph.Alignment: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.Graphics.DOM.Glyph.Alignment: unknown label ()
— Function on jBio.Graphics.DOM.Glyph.Alignment: unknown layout_sort ()
— Function on jBio.Graphics.DOM.Glyph.Alignment: unknown level ()
— Function on jBio.Graphics.DOM.Glyph.Alignment: unknown llength ()
— Function on jBio.Graphics.DOM.Glyph.Alignment: unknown make_key_name ()
— Function on jBio.Graphics.DOM.Glyph.Alignment: unknown maxdepth ()
— Function on jBio.Graphics.DOM.Glyph.Alignment: unknown no_subparts ()
— Function on jBio.Graphics.DOM.Glyph.Alignment: unknown not_ignored_subparts ()
— Function on jBio.Graphics.DOM.Glyph.Alignment: unknown overbumped ()
— Function on jBio.Graphics.DOM.Glyph.Alignment: unknown pad_bottom ()
— Function on jBio.Graphics.DOM.Glyph.Alignment: unknown pad_left ()
— Function on jBio.Graphics.DOM.Glyph.Alignment: unknown pad_right ()
— Function on jBio.Graphics.DOM.Glyph.Alignment: unknown pad_top ()
— Function on jBio.Graphics.DOM.Glyph.Alignment: unknown panel ()
— Function on jBio.Graphics.DOM.Glyph.Alignment: unknown partno ()
— Function on jBio.Graphics.DOM.Glyph.Alignment: unknown parts ()
— Function on jBio.Graphics.DOM.Glyph.Alignment: unknown point ()
— Function on jBio.Graphics.DOM.Glyph.Alignment: unknown property ()
— Function on jBio.Graphics.DOM.Glyph.Alignment: unknown start ()
— Function on jBio.Graphics.DOM.Glyph.Alignment: unknown stop ()
— Function on jBio.Graphics.DOM.Glyph.Alignment: unknown subfeat ()
— Function on jBio.Graphics.DOM.Glyph.Alignment: unknown ticks ()
— Function on jBio.Graphics.DOM.Glyph.Alignment: unknown tkcolor ()
— Function on jBio.Graphics.DOM.Glyph.Alignment: unknown total_parts ()
— Function on jBio.Graphics.DOM.Glyph.Alignment: unknown track2key ()
— Function on jBio.Graphics.DOM.Glyph.Alignment: unknown track_index ()

3.3.34 jBio.Graphics.DOM.Glyph.Arrow

— Class: jBio.Graphics.DOM.Glyph.Arrow : jBio.Root, jBio.Graphics.DOM.Glyph.Generic

Arrow glyph with major and minor ticks for scale.

Definition at line 471 of file jbio.graphics.dom.glyph.js.

— Variable of jBio.Graphics.DOM.Glyph.Arrow: static Object UNITS

This hash converts unit symbols to decimal value, e.g. M: 1e6.

— Variable of jBio.Graphics.DOM.Glyph.Arrow: String classname
— Variable of jBio.Graphics.DOM.Glyph.Arrow: Array of String parents
— Function on jBio.Graphics.DOM.Glyph.Arrow: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.Graphics.DOM.Glyph.Arrow: unknown _draw_tick_tbl ()
— Function on jBio.Graphics.DOM.Glyph.Arrow: unknown _evtgt_bind_from_hash ()
— Function on jBio.Graphics.DOM.Glyph.Arrow: unknown _gformat ()
— Function on jBio.Graphics.DOM.Glyph.Arrow: unknown _label ()
— Function on jBio.Graphics.DOM.Glyph.Arrow: unknown _subfeat ()
— Function on jBio.Graphics.DOM.Glyph.Arrow: unknown arrowheads ()
— Function on jBio.Graphics.DOM.Glyph.Arrow: unknown bgElement ()
— Function on jBio.Graphics.DOM.Glyph.Arrow: unknown bgcolor ()
— Function on jBio.Graphics.DOM.Glyph.Arrow: unknown bump ()
— Function on jBio.Graphics.DOM.Glyph.Arrow: unknown calculate_units ()
— Function on jBio.Graphics.DOM.Glyph.Arrow: unknown collision_controller ()
— Function on jBio.Graphics.DOM.Glyph.Arrow: unknown connector ()
— Function on jBio.Graphics.DOM.Glyph.Arrow: unknown do_layout ()
— Function on jBio.Graphics.DOM.Glyph.Arrow: unknown draw ()
— Function on jBio.Graphics.DOM.Glyph.Arrow: unknown draw_box ()
— Function on jBio.Graphics.DOM.Glyph.Arrow: unknown draw_component ()
— Function on jBio.Graphics.DOM.Glyph.Arrow: unknown draw_label ()
— Function on jBio.Graphics.DOM.Glyph.Arrow: unknown draw_parallel ()
— Function on jBio.Graphics.DOM.Glyph.Arrow: unknown draw_track_key ()
— Function on jBio.Graphics.DOM.Glyph.Arrow: unknown end ()
— Function on jBio.Graphics.DOM.Glyph.Arrow: unknown escapeHTML ()
— Function on jBio.Graphics.DOM.Glyph.Arrow: unknown evtgt_bind ()
— Function on jBio.Graphics.DOM.Glyph.Arrow: unknown evtgt_innervate ()
— Function on jBio.Graphics.DOM.Glyph.Arrow: unknown exceeds_depth ()
— Function on jBio.Graphics.DOM.Glyph.Arrow: unknown factory ()
— Function on jBio.Graphics.DOM.Glyph.Arrow: unknown feature ()
— Function on jBio.Graphics.DOM.Glyph.Arrow: unknown feature_has_subparts ()
— Function on jBio.Graphics.DOM.Glyph.Arrow: unknown fgcolor ()
— Function on jBio.Graphics.DOM.Glyph.Arrow: unknown get_not_ignored_subparts ()
— Function on jBio.Graphics.DOM.Glyph.Arrow: unknown get_visible_parts ()
— Function on jBio.Graphics.DOM.Glyph.Arrow: unknown get_zoomer ()
— Function on jBio.Graphics.DOM.Glyph.Arrow: unknown hbumppad ()
— Function on jBio.Graphics.DOM.Glyph.Arrow: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.Graphics.DOM.Glyph.Arrow: unknown label ()
— Function on jBio.Graphics.DOM.Glyph.Arrow: unknown layout_sort ()
— Function on jBio.Graphics.DOM.Glyph.Arrow: unknown level ()
— Function on jBio.Graphics.DOM.Glyph.Arrow: unknown llength ()
— Function on jBio.Graphics.DOM.Glyph.Arrow: unknown make_key_name ()
— Function on jBio.Graphics.DOM.Glyph.Arrow: unknown maxdepth ()
— Function on jBio.Graphics.DOM.Glyph.Arrow: unknown no_subparts ()
— Function on jBio.Graphics.DOM.Glyph.Arrow: unknown not_ignored_subparts ()
— Function on jBio.Graphics.DOM.Glyph.Arrow: unknown overbumped ()
— Function on jBio.Graphics.DOM.Glyph.Arrow: unknown pad_bottom ()
— Function on jBio.Graphics.DOM.Glyph.Arrow: unknown pad_left ()
— Function on jBio.Graphics.DOM.Glyph.Arrow: unknown pad_right ()
— Function on jBio.Graphics.DOM.Glyph.Arrow: unknown pad_top ()
— Function on jBio.Graphics.DOM.Glyph.Arrow: unknown panel ()
— Function on jBio.Graphics.DOM.Glyph.Arrow: unknown partno ()
— Function on jBio.Graphics.DOM.Glyph.Arrow: unknown parts ()
— Function on jBio.Graphics.DOM.Glyph.Arrow: unknown point ()
— Function on jBio.Graphics.DOM.Glyph.Arrow: unknown property ()
— Function on jBio.Graphics.DOM.Glyph.Arrow: unknown start ()
— Function on jBio.Graphics.DOM.Glyph.Arrow: unknown stop ()
— Function on jBio.Graphics.DOM.Glyph.Arrow: unknown subfeat ()
— Function on jBio.Graphics.DOM.Glyph.Arrow: unknown ticks ()
— Function on jBio.Graphics.DOM.Glyph.Arrow: unknown tkcolor ()
— Function on jBio.Graphics.DOM.Glyph.Arrow: unknown total_parts ()
— Function on jBio.Graphics.DOM.Glyph.Arrow: unknown track2key ()
— Function on jBio.Graphics.DOM.Glyph.Arrow: unknown track_index ()

3.3.35 jBio.Graphics.DOM.Glyph.DisoReg

— Class: jBio.Graphics.DOM.Glyph.DisoReg : jBio.Root, jBio.Graphics.DOM.Glyph.Faceted

Glyph for disordered regions.

Definition at line 1279 of file jbio.graphics.dom.glyph.js.

— Variable of jBio.Graphics.DOM.Glyph.DisoReg: String classname
— Variable of jBio.Graphics.DOM.Glyph.DisoReg: Array of String parents
— Function on jBio.Graphics.DOM.Glyph.DisoReg: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.Graphics.DOM.Glyph.DisoReg: unknown _evtgt_bind_from_hash ()
— Function on jBio.Graphics.DOM.Glyph.DisoReg: unknown _get_color_for_facet ()
— Function on jBio.Graphics.DOM.Glyph.DisoReg: unknown _get_div_facet ()
— Function on jBio.Graphics.DOM.Glyph.DisoReg: unknown _get_feat_str ()
— Function on jBio.Graphics.DOM.Glyph.DisoReg: unknown _label ()
— Function on jBio.Graphics.DOM.Glyph.DisoReg: unknown _subfeat ()
— Function on jBio.Graphics.DOM.Glyph.DisoReg: unknown bgElement ()
— Function on jBio.Graphics.DOM.Glyph.DisoReg: unknown bgcolor ()
— Function on jBio.Graphics.DOM.Glyph.DisoReg: unknown bump ()
— Function on jBio.Graphics.DOM.Glyph.DisoReg: unknown collision_controller ()
— Function on jBio.Graphics.DOM.Glyph.DisoReg: unknown connector ()
— Function on jBio.Graphics.DOM.Glyph.DisoReg: unknown do_layout ()
— Function on jBio.Graphics.DOM.Glyph.DisoReg: unknown draw ()
— Function on jBio.Graphics.DOM.Glyph.DisoReg: unknown draw_box ()
— Function on jBio.Graphics.DOM.Glyph.DisoReg: unknown draw_component ()
— Function on jBio.Graphics.DOM.Glyph.DisoReg: unknown draw_label ()
— Function on jBio.Graphics.DOM.Glyph.DisoReg: unknown draw_track_key ()
— Function on jBio.Graphics.DOM.Glyph.DisoReg: unknown end ()
— Function on jBio.Graphics.DOM.Glyph.DisoReg: unknown escapeHTML ()
— Function on jBio.Graphics.DOM.Glyph.DisoReg: unknown evtgt_bind ()
— Function on jBio.Graphics.DOM.Glyph.DisoReg: unknown evtgt_innervate ()
— Function on jBio.Graphics.DOM.Glyph.DisoReg: unknown exceeds_depth ()
— Function on jBio.Graphics.DOM.Glyph.DisoReg: unknown factory ()
— Function on jBio.Graphics.DOM.Glyph.DisoReg: unknown feature ()
— Function on jBio.Graphics.DOM.Glyph.DisoReg: unknown feature_has_subparts ()
— Function on jBio.Graphics.DOM.Glyph.DisoReg: unknown fgcolor ()
— Function on jBio.Graphics.DOM.Glyph.DisoReg: unknown get_not_ignored_subparts ()
— Function on jBio.Graphics.DOM.Glyph.DisoReg: unknown get_visible_parts ()
— Function on jBio.Graphics.DOM.Glyph.DisoReg: unknown get_zoomer ()
— Function on jBio.Graphics.DOM.Glyph.DisoReg: unknown hbumppad ()
— Function on jBio.Graphics.DOM.Glyph.DisoReg: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.Graphics.DOM.Glyph.DisoReg: unknown label ()
— Function on jBio.Graphics.DOM.Glyph.DisoReg: unknown layout_sort ()
— Function on jBio.Graphics.DOM.Glyph.DisoReg: unknown level ()
— Function on jBio.Graphics.DOM.Glyph.DisoReg: unknown llength ()
— Function on jBio.Graphics.DOM.Glyph.DisoReg: unknown make_key_name ()
— Function on jBio.Graphics.DOM.Glyph.DisoReg: unknown maxdepth ()
— Function on jBio.Graphics.DOM.Glyph.DisoReg: unknown no_subparts ()
— Function on jBio.Graphics.DOM.Glyph.DisoReg: unknown not_ignored_subparts ()
— Function on jBio.Graphics.DOM.Glyph.DisoReg: unknown overbumped ()
— Function on jBio.Graphics.DOM.Glyph.DisoReg: unknown pad_bottom ()
— Function on jBio.Graphics.DOM.Glyph.DisoReg: unknown pad_left ()
— Function on jBio.Graphics.DOM.Glyph.DisoReg: unknown pad_right ()
— Function on jBio.Graphics.DOM.Glyph.DisoReg: unknown pad_top ()
— Function on jBio.Graphics.DOM.Glyph.DisoReg: unknown panel ()
— Function on jBio.Graphics.DOM.Glyph.DisoReg: unknown partno ()
— Function on jBio.Graphics.DOM.Glyph.DisoReg: unknown parts ()
— Function on jBio.Graphics.DOM.Glyph.DisoReg: unknown point ()
— Function on jBio.Graphics.DOM.Glyph.DisoReg: unknown property ()
— Function on jBio.Graphics.DOM.Glyph.DisoReg: unknown start ()
— Function on jBio.Graphics.DOM.Glyph.DisoReg: unknown stop ()
— Function on jBio.Graphics.DOM.Glyph.DisoReg: unknown subfeat ()
— Function on jBio.Graphics.DOM.Glyph.DisoReg: unknown ticks ()
— Function on jBio.Graphics.DOM.Glyph.DisoReg: unknown tkcolor ()
— Function on jBio.Graphics.DOM.Glyph.DisoReg: unknown total_parts ()
— Function on jBio.Graphics.DOM.Glyph.DisoReg: unknown track2key ()
— Function on jBio.Graphics.DOM.Glyph.DisoReg: unknown track_index ()

3.3.36 jBio.Graphics.DOM.Glyph.Disulfide

— Class: jBio.Graphics.DOM.Glyph.Disulfide : jBio.Root, jBio.Graphics.DOM.Glyph.Generic

Glyph for disulfide bonds.

Definition at line 1353 of file jbio.graphics.dom.glyph.js.

— Variable of jBio.Graphics.DOM.Glyph.Disulfide: String classname
— Variable of jBio.Graphics.DOM.Glyph.Disulfide: Array of String parents
— Function on jBio.Graphics.DOM.Glyph.Disulfide: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.Graphics.DOM.Glyph.Disulfide: unknown _evtgt_bind_from_hash ()
— Function on jBio.Graphics.DOM.Glyph.Disulfide: unknown _label ()
— Function on jBio.Graphics.DOM.Glyph.Disulfide: unknown _subfeat ()
— Function on jBio.Graphics.DOM.Glyph.Disulfide: unknown bgElement ()
— Function on jBio.Graphics.DOM.Glyph.Disulfide: unknown bgcolor ()
— Function on jBio.Graphics.DOM.Glyph.Disulfide: unknown bump ()
— Function on jBio.Graphics.DOM.Glyph.Disulfide: unknown collision_controller ()
— Function on jBio.Graphics.DOM.Glyph.Disulfide: unknown connector ()
— Function on jBio.Graphics.DOM.Glyph.Disulfide: unknown do_layout ()
— Function on jBio.Graphics.DOM.Glyph.Disulfide: unknown draw ()
— Function on jBio.Graphics.DOM.Glyph.Disulfide: unknown draw_box ()
— Function on jBio.Graphics.DOM.Glyph.Disulfide: unknown draw_component ()
— Function on jBio.Graphics.DOM.Glyph.Disulfide: unknown draw_label ()
— Function on jBio.Graphics.DOM.Glyph.Disulfide: unknown draw_track_key ()
— Function on jBio.Graphics.DOM.Glyph.Disulfide: unknown end ()
— Function on jBio.Graphics.DOM.Glyph.Disulfide: unknown escapeHTML ()
— Function on jBio.Graphics.DOM.Glyph.Disulfide: unknown evtgt_bind ()
— Function on jBio.Graphics.DOM.Glyph.Disulfide: unknown evtgt_innervate ()
— Function on jBio.Graphics.DOM.Glyph.Disulfide: unknown exceeds_depth ()
— Function on jBio.Graphics.DOM.Glyph.Disulfide: unknown factory ()
— Function on jBio.Graphics.DOM.Glyph.Disulfide: unknown feature ()
— Function on jBio.Graphics.DOM.Glyph.Disulfide: unknown feature_has_subparts ()
— Function on jBio.Graphics.DOM.Glyph.Disulfide: unknown fgcolor ()
— Function on jBio.Graphics.DOM.Glyph.Disulfide: unknown get_not_ignored_subparts ()
— Function on jBio.Graphics.DOM.Glyph.Disulfide: unknown get_visible_parts ()
— Function on jBio.Graphics.DOM.Glyph.Disulfide: unknown get_zoomer ()
— Function on jBio.Graphics.DOM.Glyph.Disulfide: unknown hbumppad ()
— Function on jBio.Graphics.DOM.Glyph.Disulfide: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.Graphics.DOM.Glyph.Disulfide: unknown label ()
— Function on jBio.Graphics.DOM.Glyph.Disulfide: unknown layout_sort ()
— Function on jBio.Graphics.DOM.Glyph.Disulfide: unknown level ()
— Function on jBio.Graphics.DOM.Glyph.Disulfide: unknown llength ()
— Function on jBio.Graphics.DOM.Glyph.Disulfide: unknown make_key_name ()
— Function on jBio.Graphics.DOM.Glyph.Disulfide: unknown maxdepth ()
— Function on jBio.Graphics.DOM.Glyph.Disulfide: unknown no_subparts ()
— Function on jBio.Graphics.DOM.Glyph.Disulfide: unknown not_ignored_subparts ()
— Function on jBio.Graphics.DOM.Glyph.Disulfide: unknown overbumped ()
— Function on jBio.Graphics.DOM.Glyph.Disulfide: unknown pad_bottom ()
— Function on jBio.Graphics.DOM.Glyph.Disulfide: unknown pad_left ()
— Function on jBio.Graphics.DOM.Glyph.Disulfide: unknown pad_right ()
— Function on jBio.Graphics.DOM.Glyph.Disulfide: unknown pad_top ()
— Function on jBio.Graphics.DOM.Glyph.Disulfide: unknown panel ()
— Function on jBio.Graphics.DOM.Glyph.Disulfide: unknown partno ()
— Function on jBio.Graphics.DOM.Glyph.Disulfide: unknown parts ()
— Function on jBio.Graphics.DOM.Glyph.Disulfide: unknown point ()
— Function on jBio.Graphics.DOM.Glyph.Disulfide: unknown property ()
— Function on jBio.Graphics.DOM.Glyph.Disulfide: unknown start ()
— Function on jBio.Graphics.DOM.Glyph.Disulfide: unknown stop ()
— Function on jBio.Graphics.DOM.Glyph.Disulfide: unknown subfeat ()
— Function on jBio.Graphics.DOM.Glyph.Disulfide: unknown ticks ()
— Function on jBio.Graphics.DOM.Glyph.Disulfide: unknown tkcolor ()
— Function on jBio.Graphics.DOM.Glyph.Disulfide: unknown total_parts ()
— Function on jBio.Graphics.DOM.Glyph.Disulfide: unknown track2key ()
— Function on jBio.Graphics.DOM.Glyph.Disulfide: unknown track_index ()

3.3.37 jBio.Graphics.DOM.Glyph.Faceted

— Class: jBio.Graphics.DOM.Glyph.Faceted : jBio.Root, jBio.Graphics.DOM.Glyph.Generic

Base glyph for features that vary position by position and have reliability scores.

Definition at line 1143 of file jbio.graphics.dom.glyph.js.

— Variable of jBio.Graphics.DOM.Glyph.Faceted: String classname
— Variable of jBio.Graphics.DOM.Glyph.Faceted: Array of String parents
— Function on jBio.Graphics.DOM.Glyph.Faceted: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.Graphics.DOM.Glyph.Faceted: unknown _evtgt_bind_from_hash ()
— Function on jBio.Graphics.DOM.Glyph.Faceted: unknown _get_color_for_facet ()
— Function on jBio.Graphics.DOM.Glyph.Faceted: unknown _get_div_facet ()
— Function on jBio.Graphics.DOM.Glyph.Faceted: unknown _get_feat_str ()
— Function on jBio.Graphics.DOM.Glyph.Faceted: unknown _label ()
— Function on jBio.Graphics.DOM.Glyph.Faceted: unknown _subfeat ()
— Function on jBio.Graphics.DOM.Glyph.Faceted: unknown bgElement ()
— Function on jBio.Graphics.DOM.Glyph.Faceted: unknown bgcolor ()
— Function on jBio.Graphics.DOM.Glyph.Faceted: unknown bump ()
— Function on jBio.Graphics.DOM.Glyph.Faceted: unknown collision_controller ()
— Function on jBio.Graphics.DOM.Glyph.Faceted: unknown connector ()
— Function on jBio.Graphics.DOM.Glyph.Faceted: unknown do_layout ()
— Function on jBio.Graphics.DOM.Glyph.Faceted: unknown draw ()
— Function on jBio.Graphics.DOM.Glyph.Faceted: unknown draw_box ()
— Function on jBio.Graphics.DOM.Glyph.Faceted: unknown draw_component ()
— Function on jBio.Graphics.DOM.Glyph.Faceted: unknown draw_label ()
— Function on jBio.Graphics.DOM.Glyph.Faceted: unknown draw_track_key ()
— Function on jBio.Graphics.DOM.Glyph.Faceted: unknown end ()
— Function on jBio.Graphics.DOM.Glyph.Faceted: unknown escapeHTML ()
— Function on jBio.Graphics.DOM.Glyph.Faceted: unknown evtgt_bind ()
— Function on jBio.Graphics.DOM.Glyph.Faceted: unknown evtgt_innervate ()
— Function on jBio.Graphics.DOM.Glyph.Faceted: unknown exceeds_depth ()
— Function on jBio.Graphics.DOM.Glyph.Faceted: unknown factory ()
— Function on jBio.Graphics.DOM.Glyph.Faceted: unknown feature ()
— Function on jBio.Graphics.DOM.Glyph.Faceted: unknown feature_has_subparts ()
— Function on jBio.Graphics.DOM.Glyph.Faceted: unknown fgcolor ()
— Function on jBio.Graphics.DOM.Glyph.Faceted: unknown get_not_ignored_subparts ()
— Function on jBio.Graphics.DOM.Glyph.Faceted: unknown get_visible_parts ()
— Function on jBio.Graphics.DOM.Glyph.Faceted: unknown get_zoomer ()
— Function on jBio.Graphics.DOM.Glyph.Faceted: unknown hbumppad ()
— Function on jBio.Graphics.DOM.Glyph.Faceted: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.Graphics.DOM.Glyph.Faceted: unknown label ()
— Function on jBio.Graphics.DOM.Glyph.Faceted: unknown layout_sort ()
— Function on jBio.Graphics.DOM.Glyph.Faceted: unknown level ()
— Function on jBio.Graphics.DOM.Glyph.Faceted: unknown llength ()
— Function on jBio.Graphics.DOM.Glyph.Faceted: unknown make_key_name ()
— Function on jBio.Graphics.DOM.Glyph.Faceted: unknown maxdepth ()
— Function on jBio.Graphics.DOM.Glyph.Faceted: unknown no_subparts ()
— Function on jBio.Graphics.DOM.Glyph.Faceted: unknown not_ignored_subparts ()
— Function on jBio.Graphics.DOM.Glyph.Faceted: unknown overbumped ()
— Function on jBio.Graphics.DOM.Glyph.Faceted: unknown pad_bottom ()
— Function on jBio.Graphics.DOM.Glyph.Faceted: unknown pad_left ()
— Function on jBio.Graphics.DOM.Glyph.Faceted: unknown pad_right ()
— Function on jBio.Graphics.DOM.Glyph.Faceted: unknown pad_top ()
— Function on jBio.Graphics.DOM.Glyph.Faceted: unknown panel ()
— Function on jBio.Graphics.DOM.Glyph.Faceted: unknown partno ()
— Function on jBio.Graphics.DOM.Glyph.Faceted: unknown parts ()
— Function on jBio.Graphics.DOM.Glyph.Faceted: unknown point ()
— Function on jBio.Graphics.DOM.Glyph.Faceted: unknown property ()
— Function on jBio.Graphics.DOM.Glyph.Faceted: unknown start ()
— Function on jBio.Graphics.DOM.Glyph.Faceted: unknown stop ()
— Function on jBio.Graphics.DOM.Glyph.Faceted: unknown subfeat ()
— Function on jBio.Graphics.DOM.Glyph.Faceted: unknown ticks ()
— Function on jBio.Graphics.DOM.Glyph.Faceted: unknown tkcolor ()
— Function on jBio.Graphics.DOM.Glyph.Faceted: unknown total_parts ()
— Function on jBio.Graphics.DOM.Glyph.Faceted: unknown track2key ()
— Function on jBio.Graphics.DOM.Glyph.Faceted: unknown track_index ()

3.3.38 jBio.Graphics.DOM.Glyph.Generic

— Class: jBio.Graphics.DOM.Glyph.Generic : jBio.Root, jBio.Graphics.DOM.Glyph

Generic glyph.

This glyph draws a block for each feature.

Definition at line 344 of file jbio.graphics.dom.glyph.js.

— Variable of jBio.Graphics.DOM.Glyph.Generic: String classname
— Variable of jBio.Graphics.DOM.Glyph.Generic: Array of String parents
— Function on jBio.Graphics.DOM.Glyph.Generic: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.Graphics.DOM.Glyph.Generic: unknown _evtgt_bind_from_hash ()
— Function on jBio.Graphics.DOM.Glyph.Generic: unknown _label ()
— Function on jBio.Graphics.DOM.Glyph.Generic: unknown _subfeat ()
— Function on jBio.Graphics.DOM.Glyph.Generic: unknown bgElement ()
— Function on jBio.Graphics.DOM.Glyph.Generic: unknown bgcolor ()
— Function on jBio.Graphics.DOM.Glyph.Generic: unknown bump ()
— Function on jBio.Graphics.DOM.Glyph.Generic: unknown collision_controller ()
— Function on jBio.Graphics.DOM.Glyph.Generic: unknown connector ()
— Function on jBio.Graphics.DOM.Glyph.Generic: unknown do_layout ()
— Function on jBio.Graphics.DOM.Glyph.Generic: unknown draw ()
— Function on jBio.Graphics.DOM.Glyph.Generic: unknown draw_box ()
— Function on jBio.Graphics.DOM.Glyph.Generic: unknown draw_component ()
— Function on jBio.Graphics.DOM.Glyph.Generic: unknown draw_label ()
— Function on jBio.Graphics.DOM.Glyph.Generic: unknown draw_track_key ()
— Function on jBio.Graphics.DOM.Glyph.Generic: unknown end ()
— Function on jBio.Graphics.DOM.Glyph.Generic: unknown escapeHTML ()
— Function on jBio.Graphics.DOM.Glyph.Generic: unknown evtgt_bind ()
— Function on jBio.Graphics.DOM.Glyph.Generic: unknown evtgt_innervate ()
— Function on jBio.Graphics.DOM.Glyph.Generic: unknown exceeds_depth ()
— Function on jBio.Graphics.DOM.Glyph.Generic: unknown factory ()
— Function on jBio.Graphics.DOM.Glyph.Generic: unknown feature ()
— Function on jBio.Graphics.DOM.Glyph.Generic: unknown feature_has_subparts ()
— Function on jBio.Graphics.DOM.Glyph.Generic: unknown fgcolor ()
— Function on jBio.Graphics.DOM.Glyph.Generic: unknown get_not_ignored_subparts ()
— Function on jBio.Graphics.DOM.Glyph.Generic: unknown get_visible_parts ()
— Function on jBio.Graphics.DOM.Glyph.Generic: unknown get_zoomer ()
— Function on jBio.Graphics.DOM.Glyph.Generic: unknown hbumppad ()
— Function on jBio.Graphics.DOM.Glyph.Generic: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.Graphics.DOM.Glyph.Generic: unknown label ()
— Function on jBio.Graphics.DOM.Glyph.Generic: unknown layout_sort ()
— Function on jBio.Graphics.DOM.Glyph.Generic: unknown level ()
— Function on jBio.Graphics.DOM.Glyph.Generic: unknown llength ()
— Function on jBio.Graphics.DOM.Glyph.Generic: unknown make_key_name ()
— Function on jBio.Graphics.DOM.Glyph.Generic: unknown maxdepth ()
— Function on jBio.Graphics.DOM.Glyph.Generic: unknown no_subparts ()
— Function on jBio.Graphics.DOM.Glyph.Generic: unknown not_ignored_subparts ()
— Function on jBio.Graphics.DOM.Glyph.Generic: unknown overbumped ()
— Function on jBio.Graphics.DOM.Glyph.Generic: unknown pad_bottom ()
— Function on jBio.Graphics.DOM.Glyph.Generic: unknown pad_left ()
— Function on jBio.Graphics.DOM.Glyph.Generic: unknown pad_right ()
— Function on jBio.Graphics.DOM.Glyph.Generic: unknown pad_top ()
— Function on jBio.Graphics.DOM.Glyph.Generic: unknown panel ()
— Function on jBio.Graphics.DOM.Glyph.Generic: unknown partno ()
— Function on jBio.Graphics.DOM.Glyph.Generic: unknown parts ()
— Function on jBio.Graphics.DOM.Glyph.Generic: unknown point ()
— Function on jBio.Graphics.DOM.Glyph.Generic: unknown property ()
— Function on jBio.Graphics.DOM.Glyph.Generic: unknown start ()
— Function on jBio.Graphics.DOM.Glyph.Generic: unknown stop ()
— Function on jBio.Graphics.DOM.Glyph.Generic: unknown subfeat ()
— Function on jBio.Graphics.DOM.Glyph.Generic: unknown ticks ()
— Function on jBio.Graphics.DOM.Glyph.Generic: unknown tkcolor ()
— Function on jBio.Graphics.DOM.Glyph.Generic: unknown total_parts ()
— Function on jBio.Graphics.DOM.Glyph.Generic: unknown track2key ()
— Function on jBio.Graphics.DOM.Glyph.Generic: unknown track_index ()

3.3.39 jBio.Graphics.DOM.Glyph.SecondaryStructure

— Class: jBio.Graphics.DOM.Glyph.SecondaryStructure : jBio.Root, jBio.Graphics.DOM.Glyph.Generic

Simple glyph for secondary structures.

Definition at line 939 of file jbio.graphics.dom.glyph.js.

— Variable of jBio.Graphics.DOM.Glyph.SecondaryStructure: String classname
— Variable of jBio.Graphics.DOM.Glyph.SecondaryStructure: Array of String parents
— Function on jBio.Graphics.DOM.Glyph.SecondaryStructure: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.Graphics.DOM.Glyph.SecondaryStructure: unknown _evtgt_bind_from_hash ()
— Function on jBio.Graphics.DOM.Glyph.SecondaryStructure: unknown _label ()
— Function on jBio.Graphics.DOM.Glyph.SecondaryStructure: unknown _subfeat ()
— Function on jBio.Graphics.DOM.Glyph.SecondaryStructure: unknown bgElement ()
— Function on jBio.Graphics.DOM.Glyph.SecondaryStructure: unknown bgcolor ()
— Function on jBio.Graphics.DOM.Glyph.SecondaryStructure: unknown bump ()
— Function on jBio.Graphics.DOM.Glyph.SecondaryStructure: unknown collision_controller ()
— Function on jBio.Graphics.DOM.Glyph.SecondaryStructure: unknown connector ()
— Function on jBio.Graphics.DOM.Glyph.SecondaryStructure: unknown do_layout ()
— Function on jBio.Graphics.DOM.Glyph.SecondaryStructure: unknown draw ()
— Function on jBio.Graphics.DOM.Glyph.SecondaryStructure: unknown draw_box ()
— Function on jBio.Graphics.DOM.Glyph.SecondaryStructure: unknown draw_component ()
— Function on jBio.Graphics.DOM.Glyph.SecondaryStructure: unknown draw_label ()
— Function on jBio.Graphics.DOM.Glyph.SecondaryStructure: unknown draw_track_key ()
— Function on jBio.Graphics.DOM.Glyph.SecondaryStructure: unknown end ()
— Function on jBio.Graphics.DOM.Glyph.SecondaryStructure: unknown escapeHTML ()
— Function on jBio.Graphics.DOM.Glyph.SecondaryStructure: unknown evtgt_bind ()
— Function on jBio.Graphics.DOM.Glyph.SecondaryStructure: unknown evtgt_innervate ()
— Function on jBio.Graphics.DOM.Glyph.SecondaryStructure: unknown exceeds_depth ()
— Function on jBio.Graphics.DOM.Glyph.SecondaryStructure: unknown factory ()
— Function on jBio.Graphics.DOM.Glyph.SecondaryStructure: unknown feature ()
— Function on jBio.Graphics.DOM.Glyph.SecondaryStructure: unknown feature_has_subparts ()
— Function on jBio.Graphics.DOM.Glyph.SecondaryStructure: unknown fgcolor ()
— Function on jBio.Graphics.DOM.Glyph.SecondaryStructure: unknown get_not_ignored_subparts ()
— Function on jBio.Graphics.DOM.Glyph.SecondaryStructure: unknown get_visible_parts ()
— Function on jBio.Graphics.DOM.Glyph.SecondaryStructure: unknown get_zoomer ()
— Function on jBio.Graphics.DOM.Glyph.SecondaryStructure: unknown hbumppad ()
— Function on jBio.Graphics.DOM.Glyph.SecondaryStructure: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.Graphics.DOM.Glyph.SecondaryStructure: unknown label ()
— Function on jBio.Graphics.DOM.Glyph.SecondaryStructure: unknown layout_sort ()
— Function on jBio.Graphics.DOM.Glyph.SecondaryStructure: unknown level ()
— Function on jBio.Graphics.DOM.Glyph.SecondaryStructure: unknown llength ()
— Function on jBio.Graphics.DOM.Glyph.SecondaryStructure: unknown make_key_name ()
— Function on jBio.Graphics.DOM.Glyph.SecondaryStructure: unknown maxdepth ()
— Function on jBio.Graphics.DOM.Glyph.SecondaryStructure: unknown no_subparts ()
— Function on jBio.Graphics.DOM.Glyph.SecondaryStructure: unknown not_ignored_subparts ()
— Function on jBio.Graphics.DOM.Glyph.SecondaryStructure: unknown overbumped ()
— Function on jBio.Graphics.DOM.Glyph.SecondaryStructure: unknown pad_bottom ()
— Function on jBio.Graphics.DOM.Glyph.SecondaryStructure: unknown pad_left ()
— Function on jBio.Graphics.DOM.Glyph.SecondaryStructure: unknown pad_right ()
— Function on jBio.Graphics.DOM.Glyph.SecondaryStructure: unknown pad_top ()
— Function on jBio.Graphics.DOM.Glyph.SecondaryStructure: unknown panel ()
— Function on jBio.Graphics.DOM.Glyph.SecondaryStructure: unknown partno ()
— Function on jBio.Graphics.DOM.Glyph.SecondaryStructure: unknown parts ()
— Function on jBio.Graphics.DOM.Glyph.SecondaryStructure: unknown point ()
— Function on jBio.Graphics.DOM.Glyph.SecondaryStructure: unknown property ()
— Function on jBio.Graphics.DOM.Glyph.SecondaryStructure: unknown start ()
— Function on jBio.Graphics.DOM.Glyph.SecondaryStructure: unknown stop ()
— Function on jBio.Graphics.DOM.Glyph.SecondaryStructure: unknown subfeat ()
— Function on jBio.Graphics.DOM.Glyph.SecondaryStructure: unknown ticks ()
— Function on jBio.Graphics.DOM.Glyph.SecondaryStructure: unknown tkcolor ()
— Function on jBio.Graphics.DOM.Glyph.SecondaryStructure: unknown total_parts ()
— Function on jBio.Graphics.DOM.Glyph.SecondaryStructure: unknown track2key ()
— Function on jBio.Graphics.DOM.Glyph.SecondaryStructure: unknown track_index ()

3.3.40 jBio.Graphics.DOM.Glyph.SolvAcc

— Class: jBio.Graphics.DOM.Glyph.SolvAcc : jBio.Root, jBio.Graphics.DOM.Glyph.Faceted

Glyph for solvent accessibility.

Definition at line 1483 of file jbio.graphics.dom.glyph.js.

— Variable of jBio.Graphics.DOM.Glyph.SolvAcc: String classname
— Variable of jBio.Graphics.DOM.Glyph.SolvAcc: Array of String parents
— Function on jBio.Graphics.DOM.Glyph.SolvAcc: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.Graphics.DOM.Glyph.SolvAcc: unknown _evtgt_bind_from_hash ()
— Function on jBio.Graphics.DOM.Glyph.SolvAcc: unknown _get_color_for_facet ()
— Function on jBio.Graphics.DOM.Glyph.SolvAcc: unknown _get_div_facet ()
— Function on jBio.Graphics.DOM.Glyph.SolvAcc: unknown _get_feat_str ()
— Function on jBio.Graphics.DOM.Glyph.SolvAcc: unknown _label ()
— Function on jBio.Graphics.DOM.Glyph.SolvAcc: unknown _subfeat ()
— Function on jBio.Graphics.DOM.Glyph.SolvAcc: unknown bgElement ()
— Function on jBio.Graphics.DOM.Glyph.SolvAcc: unknown bgcolor ()
— Function on jBio.Graphics.DOM.Glyph.SolvAcc: unknown bump ()
— Function on jBio.Graphics.DOM.Glyph.SolvAcc: unknown collision_controller ()
— Function on jBio.Graphics.DOM.Glyph.SolvAcc: unknown connector ()
— Function on jBio.Graphics.DOM.Glyph.SolvAcc: unknown do_layout ()
— Function on jBio.Graphics.DOM.Glyph.SolvAcc: unknown draw ()
— Function on jBio.Graphics.DOM.Glyph.SolvAcc: unknown draw_box ()
— Function on jBio.Graphics.DOM.Glyph.SolvAcc: unknown draw_component ()
— Function on jBio.Graphics.DOM.Glyph.SolvAcc: unknown draw_label ()
— Function on jBio.Graphics.DOM.Glyph.SolvAcc: unknown draw_track_key ()
— Function on jBio.Graphics.DOM.Glyph.SolvAcc: unknown end ()
— Function on jBio.Graphics.DOM.Glyph.SolvAcc: unknown escapeHTML ()
— Function on jBio.Graphics.DOM.Glyph.SolvAcc: unknown evtgt_bind ()
— Function on jBio.Graphics.DOM.Glyph.SolvAcc: unknown evtgt_innervate ()
— Function on jBio.Graphics.DOM.Glyph.SolvAcc: unknown exceeds_depth ()
— Function on jBio.Graphics.DOM.Glyph.SolvAcc: unknown factory ()
— Function on jBio.Graphics.DOM.Glyph.SolvAcc: unknown feature ()
— Function on jBio.Graphics.DOM.Glyph.SolvAcc: unknown feature_has_subparts ()
— Function on jBio.Graphics.DOM.Glyph.SolvAcc: unknown fgcolor ()
— Function on jBio.Graphics.DOM.Glyph.SolvAcc: unknown get_not_ignored_subparts ()
— Function on jBio.Graphics.DOM.Glyph.SolvAcc: unknown get_visible_parts ()
— Function on jBio.Graphics.DOM.Glyph.SolvAcc: unknown get_zoomer ()
— Function on jBio.Graphics.DOM.Glyph.SolvAcc: unknown hbumppad ()
— Function on jBio.Graphics.DOM.Glyph.SolvAcc: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.Graphics.DOM.Glyph.SolvAcc: unknown label ()
— Function on jBio.Graphics.DOM.Glyph.SolvAcc: unknown layout_sort ()
— Function on jBio.Graphics.DOM.Glyph.SolvAcc: unknown level ()
— Function on jBio.Graphics.DOM.Glyph.SolvAcc: unknown llength ()
— Function on jBio.Graphics.DOM.Glyph.SolvAcc: unknown make_key_name ()
— Function on jBio.Graphics.DOM.Glyph.SolvAcc: unknown maxdepth ()
— Function on jBio.Graphics.DOM.Glyph.SolvAcc: unknown no_subparts ()
— Function on jBio.Graphics.DOM.Glyph.SolvAcc: unknown not_ignored_subparts ()
— Function on jBio.Graphics.DOM.Glyph.SolvAcc: unknown overbumped ()
— Function on jBio.Graphics.DOM.Glyph.SolvAcc: unknown pad_bottom ()
— Function on jBio.Graphics.DOM.Glyph.SolvAcc: unknown pad_left ()
— Function on jBio.Graphics.DOM.Glyph.SolvAcc: unknown pad_right ()
— Function on jBio.Graphics.DOM.Glyph.SolvAcc: unknown pad_top ()
— Function on jBio.Graphics.DOM.Glyph.SolvAcc: unknown panel ()
— Function on jBio.Graphics.DOM.Glyph.SolvAcc: unknown partno ()
— Function on jBio.Graphics.DOM.Glyph.SolvAcc: unknown parts ()
— Function on jBio.Graphics.DOM.Glyph.SolvAcc: unknown point ()
— Function on jBio.Graphics.DOM.Glyph.SolvAcc: unknown property ()
— Function on jBio.Graphics.DOM.Glyph.SolvAcc: unknown start ()
— Function on jBio.Graphics.DOM.Glyph.SolvAcc: unknown stop ()
— Function on jBio.Graphics.DOM.Glyph.SolvAcc: unknown subfeat ()
— Function on jBio.Graphics.DOM.Glyph.SolvAcc: unknown ticks ()
— Function on jBio.Graphics.DOM.Glyph.SolvAcc: unknown tkcolor ()
— Function on jBio.Graphics.DOM.Glyph.SolvAcc: unknown total_parts ()
— Function on jBio.Graphics.DOM.Glyph.SolvAcc: unknown track2key ()
— Function on jBio.Graphics.DOM.Glyph.SolvAcc: unknown track_index ()

3.3.41 jBio.Graphics.DOM.Glyph.TransmBetaBarrel

— Class: jBio.Graphics.DOM.Glyph.TransmBetaBarrel : jBio.Root, jBio.Graphics.DOM.Glyph.Generic

Simple glyph for transmembrane beta barrels.

Definition at line 1060 of file jbio.graphics.dom.glyph.js.

— Variable of jBio.Graphics.DOM.Glyph.TransmBetaBarrel: String classname
— Variable of jBio.Graphics.DOM.Glyph.TransmBetaBarrel: Array of String parents
— Function on jBio.Graphics.DOM.Glyph.TransmBetaBarrel: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.Graphics.DOM.Glyph.TransmBetaBarrel: unknown _evtgt_bind_from_hash ()
— Function on jBio.Graphics.DOM.Glyph.TransmBetaBarrel: unknown _label ()
— Function on jBio.Graphics.DOM.Glyph.TransmBetaBarrel: unknown _subfeat ()
— Function on jBio.Graphics.DOM.Glyph.TransmBetaBarrel: unknown bgElement ()
— Function on jBio.Graphics.DOM.Glyph.TransmBetaBarrel: unknown bgcolor ()
— Function on jBio.Graphics.DOM.Glyph.TransmBetaBarrel: unknown bump ()
— Function on jBio.Graphics.DOM.Glyph.TransmBetaBarrel: unknown collision_controller ()
— Function on jBio.Graphics.DOM.Glyph.TransmBetaBarrel: unknown connector ()
— Function on jBio.Graphics.DOM.Glyph.TransmBetaBarrel: unknown do_layout ()
— Function on jBio.Graphics.DOM.Glyph.TransmBetaBarrel: unknown draw ()
— Function on jBio.Graphics.DOM.Glyph.TransmBetaBarrel: unknown draw_box ()
— Function on jBio.Graphics.DOM.Glyph.TransmBetaBarrel: unknown draw_component ()
— Function on jBio.Graphics.DOM.Glyph.TransmBetaBarrel: unknown draw_label ()
— Function on jBio.Graphics.DOM.Glyph.TransmBetaBarrel: unknown draw_track_key ()
— Function on jBio.Graphics.DOM.Glyph.TransmBetaBarrel: unknown end ()
— Function on jBio.Graphics.DOM.Glyph.TransmBetaBarrel: unknown escapeHTML ()
— Function on jBio.Graphics.DOM.Glyph.TransmBetaBarrel: unknown evtgt_bind ()
— Function on jBio.Graphics.DOM.Glyph.TransmBetaBarrel: unknown evtgt_innervate ()
— Function on jBio.Graphics.DOM.Glyph.TransmBetaBarrel: unknown exceeds_depth ()
— Function on jBio.Graphics.DOM.Glyph.TransmBetaBarrel: unknown factory ()
— Function on jBio.Graphics.DOM.Glyph.TransmBetaBarrel: unknown feature ()
— Function on jBio.Graphics.DOM.Glyph.TransmBetaBarrel: unknown feature_has_subparts ()
— Function on jBio.Graphics.DOM.Glyph.TransmBetaBarrel: unknown fgcolor ()
— Function on jBio.Graphics.DOM.Glyph.TransmBetaBarrel: unknown get_not_ignored_subparts ()
— Function on jBio.Graphics.DOM.Glyph.TransmBetaBarrel: unknown get_visible_parts ()
— Function on jBio.Graphics.DOM.Glyph.TransmBetaBarrel: unknown get_zoomer ()
— Function on jBio.Graphics.DOM.Glyph.TransmBetaBarrel: unknown hbumppad ()
— Function on jBio.Graphics.DOM.Glyph.TransmBetaBarrel: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.Graphics.DOM.Glyph.TransmBetaBarrel: unknown label ()
— Function on jBio.Graphics.DOM.Glyph.TransmBetaBarrel: unknown layout_sort ()
— Function on jBio.Graphics.DOM.Glyph.TransmBetaBarrel: unknown level ()
— Function on jBio.Graphics.DOM.Glyph.TransmBetaBarrel: unknown llength ()
— Function on jBio.Graphics.DOM.Glyph.TransmBetaBarrel: unknown make_key_name ()
— Function on jBio.Graphics.DOM.Glyph.TransmBetaBarrel: unknown maxdepth ()
— Function on jBio.Graphics.DOM.Glyph.TransmBetaBarrel: unknown no_subparts ()
— Function on jBio.Graphics.DOM.Glyph.TransmBetaBarrel: unknown not_ignored_subparts ()
— Function on jBio.Graphics.DOM.Glyph.TransmBetaBarrel: unknown overbumped ()
— Function on jBio.Graphics.DOM.Glyph.TransmBetaBarrel: unknown pad_bottom ()
— Function on jBio.Graphics.DOM.Glyph.TransmBetaBarrel: unknown pad_left ()
— Function on jBio.Graphics.DOM.Glyph.TransmBetaBarrel: unknown pad_right ()
— Function on jBio.Graphics.DOM.Glyph.TransmBetaBarrel: unknown pad_top ()
— Function on jBio.Graphics.DOM.Glyph.TransmBetaBarrel: unknown panel ()
— Function on jBio.Graphics.DOM.Glyph.TransmBetaBarrel: unknown partno ()
— Function on jBio.Graphics.DOM.Glyph.TransmBetaBarrel: unknown parts ()
— Function on jBio.Graphics.DOM.Glyph.TransmBetaBarrel: unknown point ()
— Function on jBio.Graphics.DOM.Glyph.TransmBetaBarrel: unknown property ()
— Function on jBio.Graphics.DOM.Glyph.TransmBetaBarrel: unknown start ()
— Function on jBio.Graphics.DOM.Glyph.TransmBetaBarrel: unknown stop ()
— Function on jBio.Graphics.DOM.Glyph.TransmBetaBarrel: unknown subfeat ()
— Function on jBio.Graphics.DOM.Glyph.TransmBetaBarrel: unknown ticks ()
— Function on jBio.Graphics.DOM.Glyph.TransmBetaBarrel: unknown tkcolor ()
— Function on jBio.Graphics.DOM.Glyph.TransmBetaBarrel: unknown total_parts ()
— Function on jBio.Graphics.DOM.Glyph.TransmBetaBarrel: unknown track2key ()
— Function on jBio.Graphics.DOM.Glyph.TransmBetaBarrel: unknown track_index ()

3.3.42 jBio.Graphics.DOM.Glyph_zoomer

— Class: jBio.Graphics.DOM.Glyph_zoomer : jBio.Root, jBio.Graphics.DOM.Zoomer

Live element resizing (zooming) for glyphs.

Example: 

     $(rootElem).data('zoomer', new jBio.Graphics.DOM.Glyph_zoomer_FAC({ domElement: rootElem }) );

Definition at line 1796 of file jbio.graphics.dom.glyph.js.

— Variable of jBio.Graphics.DOM.Glyph_zoomer: String classname
— Variable of jBio.Graphics.DOM.Glyph_zoomer: Array of String parents
— Function on jBio.Graphics.DOM.Glyph_zoomer: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.Graphics.DOM.Glyph_zoomer: unknown _zoom_face ()
— Function on jBio.Graphics.DOM.Glyph_zoomer: unknown do_zoom ()
— Function on jBio.Graphics.DOM.Glyph_zoomer: unknown domElement ()
— Function on jBio.Graphics.DOM.Glyph_zoomer: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

3.3.43 jBio.Graphics.DOM.Label_zoomer

— Class: jBio.Graphics.DOM.Label_zoomer : jBio.Root, jBio.Graphics.DOM.Zoomer.Positioned

Live element resizing (zooming) for labels.

Example: 

     $(child).data('zoomer', new jBio.Graphics.DOM.Label_zoomer_FAC({
       domElement: child, left: ld['left'], top: ld['top'], base_font_size: ld['font-size']
     }) );

Definition at line 1856 of file jbio.graphics.dom.glyph.js.

— Variable of jBio.Graphics.DOM.Label_zoomer: String classname
— Variable of jBio.Graphics.DOM.Label_zoomer: Array of String parents
— Function on jBio.Graphics.DOM.Label_zoomer: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.Graphics.DOM.Label_zoomer: unknown _zoom_face ()
— Function on jBio.Graphics.DOM.Label_zoomer: unknown base_font_size ()
— Function on jBio.Graphics.DOM.Label_zoomer: unknown do_zoom ()
— Function on jBio.Graphics.DOM.Label_zoomer: unknown domElement ()
— Function on jBio.Graphics.DOM.Label_zoomer: unknown height ()
— Function on jBio.Graphics.DOM.Label_zoomer: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.Graphics.DOM.Label_zoomer: unknown left ()
— Function on jBio.Graphics.DOM.Label_zoomer: unknown top ()
— Function on jBio.Graphics.DOM.Label_zoomer: unknown width ()

3.3.44 jBio.Graphics.DOM.Panel

— Class: jBio.Graphics.DOM.Panel : jBio.Root, jBio.Graphics.DOMbase, jBio.Graphics.Panel

DOM panel.

Definition at line 56 of file jbio.graphics.dom.panel.js.

— Variable of jBio.Graphics.DOM.Panel: static Number DOMindex

Initial value of index used to generate unique ids. Default: ‘0’.

— Variable of jBio.Graphics.DOM.Panel: static Number EXTRA_RIGHT_PADDING

Default: ‘30’.

— Variable of jBio.Graphics.DOM.Panel: static String GRIDCOLOR

Default: ‘#E0FFFF’.

— Variable of jBio.Graphics.DOM.Panel: static String KEYALIGN

Default: ‘left’.

— Variable of jBio.Graphics.DOM.Panel: static String KEYCOLOR

Default: ‘#F5DEB3’.

— Variable of jBio.Graphics.DOM.Panel: static String KEYLABELFONT

Default: ‘sans-serif’.

— Variable of jBio.Graphics.DOM.Panel: static Number KEYLABELFONTSIZE

Default: ‘12’.

— Variable of jBio.Graphics.DOM.Panel: static String KEYLABELFONTWEIGHT

Default: ‘bold’.

— Variable of jBio.Graphics.DOM.Panel: static Number KEYPADTOP

Default: ‘5’.

— Variable of jBio.Graphics.DOM.Panel: static Number KEYSPACING

Default: ‘5’.

— Variable of jBio.Graphics.DOM.Panel: static String KEYSTYLE

Default: ‘bottom’.

— Variable of jBio.Graphics.DOM.Panel: static String MISSING_TRACK_COLOR

Default: ‘gray’.

— Variable of jBio.Graphics.DOM.Panel: static Number Z_INDEX_GRID

Default: ‘3’.

— Variable of jBio.Graphics.DOM.Panel: static Number Z_INDEX_PANEL_BG

Default: ‘1’.

— Variable of jBio.Graphics.DOM.Panel: static Number Z_INDEX_POSTGRID

Default: ‘4’.

— Variable of jBio.Graphics.DOM.Panel: static Number Z_INDEX_TRACK_BG

Default: ‘2’.

— Variable of jBio.Graphics.DOM.Panel: static Number Z_INDEX_TRACK_FG

Default: ‘5’.

— Variable of jBio.Graphics.DOM.Panel: static Number api_version

Default: ‘1.0’.

— Variable of jBio.Graphics.DOM.Panel: String classname
— Variable of jBio.Graphics.DOM.Panel: Array of String parents
— Function on jBio.Graphics.DOM.Panel: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.Graphics.DOM.Panel: unknown _add_track ()
— Function on jBio.Graphics.DOM.Panel: unknown _do_add_track ()
— Function on jBio.Graphics.DOM.Panel: unknown _id_prefix ()
— Function on jBio.Graphics.DOM.Panel: unknown add_category_labels ()
— Function on jBio.Graphics.DOM.Panel: unknown add_track ()
— Function on jBio.Graphics.DOM.Panel: unknown all_callbacks ()
— Function on jBio.Graphics.DOM.Panel: unknown autopad ()
— Function on jBio.Graphics.DOM.Panel: unknown background ()
— Function on jBio.Graphics.DOM.Panel: unknown bgcolor ()
— Function on jBio.Graphics.DOM.Panel: unknown collision_controller ()
— Function on jBio.Graphics.DOM.Panel: unknown display_length ()
— Function on jBio.Graphics.DOM.Panel: unknown display_start ()
— Function on jBio.Graphics.DOM.Panel: unknown draftArea ()
— Function on jBio.Graphics.DOM.Panel: unknown draw ()
— Function on jBio.Graphics.DOM.Panel: unknown empty_track_style ()
— Function on jBio.Graphics.DOM.Panel: unknown escapeHTML ()
— Function on jBio.Graphics.DOM.Panel: unknown extend_grid ()
— Function on jBio.Graphics.DOM.Panel: unknown format_key ()
— Function on jBio.Graphics.DOM.Panel: unknown get_zoomer ()
— Function on jBio.Graphics.DOM.Panel: unknown grid ()
— Function on jBio.Graphics.DOM.Panel: unknown gridcolor ()
— Function on jBio.Graphics.DOM.Panel: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.Graphics.DOM.Panel: unknown key_align ()
— Function on jBio.Graphics.DOM.Panel: unknown key_boxes ()
— Function on jBio.Graphics.DOM.Panel: unknown key_color ()
— Function on jBio.Graphics.DOM.Panel: unknown key_font ()
— Function on jBio.Graphics.DOM.Panel: unknown key_font_size ()
— Function on jBio.Graphics.DOM.Panel: unknown key_font_weight ()
— Function on jBio.Graphics.DOM.Panel: unknown key_spacing ()
— Function on jBio.Graphics.DOM.Panel: unknown key_style ()
— Function on jBio.Graphics.DOM.Panel: unknown media ()
— Function on jBio.Graphics.DOM.Panel: unknown pad_bottom ()
— Function on jBio.Graphics.DOM.Panel: unknown pad_left ()
— Function on jBio.Graphics.DOM.Panel: unknown pad_right ()
— Function on jBio.Graphics.DOM.Panel: unknown pad_top ()
— Function on jBio.Graphics.DOM.Panel: unknown postgrid ()
— Function on jBio.Graphics.DOM.Panel: unknown track_spacing ()
— Function on jBio.Graphics.DOM.Panel: unknown tracks ()

3.3.45 jBio.Graphics.DOM.Panel_zoomer

— Class: jBio.Graphics.DOM.Panel_zoomer : jBio.Root, jBio.Graphics.DOM.Zoomer

Live panel resizer (zoomer).

Definition at line 330 of file jbio.graphics.dom.panel.js.

— Variable of jBio.Graphics.DOM.Panel_zoomer: String classname
— Variable of jBio.Graphics.DOM.Panel_zoomer: Array of String parents
— Function on jBio.Graphics.DOM.Panel_zoomer: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.Graphics.DOM.Panel_zoomer: unknown _zoom_face ()
— Function on jBio.Graphics.DOM.Panel_zoomer: unknown do_zoom ()
— Function on jBio.Graphics.DOM.Panel_zoomer: unknown domElement ()
— Function on jBio.Graphics.DOM.Panel_zoomer: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

3.3.46 jBio.Graphics.DOM.Position

— Class: jBio.Graphics.DOM.Position : jBio.Root, jBio.Graphics.Position

Rendered glyph position for DOM rendering.

Definition at line 376 of file jbio.graphics.dom.js.

— Variable of jBio.Graphics.DOM.Position: String classname
— Variable of jBio.Graphics.DOM.Position: Array of String parents
— Function on jBio.Graphics.DOM.Position: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.Graphics.DOM.Position: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.Graphics.DOM.Position: unknown layout ()
— Function on jBio.Graphics.DOM.Position: unknown move ()
— Function on jBio.Graphics.DOM.Position: unknown parent_bottom ()
— Function on jBio.Graphics.DOM.Position: unknown parent_left ()
— Function on jBio.Graphics.DOM.Position: unknown parent_right ()
— Function on jBio.Graphics.DOM.Position: unknown parent_top ()
— Function on jBio.Graphics.DOM.Position: unknown rendering ()

3.3.47 jBio.Graphics.DOM.Px2pt

— Class: jBio.Graphics.DOM.Px2pt : jBio.Root, jBio.Graphics.DOMbase, jBio.Graphics.Px2pt

Point to pixel conversion for DOM.

Definition at line 292 of file jbio.graphics.dom.js.

— Variable of jBio.Graphics.DOM.Px2pt: String classname
— Variable of jBio.Graphics.DOM.Px2pt: Array of String parents
— Function on jBio.Graphics.DOM.Px2pt: unknown DPI ()
— Function on jBio.Graphics.DOM.Px2pt: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.Graphics.DOM.Px2pt: unknown _obtainDPI ()
— Function on jBio.Graphics.DOM.Px2pt: unknown escapeHTML ()
— Function on jBio.Graphics.DOM.Px2pt: unknown get_zoomer ()
— Function on jBio.Graphics.DOM.Px2pt: unknown hookElement ()
— Function on jBio.Graphics.DOM.Px2pt: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.Graphics.DOM.Px2pt: unknown ptXpx ()
— Function on jBio.Graphics.DOM.Px2pt: unknown ptYpx ()
— Function on jBio.Graphics.DOM.Px2pt: unknown pxXpt ()
— Function on jBio.Graphics.DOM.Px2pt: unknown pxYpt ()
— Function on jBio.Graphics.DOM.Px2pt: unknown stringbounds ()

3.3.48 jBio.Graphics.DOM.Rendering

— Class: jBio.Graphics.DOM.Rendering : jBio.Root, jBio.Graphics.Rendering, jBio.Graphics.DOMbase

Document object model (DOM) rendering of glyph.

Definition at line 410 of file jbio.graphics.dom.js.

— Variable of jBio.Graphics.DOM.Rendering: String classname
— Variable of jBio.Graphics.DOM.Rendering: Array of String parents
— Function on jBio.Graphics.DOM.Rendering: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.Graphics.DOM.Rendering: unknown ca_elem ()
— Function on jBio.Graphics.DOM.Rendering: unknown escapeHTML ()
— Function on jBio.Graphics.DOM.Rendering: unknown get_zoomer ()
— Function on jBio.Graphics.DOM.Rendering: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.Graphics.DOM.Rendering: unknown part_renderings ()
— Function on jBio.Graphics.DOM.Rendering: unknown pe_rendering ()
— Function on jBio.Graphics.DOM.Rendering: unknown position ()
— Function on jBio.Graphics.DOM.Rendering: unknown root_elem ()
— Function on jBio.Graphics.DOM.Rendering: unknown root_elem_ca_elem_update ()
— Function on jBio.Graphics.DOM.Rendering: unknown root_elem_outline ()
— Function on jBio.Graphics.DOM.Rendering: unknown tk_elem ()

3.3.49 jBio.Graphics.DOM.Zoomer

— Class: jBio.Graphics.DOM.Zoomer : jBio.Root

Live element resizer (zoomer).

Definition at line 164 of file jbio.graphics.dom.js.

— Variable of jBio.Graphics.DOM.Zoomer: String classname
— Variable of jBio.Graphics.DOM.Zoomer: Array of String parents
— Function on jBio.Graphics.DOM.Zoomer: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.Graphics.DOM.Zoomer: unknown _zoom_face ()
— Function on jBio.Graphics.DOM.Zoomer: unknown do_zoom ()
— Function on jBio.Graphics.DOM.Zoomer: unknown domElement ()
— Function on jBio.Graphics.DOM.Zoomer: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

3.3.50 jBio.Graphics.DOM.Zoomer.Positioned

— Class: jBio.Graphics.DOM.Zoomer.Positioned : jBio.Root, jBio.Graphics.DOM.Zoomer

Live element resizer (zoomer) for simple positioned elements.

Definition at line 238 of file jbio.graphics.dom.js.

— Variable of jBio.Graphics.DOM.Zoomer.Positioned: String classname
— Variable of jBio.Graphics.DOM.Zoomer.Positioned: Array of String parents
— Function on jBio.Graphics.DOM.Zoomer.Positioned: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.Graphics.DOM.Zoomer.Positioned: unknown _zoom_face ()
— Function on jBio.Graphics.DOM.Zoomer.Positioned: unknown do_zoom ()
— Function on jBio.Graphics.DOM.Zoomer.Positioned: unknown domElement ()
— Function on jBio.Graphics.DOM.Zoomer.Positioned: unknown height ()
— Function on jBio.Graphics.DOM.Zoomer.Positioned: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.Graphics.DOM.Zoomer.Positioned: unknown left ()
— Function on jBio.Graphics.DOM.Zoomer.Positioned: unknown top ()
— Function on jBio.Graphics.DOM.Zoomer.Positioned: unknown width ()

3.3.51 jBio.Graphics.DOMbase

— Class: jBio.Graphics.DOMbase : jBio.Root

Base class for glyphs that draw through the document object model (DOM).

Definition at line 118 of file jbio.graphics.dom.js.

— Variable of jBio.Graphics.DOMbase: String classname
— Variable of jBio.Graphics.DOMbase: Array of String parents
— Function on jBio.Graphics.DOMbase: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.Graphics.DOMbase: unknown escapeHTML ()
— Function on jBio.Graphics.DOMbase: unknown get_zoomer ()
— Function on jBio.Graphics.DOMbase: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

3.3.52 jBio.Graphics.DOMevents_binderI

— Class: jBio.Graphics.DOMevents_binderI : jBio.Root

Base class for glyphs that receive DOM events.

Definition at line 29 of file jbio.graphics.dom.js.

— Variable of jBio.Graphics.DOMevents_binderI: String classname
— Variable of jBio.Graphics.DOMevents_binderI: Array of String parents
— Function on jBio.Graphics.DOMevents_binderI: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.Graphics.DOMevents_binderI: unknown _evtgt_bind_from_hash ()
— Function on jBio.Graphics.DOMevents_binderI: unknown evtgt_bind ()
— Function on jBio.Graphics.DOMevents_binderI: unknown evtgt_innervate ()
— Function on jBio.Graphics.DOMevents_binderI: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

3.3.53 jBio.Graphics.Exception.DOM

— Class: jBio.Graphics.Exception.DOM : jBio.Root

jBio.Graphics DOM exception.

Definition at line 48 of file jbio.graphics.js.

— Variable of jBio.Graphics.Exception.DOM: String classname
— Variable of jBio.Graphics.Exception.DOM: Array of String parents
— Function on jBio.Graphics.Exception.DOM: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.Graphics.Exception.DOM: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

3.3.54 jBio.Graphics.Feature

— Class: jBio.Graphics.Feature : jBio.Root, jBio.SeqFeature.Generic

Generic feature.

Essentially jBio.SeqFeature.Generic, the only modification is to the parameters of its constructor.

Definition at line 856 of file jbio.graphics.js.

— Variable of jBio.Graphics.Feature: String classname
— Variable of jBio.Graphics.Feature: Array of String parents
— Function on jBio.Graphics.Feature: unknown _add_flattened_SeqFeatures ()
— Function on jBio.Graphics.Feature: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.Graphics.Feature: unknown _expand_region ()
— Function on jBio.Graphics.Feature: unknown _testStrand ()

Private method for strand testing.

Definition at line 411 of file jbio.js.

— Function on jBio.Graphics.Feature: unknown add_SeqFeature ()
— Function on jBio.Graphics.Feature: unknown annotation ()
— Function on jBio.Graphics.Feature: Boolean contains (jBio.RangeI __other, Object __p)

Tests whether the range contains another.

Parameters:
__other
Other range.
__p
Parameter hash:
String strand-testing
‘strong’: Match if strands are defined and match.

‘weak’: Match if either strand is 0 or strands match.

‘ignore’: Disregard strands.


Returns:
‘true’ if range contains the other, ‘false’ otherwise.
Definition at line 455 of file jbio.js.

— Function on jBio.Graphics.Feature: unknown display_name ()
— Function on jBio.Graphics.Feature: unknown end ()
— Function on jBio.Graphics.Feature: unknown feature_count ()
— Function on jBio.Graphics.Feature: unknown get_SeqFeatures ()
— Function on jBio.Graphics.Feature: unknown get_all_SeqFeatures ()
— Function on jBio.Graphics.Feature: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.Graphics.Feature: size type llength ()

Get length of range: end()-start()+1.

Returns:
Current length: positive integer or ‘0’.
Definition at line 367 of file jbio.js.

— Function on jBio.Graphics.Feature: unknown location ()
— Function on jBio.Graphics.Feature: unknown primary_tag ()
— Function on jBio.Graphics.Feature: unknown remove_SeqFeatures ()
— Function on jBio.Graphics.Feature: unknown source_tag ()
— Function on jBio.Graphics.Feature: unknown start ()
— Function on jBio.Graphics.Feature: unknown strand ()

3.3.55 jBio.Graphics.Glyph.Factory

— Class: jBio.Graphics.Glyph.Factory : jBio.Root

Factory for glyph instances.

Definition at line 655 of file jbio.graphics.glyph.js.

— Variable of jBio.Graphics.Glyph.Factory: static Object DEFAULT_PROPERTIES

Default glyph properties:

String bgcolor
Background colour.
Number bump
Bump parameter for collision control.
Number bump_spacing
Bump spacing for collision control.
String fgcolor
Foreground colour.
String fontcolor
Font colour.
String font2color
Second font colour.
String font
Font.
Number font_size
Font size.
String font_weight
Font weight.
Number height
Glyph height.
String label_position
Label position.
Number linewidth
Line width.
Number quill_interval
Interval of a decorated line with small arrows indicating strandedness.
— Variable of jBio.Graphics.Glyph.Factory: String classname
— Variable of jBio.Graphics.Glyph.Factory: Array of String parents
— Function on jBio.Graphics.Glyph.Factory: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.Graphics.Glyph.Factory: unknown feature_to_glyph ()
— Function on jBio.Graphics.Glyph.Factory: unknown font ()
— Function on jBio.Graphics.Glyph.Factory: unknown get_glyph_property ()
— Function on jBio.Graphics.Glyph.Factory: unknown glyph_map ()
— Function on jBio.Graphics.Glyph.Factory: unknown glyph_properties ()
— Function on jBio.Graphics.Glyph.Factory: unknown glyph_property ()
— Function on jBio.Graphics.Glyph.Factory: unknown glyph_property_names ()
— Function on jBio.Graphics.Glyph.Factory: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.Graphics.Glyph.Factory: unknown make_glyph ()
— Function on jBio.Graphics.Glyph.Factory: unknown map_no_trunc ()
— Function on jBio.Graphics.Glyph.Factory: unknown overriding_glyph_properties ()
— Function on jBio.Graphics.Glyph.Factory: unknown panel ()
— Function on jBio.Graphics.Glyph.Factory: unknown scale ()
— Function on jBio.Graphics.Glyph.Factory: unknown set_glyph_property ()
— Function on jBio.Graphics.Glyph.Factory: unknown specialclass ()
— Function on jBio.Graphics.Glyph.Factory: unknown stylesheet ()

3.3.56 jBio.Graphics.GlyphI

— Class: jBio.Graphics.GlyphI : jBio.Root

Glyph.

A glyph provides visualisation for its associated feature.

Definition at line 96 of file jbio.graphics.glyph.js.

— Variable of jBio.Graphics.GlyphI: String classname
— Variable of jBio.Graphics.GlyphI: Array of String parents
— Function on jBio.Graphics.GlyphI: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.Graphics.GlyphI: unknown _subfeat ()
— Function on jBio.Graphics.GlyphI: unknown bgcolor ()
— Function on jBio.Graphics.GlyphI: unknown bump ()
— Function on jBio.Graphics.GlyphI: unknown collision_controller ()
— Function on jBio.Graphics.GlyphI: unknown connector ()
— Function on jBio.Graphics.GlyphI: unknown do_layout ()
— Function on jBio.Graphics.GlyphI: unknown draw ()
— Function on jBio.Graphics.GlyphI: unknown draw_track_key ()
— Function on jBio.Graphics.GlyphI: unknown end ()
— Function on jBio.Graphics.GlyphI: unknown exceeds_depth ()
— Function on jBio.Graphics.GlyphI: unknown factory ()
— Function on jBio.Graphics.GlyphI: unknown feature ()
— Function on jBio.Graphics.GlyphI: unknown feature_has_subparts ()
— Function on jBio.Graphics.GlyphI: unknown fgcolor ()
— Function on jBio.Graphics.GlyphI: unknown get_not_ignored_subparts ()
— Function on jBio.Graphics.GlyphI: unknown get_visible_parts ()
— Function on jBio.Graphics.GlyphI: unknown hbumppad ()
— Function on jBio.Graphics.GlyphI: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.Graphics.GlyphI: unknown layout_sort ()
— Function on jBio.Graphics.GlyphI: unknown level ()
— Function on jBio.Graphics.GlyphI: unknown llength ()
— Function on jBio.Graphics.GlyphI: unknown make_key_name ()
— Function on jBio.Graphics.GlyphI: unknown maxdepth ()
— Function on jBio.Graphics.GlyphI: unknown no_subparts ()
— Function on jBio.Graphics.GlyphI: unknown not_ignored_subparts ()
— Function on jBio.Graphics.GlyphI: unknown overbumped ()
— Function on jBio.Graphics.GlyphI: unknown pad_bottom ()
— Function on jBio.Graphics.GlyphI: unknown pad_left ()
— Function on jBio.Graphics.GlyphI: unknown pad_right ()
— Function on jBio.Graphics.GlyphI: unknown pad_top ()
— Function on jBio.Graphics.GlyphI: unknown panel ()
— Function on jBio.Graphics.GlyphI: unknown partno ()
— Function on jBio.Graphics.GlyphI: unknown parts ()
— Function on jBio.Graphics.GlyphI: unknown point ()
— Function on jBio.Graphics.GlyphI: unknown property ()
— Function on jBio.Graphics.GlyphI: unknown start ()
— Function on jBio.Graphics.GlyphI: unknown stop ()
— Function on jBio.Graphics.GlyphI: unknown subfeat ()
— Function on jBio.Graphics.GlyphI: unknown ticks ()
— Function on jBio.Graphics.GlyphI: unknown tkcolor ()
— Function on jBio.Graphics.GlyphI: unknown total_parts ()
— Function on jBio.Graphics.GlyphI: unknown track2key ()
— Function on jBio.Graphics.GlyphI: unknown track_index ()

3.3.57 jBio.Graphics.Layout

— Class: jBio.Graphics.Layout : jBio.Root

A layout of a visual element, such as a panel or glyph.

Definition at line 259 of file jbio.graphics.js.

— Variable of jBio.Graphics.Layout: String classname
— Variable of jBio.Graphics.Layout: Array of String parents
— Function on jBio.Graphics.Layout: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.Graphics.Layout: unknown content_height ()
— Function on jBio.Graphics.Layout: unknown content_width ()
— Function on jBio.Graphics.Layout: unknown display_end ()
— Function on jBio.Graphics.Layout: unknown display_length ()
— Function on jBio.Graphics.Layout: unknown display_start ()
— Function on jBio.Graphics.Layout: unknown full_height ()
— Function on jBio.Graphics.Layout: unknown full_width ()
— Function on jBio.Graphics.Layout: unknown ge ()
— Function on jBio.Graphics.Layout: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.Graphics.Layout: unknown pt2res ()
— Function on jBio.Graphics.Layout: unknown res2pt ()
— Function on jBio.Graphics.Layout: unknown scale ()
— Function on jBio.Graphics.Layout: unknown visible_parts ()
— Function on jBio.Graphics.Layout: unknown zooming ()

3.3.58 jBio.Graphics.Media

— Class: jBio.Graphics.Media : jBio.Root

Target media type base class.

The concept of tagets media types is similar to the CSS concept.

Definition at line 81 of file jbio.graphics.js.

— Variable of jBio.Graphics.Media: String classname
— Variable of jBio.Graphics.Media: Array of String parents
— Function on jBio.Graphics.Media: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.Graphics.Media: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.Graphics.Media: unknown minXpt ()
— Function on jBio.Graphics.Media: unknown minYpt ()
— Function on jBio.Graphics.Media: unknown px2pt ()

3.3.59 jBio.Graphics.Media.Print

— Class: jBio.Graphics.Media.Print : jBio.Root, jBio.Graphics.Media

Print target media type.

Definition at line 149 of file jbio.graphics.js.

— Variable of jBio.Graphics.Media.Print: String classname
— Variable of jBio.Graphics.Media.Print: Array of String parents
— Function on jBio.Graphics.Media.Print: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.Graphics.Media.Print: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.Graphics.Media.Print: unknown minXpt ()
— Function on jBio.Graphics.Media.Print: unknown minYpt ()
— Function on jBio.Graphics.Media.Print: unknown px2pt ()

3.3.60 jBio.Graphics.Media.Screen

— Class: jBio.Graphics.Media.Screen : jBio.Root, jBio.Graphics.Media

Screen target media type.

Definition at line 117 of file jbio.graphics.js.

— Variable of jBio.Graphics.Media.Screen: String classname
— Variable of jBio.Graphics.Media.Screen: Array of String parents
— Function on jBio.Graphics.Media.Screen: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.Graphics.Media.Screen: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.Graphics.Media.Screen: unknown minXpt ()
— Function on jBio.Graphics.Media.Screen: unknown minYpt ()
— Function on jBio.Graphics.Media.Screen: unknown px2pt ()

3.3.61 jBio.Graphics.Panel

— Class: jBio.Graphics.Panel : jBio.Root

Panel.

Definition at line 111 of file jbio.graphics.panel.js.

— Variable of jBio.Graphics.Panel: static Number EXTRA_RIGHT_PADDING

Default: ‘30’.

— Variable of jBio.Graphics.Panel: static String GRIDCOLOR

Default: ‘#E0FFFF’.

— Variable of jBio.Graphics.Panel: static String KEYALIGN

Default: ‘left’.

— Variable of jBio.Graphics.Panel: static String KEYCOLOR

Default: ‘#F5DEB3’.

— Variable of jBio.Graphics.Panel: static String KEYLABELFONT

Default: ‘sans-serif’.

— Variable of jBio.Graphics.Panel: static Number KEYLABELFONTSIZE

Default: ‘12’.

— Variable of jBio.Graphics.Panel: static String KEYLABELFONTWEIGHT

Default: ‘bold’.

— Variable of jBio.Graphics.Panel: static Number KEYPADTOP

Default: ‘5’.

— Variable of jBio.Graphics.Panel: static Number KEYSPACING

Default: ‘5’.

— Variable of jBio.Graphics.Panel: static String KEYSTYLE

Default: ‘bottom’.

— Variable of jBio.Graphics.Panel: static String MISSING_TRACK_COLOR

Default: ‘gray’.

— Variable of jBio.Graphics.Panel: static Number api_version

Default: ‘1.0’.

— Variable of jBio.Graphics.Panel: String classname
— Variable of jBio.Graphics.Panel: Array of String parents
— Function on jBio.Graphics.Panel: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.Graphics.Panel: unknown _add_track ()
— Function on jBio.Graphics.Panel: unknown _do_add_track ()
— Function on jBio.Graphics.Panel: unknown add_category_labels ()
— Function on jBio.Graphics.Panel: unknown add_track ()
— Function on jBio.Graphics.Panel: unknown all_callbacks ()
— Function on jBio.Graphics.Panel: unknown autopad ()
— Function on jBio.Graphics.Panel: unknown background ()
— Function on jBio.Graphics.Panel: unknown bgcolor ()
— Function on jBio.Graphics.Panel: unknown bottom ()
— Function on jBio.Graphics.Panel: unknown display_length ()
— Function on jBio.Graphics.Panel: unknown display_start ()
— Function on jBio.Graphics.Panel: unknown draw ()
— Function on jBio.Graphics.Panel: unknown empty_track_style ()
— Function on jBio.Graphics.Panel: unknown extend_grid ()
— Function on jBio.Graphics.Panel: unknown grid ()
— Function on jBio.Graphics.Panel: unknown gridcolor ()
— Function on jBio.Graphics.Panel: unknown image_class ()
— Function on jBio.Graphics.Panel: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.Graphics.Panel: unknown key_align ()
— Function on jBio.Graphics.Panel: unknown key_boxes ()
— Function on jBio.Graphics.Panel: unknown key_color ()
— Function on jBio.Graphics.Panel: unknown key_font ()
— Function on jBio.Graphics.Panel: unknown key_font_size ()
— Function on jBio.Graphics.Panel: unknown key_font_weight ()
— Function on jBio.Graphics.Panel: unknown key_spacing ()
— Function on jBio.Graphics.Panel: unknown key_style ()
— Function on jBio.Graphics.Panel: unknown left ()
— Function on jBio.Graphics.Panel: unknown llength ()
— Function on jBio.Graphics.Panel: unknown max_height ()
— Function on jBio.Graphics.Panel: unknown media ()
— Function on jBio.Graphics.Panel: unknown pad_bottom ()
— Function on jBio.Graphics.Panel: unknown pad_left ()
— Function on jBio.Graphics.Panel: unknown pad_right ()
— Function on jBio.Graphics.Panel: unknown pad_top ()
— Function on jBio.Graphics.Panel: unknown postgrid ()
— Function on jBio.Graphics.Panel: unknown right ()
— Function on jBio.Graphics.Panel: unknown top ()
— Function on jBio.Graphics.Panel: unknown track_spacing ()
— Function on jBio.Graphics.Panel: unknown tracks ()

3.3.62 jBio.Graphics.Position

— Class: jBio.Graphics.Position : jBio.Root

Rendered glyph position.

Definition at line 350 of file jbio.graphics.js.

— Variable of jBio.Graphics.Position: String classname
— Variable of jBio.Graphics.Position: Array of String parents
— Function on jBio.Graphics.Position: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.Graphics.Position: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.Graphics.Position: unknown layout ()
— Function on jBio.Graphics.Position: unknown move ()
— Function on jBio.Graphics.Position: unknown parent_bottom ()
— Function on jBio.Graphics.Position: unknown parent_left ()
— Function on jBio.Graphics.Position: unknown parent_right ()
— Function on jBio.Graphics.Position: unknown parent_top ()
— Function on jBio.Graphics.Position: unknown rendering ()

3.3.63 jBio.Graphics.Px2pt

— Class: jBio.Graphics.Px2pt : jBio.Root

Point to pixel conversion.

Definition at line 185 of file jbio.graphics.js.

— Variable of jBio.Graphics.Px2pt: String classname
— Variable of jBio.Graphics.Px2pt: Array of String parents
— Function on jBio.Graphics.Px2pt: unknown DPI ()
— Function on jBio.Graphics.Px2pt: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.Graphics.Px2pt: unknown _obtainDPI ()
— Function on jBio.Graphics.Px2pt: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.Graphics.Px2pt: unknown ptXpx ()
— Function on jBio.Graphics.Px2pt: unknown ptYpx ()
— Function on jBio.Graphics.Px2pt: unknown pxXpt ()
— Function on jBio.Graphics.Px2pt: unknown pxYpt ()
— Function on jBio.Graphics.Px2pt: unknown stringbounds ()

3.3.64 jBio.Graphics.Rendering

— Class: jBio.Graphics.Rendering : jBio.Root

A rendering of a visual element, such as a panel or glyph.

Definition at line 429 of file jbio.graphics.js.

— Variable of jBio.Graphics.Rendering: String classname
— Variable of jBio.Graphics.Rendering: Array of String parents
— Function on jBio.Graphics.Rendering: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.Graphics.Rendering: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.Graphics.Rendering: unknown part_renderings ()
— Function on jBio.Graphics.Rendering: unknown pe_rendering ()
— Function on jBio.Graphics.Rendering: unknown position ()

3.3.65 jBio.Graphics.Spacecentre

— Class: jBio.Graphics.Spacecentre : jBio.Root

Drawing space manager for alignment glyphs.

Keeps track of allocated segments of the drawing space and finds empty space for more drawing.

Definition at line 485 of file jbio.graphics.js.

— Variable of jBio.Graphics.Spacecentre: String classname
— Variable of jBio.Graphics.Spacecentre: Array of String parents
— Function on jBio.Graphics.Spacecentre: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.Graphics.Spacecentre: unknown _find_max_width ()
— Function on jBio.Graphics.Spacecentre: unknown _get_bigger_bins ()
— Function on jBio.Graphics.Spacecentre: unknown _get_bin ()
— Function on jBio.Graphics.Spacecentre: unknown _get_smaller_bins ()
— Function on jBio.Graphics.Spacecentre: unknown add_glyph_into_space ()
— Function on jBio.Graphics.Spacecentre: unknown add_new_glyph ()
— Function on jBio.Graphics.Spacecentre: unknown add_space ()
— Function on jBio.Graphics.Spacecentre: unknown binw ()
— Function on jBio.Graphics.Spacecentre: unknown find_space ()
— Function on jBio.Graphics.Spacecentre: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.Graphics.Spacecentre: unknown llength ()
— Function on jBio.Graphics.Spacecentre: unknown width ()

3.3.66 jBio.IdentifiableI

— Class: jBio.IdentifiableI : jBio.Root

Class with identifiers.

Pure abstract class.

Definition at line 1035 of file jbio.js.

— Variable of jBio.IdentifiableI: String classname
— Variable of jBio.IdentifiableI: Array of String parents
— Function on jBio.IdentifiableI: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.IdentifiableI: unknown authority ()
— Function on jBio.IdentifiableI: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.IdentifiableI: unknown namespace ()
— Function on jBio.IdentifiableI: unknown object_id ()
— Function on jBio.IdentifiableI: unknown version ()

3.3.67 jBio.Location.Atomic

— Class: jBio.Location.Atomic : jBio.Root, jBio.LocationI

Atomic location on sequence.

Definition at line 1263 of file jbio.js.

— Variable of jBio.Location.Atomic: String classname
— Variable of jBio.Location.Atomic: Array of String parents
— Function on jBio.Location.Atomic: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.Location.Atomic: unknown _testStrand ()

Private method for strand testing.

Definition at line 411 of file jbio.js.

— Function on jBio.Location.Atomic: Boolean contains (jBio.RangeI __other, Object __p)

Tests whether the range contains another.

Parameters:
__other
Other range.
__p
Parameter hash:
String strand-testing
‘strong’: Match if strands are defined and match.

‘weak’: Match if either strand is 0 or strands match.

‘ignore’: Disregard strands.


Returns:
‘true’ if range contains the other, ‘false’ otherwise.
Definition at line 455 of file jbio.js.

— Function on jBio.Location.Atomic: Object coordinate_policy (Object __nv)

Get/set coordinate policy.

Parameters:
__nv
New value. Optional.

Returns:
Current value.
Definition at line 567 of file jbio.js.

— Function on jBio.Location.Atomic: Number end (Number __nv)

Get/set end.

Parameters:
__nv
New value. Optional.

Returns:
Current value.
Definition at line 522 of file jbio.js.

— Function on jBio.Location.Atomic: String end_pos_type (String __nv)

Get/set end position type.

Parameters:
__nv
New value. Optional.

Returns:
Current value.
One of [‘BEFORE’|‘AFTER’|‘EXACT’|‘WITHIN’|‘BETWEEN’].

Definition at line 577 of file jbio.js.

— Function on jBio.Location.Atomic: Number flip_strand ()

Flip strand: strand *= -1.

Returns:
Current strand.
Definition at line 558 of file jbio.js.

— Function on jBio.Location.Atomic: Boolean is_remote (Boolean __nv)

Get/set remoteness.

Parameters:
__nv
New value. Optional.

Returns:
Current value.
BioPerl: A location is said to be remote if it is on a different `object' than the object which `has' this location.

Definition at line 587 of file jbio.js.

— Function on jBio.Location.Atomic: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.Location.Atomic: size type llength ()

Get length of range: end()-start()+1.

Returns:
Current length: positive integer or ‘0’.
Definition at line 367 of file jbio.js.

— Function on jBio.Location.Atomic: String location_type (String __nv)

Get/set location type.

Parameters:
__nv
New value. Optional.

Returns:
Current value.
One of: [‘..’|‘EXACT’|‘^’|‘IN-BETWEEN’].

Definition at line 506 of file jbio.js.

— Function on jBio.Location.Atomic: Number max_end (Number __nv)

Get/set maximum end.

Parameters:
__nv
New value. Optional.

Returns:
Current value.
Definition at line 596 of file jbio.js.

— Function on jBio.Location.Atomic: Number max_start (Number __nv)

Get/set maximum start.

Parameters:
__nv
New value. Optional.

Returns:
Current value.
Definition at line 540 of file jbio.js.

— Function on jBio.Location.Atomic: Number min_end (Number __nv)

Get/set minimum end.

Parameters:
__nv
New value. Optional.

Returns:
Current value.
Definition at line 605 of file jbio.js.

— Function on jBio.Location.Atomic: Number min_start (Number __nv)

Get/set minimum start.

Parameters:
__nv
New value. Optional.

Returns:
Current value.
Definition at line 531 of file jbio.js.

— Function on jBio.Location.Atomic: Object seq_id (Object __nv)

Get/set the identifier of sequence this location is related to.

Parameters:
__nv
New value. Optional.

Returns:
Current value.
Definition at line 614 of file jbio.js.

— Function on jBio.Location.Atomic: Number start (Number __nv)

Get/set start.

Parameters:
__nv
New value. Optional.

Returns:
Current value.
Definition at line 514 of file jbio.js.

— Function on jBio.Location.Atomic: String start_pos_type (String __nv)

Get/set start position type.

Parameters:
__nv
New value. Optional.

Returns:
Current value.
One of [‘BEFORE’|‘AFTER’|‘EXACT’|‘WITHIN’|‘BETWEEN’].

Definition at line 550 of file jbio.js.

— Function on jBio.Location.Atomic: unknown strand ()
— Function on jBio.Location.Atomic: String to_FTstring ()

Get textual representation.

Returns:
String representation of this location.
Definition at line 635 of file jbio.js.

3.3.68 jBio.Location.Ppxml.Alignment

— Class: jBio.Location.Ppxml.Alignment : jBio.Root, jBio.LocationI, jBio.XMLelementI

Location in a PredictProtein XML alignment.

See also the PredictProtein XML schema.

Definition at line 1495 of file jbio.js.

— Variable of jBio.Location.Ppxml.Alignment: String classname
— Variable of jBio.Location.Ppxml.Alignment: Array of String parents
— Function on jBio.Location.Ppxml.Alignment: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.Location.Ppxml.Alignment: unknown _testStrand ()

Private method for strand testing.

Definition at line 411 of file jbio.js.

— Function on jBio.Location.Ppxml.Alignment: Boolean contains (jBio.RangeI __other, Object __p)

Tests whether the range contains another.

Parameters:
__other
Other range.
__p
Parameter hash:
String strand-testing
‘strong’: Match if strands are defined and match.

‘weak’: Match if either strand is 0 or strands match.

‘ignore’: Disregard strands.


Returns:
‘true’ if range contains the other, ‘false’ otherwise.
Definition at line 455 of file jbio.js.

— Function on jBio.Location.Ppxml.Alignment: Object coordinate_policy (Object __nv)

Get/set coordinate policy.

Parameters:
__nv
New value. Optional.

Returns:
Current value.
Definition at line 567 of file jbio.js.

— Function on jBio.Location.Ppxml.Alignment: unknown end ()
— Function on jBio.Location.Ppxml.Alignment: String end_pos_type (String __nv)

Get/set end position type.

Parameters:
__nv
New value. Optional.

Returns:
Current value.
One of [‘BEFORE’|‘AFTER’|‘EXACT’|‘WITHIN’|‘BETWEEN’].

Definition at line 577 of file jbio.js.

— Function on jBio.Location.Ppxml.Alignment: Number flip_strand ()

Flip strand: strand *= -1.

Returns:
Current strand.
Definition at line 558 of file jbio.js.

— Function on jBio.Location.Ppxml.Alignment: unknown getElementsByTagNameAndAttr ()
— Function on jBio.Location.Ppxml.Alignment: Boolean is_remote (Boolean __nv)

Get/set remoteness.

Parameters:
__nv
New value. Optional.

Returns:
Current value.
BioPerl: A location is said to be remote if it is on a different `object' than the object which `has' this location.

Definition at line 587 of file jbio.js.

— Function on jBio.Location.Ppxml.Alignment: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.Location.Ppxml.Alignment: size type llength ()

Get length of range: end()-start()+1.

Returns:
Current length: positive integer or ‘0’.
Definition at line 367 of file jbio.js.

— Function on jBio.Location.Ppxml.Alignment: String location_type (String __nv)

Get/set location type.

Parameters:
__nv
New value. Optional.

Returns:
Current value.
One of: [‘..’|‘EXACT’|‘^’|‘IN-BETWEEN’].

Definition at line 506 of file jbio.js.

— Function on jBio.Location.Ppxml.Alignment: Number max_end (Number __nv)

Get/set maximum end.

Parameters:
__nv
New value. Optional.

Returns:
Current value.
Definition at line 596 of file jbio.js.

— Function on jBio.Location.Ppxml.Alignment: Number max_start (Number __nv)

Get/set maximum start.

Parameters:
__nv
New value. Optional.

Returns:
Current value.
Definition at line 540 of file jbio.js.

— Function on jBio.Location.Ppxml.Alignment: Number min_end (Number __nv)

Get/set minimum end.

Parameters:
__nv
New value. Optional.

Returns:
Current value.
Definition at line 605 of file jbio.js.

— Function on jBio.Location.Ppxml.Alignment: Number min_start (Number __nv)

Get/set minimum start.

Parameters:
__nv
New value. Optional.

Returns:
Current value.
Definition at line 531 of file jbio.js.

— Function on jBio.Location.Ppxml.Alignment: Object seq_id (Object __nv)

Get/set the identifier of sequence this location is related to.

Parameters:
__nv
New value. Optional.

Returns:
Current value.
Definition at line 614 of file jbio.js.

— Function on jBio.Location.Ppxml.Alignment: unknown start ()
— Function on jBio.Location.Ppxml.Alignment: String start_pos_type (String __nv)

Get/set start position type.

Parameters:
__nv
New value. Optional.

Returns:
Current value.
One of [‘BEFORE’|‘AFTER’|‘EXACT’|‘WITHIN’|‘BETWEEN’].

Definition at line 550 of file jbio.js.

— Function on jBio.Location.Ppxml.Alignment: Number strand (String __nv)

Get/set strand.

Parameters:
__nv
New value. Optional.

Returns:
Current numeric strand identifier.
Strand types are represented by three numerical values: ‘-1’, ‘0’ and ‘1’. These correspond to the ‘-’, ‘.’ (not applicable/not defined) and ‘+’ strands respectively. These symbols are also accepted when setting the value.

Definition at line 625 of file jbio.js.

— Function on jBio.Location.Ppxml.Alignment: String to_FTstring ()

Get textual representation.

Returns:
String representation of this location.
Definition at line 635 of file jbio.js.

— Function on jBio.Location.Ppxml.Alignment: unknown xml_instance ()

3.3.69 jBio.Location.Simple

— Class: jBio.Location.Simple : jBio.Root, jBio.Location.Atomic

Simple location.

Location with type ‘EXACT’ or ‘IN-BETWEEN’ (e.g. ‘12..15’ or ‘16^17’).

Definition at line 1320 of file jbio.js.

— Variable of jBio.Location.Simple: static const Object RANGEDECODE

Range symbol decoding hash: { 'EXACT': '..', 'IN-BETWEEN': '^' }.

— Variable of jBio.Location.Simple: static const Object RANGEENCODE

Range symbol encoding hash: { '\.\.': 'EXACT', '\^': 'IN-BETWEEN' }.

— Variable of jBio.Location.Simple: String classname
— Variable of jBio.Location.Simple: Array of String parents
— Function on jBio.Location.Simple: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.Location.Simple: unknown _testStrand ()

Private method for strand testing.

Definition at line 411 of file jbio.js.

— Function on jBio.Location.Simple: Boolean contains (jBio.RangeI __other, Object __p)

Tests whether the range contains another.

Parameters:
__other
Other range.
__p
Parameter hash:
String strand-testing
‘strong’: Match if strands are defined and match.

‘weak’: Match if either strand is 0 or strands match.

‘ignore’: Disregard strands.


Returns:
‘true’ if range contains the other, ‘false’ otherwise.
Definition at line 455 of file jbio.js.

— Function on jBio.Location.Simple: Object coordinate_policy (Object __nv)

Get/set coordinate policy.

Parameters:
__nv
New value. Optional.

Returns:
Current value.
Definition at line 567 of file jbio.js.

— Function on jBio.Location.Simple: unknown end ()
— Function on jBio.Location.Simple: String end_pos_type (String __nv)

Get/set end position type.

Parameters:
__nv
New value. Optional.

Returns:
Current value.
One of [‘BEFORE’|‘AFTER’|‘EXACT’|‘WITHIN’|‘BETWEEN’].

Definition at line 577 of file jbio.js.

— Function on jBio.Location.Simple: Number flip_strand ()

Flip strand: strand *= -1.

Returns:
Current strand.
Definition at line 558 of file jbio.js.

— Function on jBio.Location.Simple: Boolean is_remote (Boolean __nv)

Get/set remoteness.

Parameters:
__nv
New value. Optional.

Returns:
Current value.
BioPerl: A location is said to be remote if it is on a different `object' than the object which `has' this location.

Definition at line 587 of file jbio.js.

— Function on jBio.Location.Simple: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.Location.Simple: size type llength ()

Get length of range: end()-start()+1.

Returns:
Current length: positive integer or ‘0’.
Definition at line 367 of file jbio.js.

— Function on jBio.Location.Simple: unknown location_type ()
— Function on jBio.Location.Simple: Number max_end (Number __nv)

Get/set maximum end.

Parameters:
__nv
New value. Optional.

Returns:
Current value.
Definition at line 596 of file jbio.js.

— Function on jBio.Location.Simple: Number max_start (Number __nv)

Get/set maximum start.

Parameters:
__nv
New value. Optional.

Returns:
Current value.
Definition at line 540 of file jbio.js.

— Function on jBio.Location.Simple: Number min_end (Number __nv)

Get/set minimum end.

Parameters:
__nv
New value. Optional.

Returns:
Current value.
Definition at line 605 of file jbio.js.

— Function on jBio.Location.Simple: Number min_start (Number __nv)

Get/set minimum start.

Parameters:
__nv
New value. Optional.

Returns:
Current value.
Definition at line 531 of file jbio.js.

— Function on jBio.Location.Simple: Object seq_id (Object __nv)

Get/set the identifier of sequence this location is related to.

Parameters:
__nv
New value. Optional.

Returns:
Current value.
Definition at line 614 of file jbio.js.

— Function on jBio.Location.Simple: unknown start ()
— Function on jBio.Location.Simple: String start_pos_type (String __nv)

Get/set start position type.

Parameters:
__nv
New value. Optional.

Returns:
Current value.
One of [‘BEFORE’|‘AFTER’|‘EXACT’|‘WITHIN’|‘BETWEEN’].

Definition at line 550 of file jbio.js.

— Function on jBio.Location.Simple: unknown strand ()
— Function on jBio.Location.Simple: String to_FTstring ()

Get textual representation.

Returns:
String representation of this location.
Definition at line 635 of file jbio.js.

3.3.70 jBio.Location.Split

— Class: jBio.Location.Split : jBio.Root, jBio.Location.Atomic, jBio.Location.SplitLocationI

A location that has multiple start/end points, e.g. a set of exons.

Brings together jBio.Location.Atomic and jBio.Location.SplitLocationI.

Definition at line 1454 of file jbio.js.

— Variable of jBio.Location.Split: String classname
— Variable of jBio.Location.Split: Array of String parents
— Function on jBio.Location.Split: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.Location.Split: unknown _testStrand ()

Private method for strand testing.

Definition at line 411 of file jbio.js.

— Function on jBio.Location.Split: Boolean contains (jBio.RangeI __other, Object __p)

Tests whether the range contains another.

Parameters:
__other
Other range.
__p
Parameter hash:
String strand-testing
‘strong’: Match if strands are defined and match.

‘weak’: Match if either strand is 0 or strands match.

‘ignore’: Disregard strands.


Returns:
‘true’ if range contains the other, ‘false’ otherwise.
Definition at line 455 of file jbio.js.

— Function on jBio.Location.Split: Object coordinate_policy (Object __nv)

Get/set coordinate policy.

Parameters:
__nv
New value. Optional.

Returns:
Current value.
Definition at line 567 of file jbio.js.

— Function on jBio.Location.Split: Number end (Number __nv)

Get/set end.

Parameters:
__nv
New value. Optional.

Returns:
Current value.
Definition at line 522 of file jbio.js.

— Function on jBio.Location.Split: String end_pos_type (String __nv)

Get/set end position type.

Parameters:
__nv
New value. Optional.

Returns:
Current value.
One of [‘BEFORE’|‘AFTER’|‘EXACT’|‘WITHIN’|‘BETWEEN’].

Definition at line 577 of file jbio.js.

— Function on jBio.Location.Split: Number flip_strand ()

Flip strand: strand *= -1.

Returns:
Current strand.
Definition at line 558 of file jbio.js.

— Function on jBio.Location.Split: Boolean is_remote (Boolean __nv)

Get/set remoteness.

Parameters:
__nv
New value. Optional.

Returns:
Current value.
BioPerl: A location is said to be remote if it is on a different `object' than the object which `has' this location.

Definition at line 587 of file jbio.js.

— Function on jBio.Location.Split: unknown is_single_sequence ()
— Function on jBio.Location.Split: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.Location.Split: size type llength ()

Get length of range: end()-start()+1.

Returns:
Current length: positive integer or ‘0’.
Definition at line 367 of file jbio.js.

— Function on jBio.Location.Split: String location_type (String __nv)

Get/set location type.

Parameters:
__nv
New value. Optional.

Returns:
Current value.
One of: [‘..’|‘EXACT’|‘^’|‘IN-BETWEEN’].

Definition at line 506 of file jbio.js.

— Function on jBio.Location.Split: Number max_end (Number __nv)

Get/set maximum end.

Parameters:
__nv
New value. Optional.

Returns:
Current value.
Definition at line 596 of file jbio.js.

— Function on jBio.Location.Split: Number max_start (Number __nv)

Get/set maximum start.

Parameters:
__nv
New value. Optional.

Returns:
Current value.
Definition at line 540 of file jbio.js.

— Function on jBio.Location.Split: Number min_end (Number __nv)

Get/set minimum end.

Parameters:
__nv
New value. Optional.

Returns:
Current value.
Definition at line 605 of file jbio.js.

— Function on jBio.Location.Split: Number min_start (Number __nv)

Get/set minimum start.

Parameters:
__nv
New value. Optional.

Returns:
Current value.
Definition at line 531 of file jbio.js.

— Function on jBio.Location.Split: Object seq_id (Object __nv)

Get/set the identifier of sequence this location is related to.

Parameters:
__nv
New value. Optional.

Returns:
Current value.
Definition at line 614 of file jbio.js.

— Function on jBio.Location.Split: unknown splittype ()
— Function on jBio.Location.Split: Number start (Number __nv)

Get/set start.

Parameters:
__nv
New value. Optional.

Returns:
Current value.
Definition at line 514 of file jbio.js.

— Function on jBio.Location.Split: String start_pos_type (String __nv)

Get/set start position type.

Parameters:
__nv
New value. Optional.

Returns:
Current value.
One of [‘BEFORE’|‘AFTER’|‘EXACT’|‘WITHIN’|‘BETWEEN’].

Definition at line 550 of file jbio.js.

— Function on jBio.Location.Split: unknown strand ()
— Function on jBio.Location.Split: unknown sub_Location ()
— Function on jBio.Location.Split: String to_FTstring ()

Get textual representation.

Returns:
String representation of this location.
Definition at line 635 of file jbio.js.

3.3.71 jBio.Location.SplitLocationI

— Class: jBio.Location.SplitLocationI : jBio.Root, jBio.LocationI

A location that has multiple start/end points, e.g. a set of exons.

Definition at line 679 of file jbio.js.

— Variable of jBio.Location.SplitLocationI: String classname
— Variable of jBio.Location.SplitLocationI: Array of String parents
— Function on jBio.Location.SplitLocationI: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.Location.SplitLocationI: unknown _testStrand ()

Private method for strand testing.

Definition at line 411 of file jbio.js.

— Function on jBio.Location.SplitLocationI: Boolean contains (jBio.RangeI __other, Object __p)

Tests whether the range contains another.

Parameters:
__other
Other range.
__p
Parameter hash:
String strand-testing
‘strong’: Match if strands are defined and match.

‘weak’: Match if either strand is 0 or strands match.

‘ignore’: Disregard strands.


Returns:
‘true’ if range contains the other, ‘false’ otherwise.
Definition at line 455 of file jbio.js.

— Function on jBio.Location.SplitLocationI: Object coordinate_policy (Object __nv)

Get/set coordinate policy.

Parameters:
__nv
New value. Optional.

Returns:
Current value.
Definition at line 567 of file jbio.js.

— Function on jBio.Location.SplitLocationI: Number end (Number __nv)

Get/set end.

Parameters:
__nv
New value. Optional.

Returns:
Current value.
Definition at line 522 of file jbio.js.

— Function on jBio.Location.SplitLocationI: String end_pos_type (String __nv)

Get/set end position type.

Parameters:
__nv
New value. Optional.

Returns:
Current value.
One of [‘BEFORE’|‘AFTER’|‘EXACT’|‘WITHIN’|‘BETWEEN’].

Definition at line 577 of file jbio.js.

— Function on jBio.Location.SplitLocationI: Number flip_strand ()

Flip strand: strand *= -1.

Returns:
Current strand.
Definition at line 558 of file jbio.js.

— Function on jBio.Location.SplitLocationI: Boolean is_remote (Boolean __nv)

Get/set remoteness.

Parameters:
__nv
New value. Optional.

Returns:
Current value.
BioPerl: A location is said to be remote if it is on a different `object' than the object which `has' this location.

Definition at line 587 of file jbio.js.

— Function on jBio.Location.SplitLocationI: unknown is_single_sequence ()
— Function on jBio.Location.SplitLocationI: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.Location.SplitLocationI: size type llength ()

Get length of range: end()-start()+1.

Returns:
Current length: positive integer or ‘0’.
Definition at line 367 of file jbio.js.

— Function on jBio.Location.SplitLocationI: String location_type (String __nv)

Get/set location type.

Parameters:
__nv
New value. Optional.

Returns:
Current value.
One of: [‘..’|‘EXACT’|‘^’|‘IN-BETWEEN’].

Definition at line 506 of file jbio.js.

— Function on jBio.Location.SplitLocationI: Number max_end (Number __nv)

Get/set maximum end.

Parameters:
__nv
New value. Optional.

Returns:
Current value.
Definition at line 596 of file jbio.js.

— Function on jBio.Location.SplitLocationI: Number max_start (Number __nv)

Get/set maximum start.

Parameters:
__nv
New value. Optional.

Returns:
Current value.
Definition at line 540 of file jbio.js.

— Function on jBio.Location.SplitLocationI: Number min_end (Number __nv)

Get/set minimum end.

Parameters:
__nv
New value. Optional.

Returns:
Current value.
Definition at line 605 of file jbio.js.

— Function on jBio.Location.SplitLocationI: Number min_start (Number __nv)

Get/set minimum start.

Parameters:
__nv
New value. Optional.

Returns:
Current value.
Definition at line 531 of file jbio.js.

— Function on jBio.Location.SplitLocationI: Object seq_id (Object __nv)

Get/set the identifier of sequence this location is related to.

Parameters:
__nv
New value. Optional.

Returns:
Current value.
Definition at line 614 of file jbio.js.

— Function on jBio.Location.SplitLocationI: unknown splittype ()
— Function on jBio.Location.SplitLocationI: Number start (Number __nv)

Get/set start.

Parameters:
__nv
New value. Optional.

Returns:
Current value.
Definition at line 514 of file jbio.js.

— Function on jBio.Location.SplitLocationI: String start_pos_type (String __nv)

Get/set start position type.

Parameters:
__nv
New value. Optional.

Returns:
Current value.
One of [‘BEFORE’|‘AFTER’|‘EXACT’|‘WITHIN’|‘BETWEEN’].

Definition at line 550 of file jbio.js.

— Function on jBio.Location.SplitLocationI: Number strand (String __nv)

Get/set strand.

Parameters:
__nv
New value. Optional.

Returns:
Current numeric strand identifier.
Strand types are represented by three numerical values: ‘-1’, ‘0’ and ‘1’. These correspond to the ‘-’, ‘.’ (not applicable/not defined) and ‘+’ strands respectively. These symbols are also accepted when setting the value.

Definition at line 625 of file jbio.js.

— Function on jBio.Location.SplitLocationI: unknown sub_Location ()
— Function on jBio.Location.SplitLocationI: String to_FTstring ()

Get textual representation.

Returns:
String representation of this location.
Definition at line 635 of file jbio.js.

3.3.72 jBio.Location.UniProtKBXML

— Class: jBio.Location.UniProtKBXML : jBio.Root, jBio.LocationI, jBio.XMLelementI

Location in a UniProtKB XML document.

See also the UniProtKB XML schema.

Definition at line 1403 of file jbio.js.

— Variable of jBio.Location.UniProtKBXML: String classname
— Variable of jBio.Location.UniProtKBXML: Array of String parents
— Function on jBio.Location.UniProtKBXML: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.Location.UniProtKBXML: unknown _testStrand ()

Private method for strand testing.

Definition at line 411 of file jbio.js.

— Function on jBio.Location.UniProtKBXML: Boolean contains (jBio.RangeI __other, Object __p)

Tests whether the range contains another.

Parameters:
__other
Other range.
__p
Parameter hash:
String strand-testing
‘strong’: Match if strands are defined and match.

‘weak’: Match if either strand is 0 or strands match.

‘ignore’: Disregard strands.


Returns:
‘true’ if range contains the other, ‘false’ otherwise.
Definition at line 455 of file jbio.js.

— Function on jBio.Location.UniProtKBXML: Object coordinate_policy (Object __nv)

Get/set coordinate policy.

Parameters:
__nv
New value. Optional.

Returns:
Current value.
Definition at line 567 of file jbio.js.

— Function on jBio.Location.UniProtKBXML: unknown end ()
— Function on jBio.Location.UniProtKBXML: String end_pos_type (String __nv)

Get/set end position type.

Parameters:
__nv
New value. Optional.

Returns:
Current value.
One of [‘BEFORE’|‘AFTER’|‘EXACT’|‘WITHIN’|‘BETWEEN’].

Definition at line 577 of file jbio.js.

— Function on jBio.Location.UniProtKBXML: Number flip_strand ()

Flip strand: strand *= -1.

Returns:
Current strand.
Definition at line 558 of file jbio.js.

— Function on jBio.Location.UniProtKBXML: unknown getElementsByTagNameAndAttr ()
— Function on jBio.Location.UniProtKBXML: Boolean is_remote (Boolean __nv)

Get/set remoteness.

Parameters:
__nv
New value. Optional.

Returns:
Current value.
BioPerl: A location is said to be remote if it is on a different `object' than the object which `has' this location.

Definition at line 587 of file jbio.js.

— Function on jBio.Location.UniProtKBXML: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.Location.UniProtKBXML: size type llength ()

Get length of range: end()-start()+1.

Returns:
Current length: positive integer or ‘0’.
Definition at line 367 of file jbio.js.

— Function on jBio.Location.UniProtKBXML: String location_type (String __nv)

Get/set location type.

Parameters:
__nv
New value. Optional.

Returns:
Current value.
One of: [‘..’|‘EXACT’|‘^’|‘IN-BETWEEN’].

Definition at line 506 of file jbio.js.

— Function on jBio.Location.UniProtKBXML: Number max_end (Number __nv)

Get/set maximum end.

Parameters:
__nv
New value. Optional.

Returns:
Current value.
Definition at line 596 of file jbio.js.

— Function on jBio.Location.UniProtKBXML: Number max_start (Number __nv)

Get/set maximum start.

Parameters:
__nv
New value. Optional.

Returns:
Current value.
Definition at line 540 of file jbio.js.

— Function on jBio.Location.UniProtKBXML: Number min_end (Number __nv)

Get/set minimum end.

Parameters:
__nv
New value. Optional.

Returns:
Current value.
Definition at line 605 of file jbio.js.

— Function on jBio.Location.UniProtKBXML: Number min_start (Number __nv)

Get/set minimum start.

Parameters:
__nv
New value. Optional.

Returns:
Current value.
Definition at line 531 of file jbio.js.

— Function on jBio.Location.UniProtKBXML: Object seq_id (Object __nv)

Get/set the identifier of sequence this location is related to.

Parameters:
__nv
New value. Optional.

Returns:
Current value.
Definition at line 614 of file jbio.js.

— Function on jBio.Location.UniProtKBXML: unknown start ()
— Function on jBio.Location.UniProtKBXML: String start_pos_type (String __nv)

Get/set start position type.

Parameters:
__nv
New value. Optional.

Returns:
Current value.
One of [‘BEFORE’|‘AFTER’|‘EXACT’|‘WITHIN’|‘BETWEEN’].

Definition at line 550 of file jbio.js.

— Function on jBio.Location.UniProtKBXML: Number strand (String __nv)

Get/set strand.

Parameters:
__nv
New value. Optional.

Returns:
Current numeric strand identifier.
Strand types are represented by three numerical values: ‘-1’, ‘0’ and ‘1’. These correspond to the ‘-’, ‘.’ (not applicable/not defined) and ‘+’ strands respectively. These symbols are also accepted when setting the value.

Definition at line 625 of file jbio.js.

— Function on jBio.Location.UniProtKBXML: String to_FTstring ()

Get textual representation.

Returns:
String representation of this location.
Definition at line 635 of file jbio.js.

— Function on jBio.Location.UniProtKBXML: unknown xml_instance ()

3.3.73 jBio.LocationI

— Class: jBio.LocationI : jBio.Root, jBio.RangeI

Location.

This is an abstract class, defining the interface only.

Definition at line 496 of file jbio.js.

— Variable of jBio.LocationI: String classname
— Variable of jBio.LocationI: Array of String parents
— Function on jBio.LocationI: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.LocationI: unknown _testStrand ()

Private method for strand testing.

Definition at line 411 of file jbio.js.

— Function on jBio.LocationI: Boolean contains (jBio.RangeI __other, Object __p)

Tests whether the range contains another.

Parameters:
__other
Other range.
__p
Parameter hash:
String strand-testing
‘strong’: Match if strands are defined and match.

‘weak’: Match if either strand is 0 or strands match.

‘ignore’: Disregard strands.


Returns:
‘true’ if range contains the other, ‘false’ otherwise.
Definition at line 455 of file jbio.js.

— Function on jBio.LocationI: Object coordinate_policy (Object __nv)

Get/set coordinate policy.

Parameters:
__nv
New value. Optional.

Returns:
Current value.
Definition at line 567 of file jbio.js.

— Function on jBio.LocationI: Number end (Number __nv)

Get/set end.

Parameters:
__nv
New value. Optional.

Returns:
Current value.
Definition at line 522 of file jbio.js.

— Function on jBio.LocationI: String end_pos_type (String __nv)

Get/set end position type.

Parameters:
__nv
New value. Optional.

Returns:
Current value.
One of [‘BEFORE’|‘AFTER’|‘EXACT’|‘WITHIN’|‘BETWEEN’].

Definition at line 577 of file jbio.js.

— Function on jBio.LocationI: Number flip_strand ()

Flip strand: strand *= -1.

Returns:
Current strand.
Definition at line 558 of file jbio.js.

— Function on jBio.LocationI: Boolean is_remote (Boolean __nv)

Get/set remoteness.

Parameters:
__nv
New value. Optional.

Returns:
Current value.
BioPerl: A location is said to be remote if it is on a different `object' than the object which `has' this location.

Definition at line 587 of file jbio.js.

— Function on jBio.LocationI: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.LocationI: size type llength ()

Get length of range: end()-start()+1.

Returns:
Current length: positive integer or ‘0’.
Definition at line 367 of file jbio.js.

— Function on jBio.LocationI: String location_type (String __nv)

Get/set location type.

Parameters:
__nv
New value. Optional.

Returns:
Current value.
One of: [‘..’|‘EXACT’|‘^’|‘IN-BETWEEN’].

Definition at line 506 of file jbio.js.

— Function on jBio.LocationI: Number max_end (Number __nv)

Get/set maximum end.

Parameters:
__nv
New value. Optional.

Returns:
Current value.
Definition at line 596 of file jbio.js.

— Function on jBio.LocationI: Number max_start (Number __nv)

Get/set maximum start.

Parameters:
__nv
New value. Optional.

Returns:
Current value.
Definition at line 540 of file jbio.js.

— Function on jBio.LocationI: Number min_end (Number __nv)

Get/set minimum end.

Parameters:
__nv
New value. Optional.

Returns:
Current value.
Definition at line 605 of file jbio.js.

— Function on jBio.LocationI: Number min_start (Number __nv)

Get/set minimum start.

Parameters:
__nv
New value. Optional.

Returns:
Current value.
Definition at line 531 of file jbio.js.

— Function on jBio.LocationI: Object seq_id (Object __nv)

Get/set the identifier of sequence this location is related to.

Parameters:
__nv
New value. Optional.

Returns:
Current value.
Definition at line 614 of file jbio.js.

— Function on jBio.LocationI: Number start (Number __nv)

Get/set start.

Parameters:
__nv
New value. Optional.

Returns:
Current value.
Definition at line 514 of file jbio.js.

— Function on jBio.LocationI: String start_pos_type (String __nv)

Get/set start position type.

Parameters:
__nv
New value. Optional.

Returns:
Current value.
One of [‘BEFORE’|‘AFTER’|‘EXACT’|‘WITHIN’|‘BETWEEN’].

Definition at line 550 of file jbio.js.

— Function on jBio.LocationI: Number strand (String __nv)

Get/set strand.

Parameters:
__nv
New value. Optional.

Returns:
Current numeric strand identifier.
Strand types are represented by three numerical values: ‘-1’, ‘0’ and ‘1’. These correspond to the ‘-’, ‘.’ (not applicable/not defined) and ‘+’ strands respectively. These symbols are also accepted when setting the value.

Definition at line 625 of file jbio.js.

— Function on jBio.LocationI: String to_FTstring ()

Get textual representation.

Returns:
String representation of this location.
Definition at line 635 of file jbio.js.

3.3.74 jBio.PrimarySeq

— Class: jBio.PrimarySeq : jBio.Root, jBio.PrimarySeqI

`Lightweight' sequence.

Definition at line 1961 of file jbio.js.

— Variable of jBio.PrimarySeq: String classname
— Variable of jBio.PrimarySeq: Array of String parents
— Function on jBio.PrimarySeq: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.PrimarySeq: unknown _guess_alphabet ()
— Function on jBio.PrimarySeq: unknown accession_number ()
— Function on jBio.PrimarySeq: unknown alphabet ()
— Function on jBio.PrimarySeq: unknown authority ()
— Function on jBio.PrimarySeq: unknown description ()
— Function on jBio.PrimarySeq: unknown display_id ()
— Function on jBio.PrimarySeq: unknown display_name ()
— Function on jBio.PrimarySeq: unknown id ()
— Function on jBio.PrimarySeq: unknown is_circular ()
— Function on jBio.PrimarySeq: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.PrimarySeq: unknown llength ()
— Function on jBio.PrimarySeq: unknown namespace ()
— Function on jBio.PrimarySeq: unknown object_id ()
— Function on jBio.PrimarySeq: unknown primary_id ()
— Function on jBio.PrimarySeq: unknown seq ()
— Function on jBio.PrimarySeq: unknown subseq ()
— Function on jBio.PrimarySeq: unknown validate_seq ()
— Function on jBio.PrimarySeq: unknown version ()

3.3.75 jBio.PrimarySeqI

— Class: jBio.PrimarySeqI : jBio.Root, jBio.IdentifiableI, jBio.DescribableI

Sequence.

This is a simple sequence class, it is to bring together jBio.IdentifiableI and jBio.DescribableI and define some methods.

Definition at line 1103 of file jbio.js.

— Variable of jBio.PrimarySeqI: String classname
— Variable of jBio.PrimarySeqI: Array of String parents
— Function on jBio.PrimarySeqI: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.PrimarySeqI: unknown accession_number ()
— Function on jBio.PrimarySeqI: unknown alphabet ()
— Function on jBio.PrimarySeqI: unknown authority ()
— Function on jBio.PrimarySeqI: unknown description ()
— Function on jBio.PrimarySeqI: unknown display_id ()
— Function on jBio.PrimarySeqI: unknown display_name ()
— Function on jBio.PrimarySeqI: unknown is_circular ()
— Function on jBio.PrimarySeqI: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.PrimarySeqI: unknown llength ()
— Function on jBio.PrimarySeqI: unknown namespace ()
— Function on jBio.PrimarySeqI: unknown object_id ()
— Function on jBio.PrimarySeqI: unknown primary_id ()
— Function on jBio.PrimarySeqI: unknown seq ()
— Function on jBio.PrimarySeqI: unknown subseq ()
— Function on jBio.PrimarySeqI: unknown validate_seq ()
— Function on jBio.PrimarySeqI: unknown version ()

3.3.76 jBio.RangeI

— Class: jBio.RangeI : jBio.Root

Range of integer coordinates.

Definition at line 347 of file jbio.js.

— Variable of jBio.RangeI: String classname
— Variable of jBio.RangeI: Array of String parents
— Function on jBio.RangeI: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.RangeI: unknown _testStrand ()

Private method for strand testing.

Definition at line 411 of file jbio.js.

— Function on jBio.RangeI: Boolean contains (jBio.RangeI __other, Object __p)

Tests whether the range contains another.

Parameters:
__other
Other range.
__p
Parameter hash:
String strand-testing
‘strong’: Match if strands are defined and match.

‘weak’: Match if either strand is 0 or strands match.

‘ignore’: Disregard strands.


Returns:
‘true’ if range contains the other, ‘false’ otherwise.
Definition at line 455 of file jbio.js.

— Function on jBio.RangeI: positive integer end (positive integer __nv)

Get/set end of range.

Parameters:
__nv
New value. Optional.

Returns:
Current value.
Definition at line 358 of file jbio.js.

— Function on jBio.RangeI: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.RangeI: size type llength ()

Get length of range: end()-start()+1.

Returns:
Current length: positive integer or ‘0’.
Definition at line 367 of file jbio.js.

— Function on jBio.RangeI: positive integer start (positive integer __nv)

Get/set start of range.

Parameters:
__nv
New value. Optional.

Returns:
Current value.
Definition at line 376 of file jbio.js.

— Function on jBio.RangeI: Number strand (String __nv)

Get/set strand.

Parameters:
__nv
New value. Optional.

Returns:
Current numeric strand identifier.
Strand types are represented by three numerical values: ‘-1’, ‘0’ and ‘1’. These correspond to the ‘-’, ‘.’ (not applicable/not defined) and ‘+’ strands respectively. The symbols are also accepted when setting the value.

Definition at line 387 of file jbio.js.

3.3.77 jBio.Root

— Class: jBio.Root

This class provides type information handling.

All type-aware classes descend from jBio.Root.

Definition at line 125 of file jbio.js.

— Variable of jBio.Root: String classname
— Variable of jBio.Root: Array of String parents
— Function on jBio.Root: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.Root: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

3.3.78 jBio.Root.IO

— Class: jBio.Root.IO : jBio.Root

IO base.

Definition at line 3395 of file jbio.js.

— Variable of jBio.Root.IO: String classname
— Variable of jBio.Root.IO: Array of String parents
— Function on jBio.Root.IO: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.Root.IO: unknown _readbuffer ()
— Function on jBio.Root.IO: unknown _readline ()
— Function on jBio.Root.IO: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.Root.IO: unknown open ()

3.3.79 jBio.Root.SeqIO

— Class: jBio.Root.SeqIO : jBio.Root, jBio.Factory.SequenceStreamI, jBio.Root.IO

Sequence IO base.

Definition at line 3469 of file jbio.js.

— Variable of jBio.Root.SeqIO: String classname
— Variable of jBio.Root.SeqIO: Array of String parents
— Function on jBio.Root.SeqIO: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.Root.SeqIO: unknown _readbuffer ()
— Function on jBio.Root.SeqIO: unknown _readline ()
— Function on jBio.Root.SeqIO: unknown alphabet ()
— Function on jBio.Root.SeqIO: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.Root.SeqIO: unknown location_factory ()
— Function on jBio.Root.SeqIO: unknown next_seq ()
— Function on jBio.Root.SeqIO: unknown object_factory ()
— Function on jBio.Root.SeqIO: unknown open ()
— Function on jBio.Root.SeqIO: unknown sequence_builder ()
— Function on jBio.Root.SeqIO: unknown sequence_factory ()
— Function on jBio.Root.SeqIO: unknown write_seq ()

3.3.80 jBio.Seq

— Class: jBio.Seq : jBio.Root, jBio.Seqbase

Sequence.

This is the one you are looking for.

Definition at line 2912 of file jbio.js.

— Variable of jBio.Seq: String classname
— Variable of jBio.Seq: Array of String parents
— Function on jBio.Seq: unknown _add_flattened_SeqFeatures ()
— Function on jBio.Seq: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.Seq: unknown accession_number ()
— Function on jBio.Seq: unknown add_SeqFeature ()
— Function on jBio.Seq: unknown all_SeqFeatures ()
— Function on jBio.Seq: unknown alphabet ()
— Function on jBio.Seq: unknown annotation ()
— Function on jBio.Seq: unknown authority ()
— Function on jBio.Seq: unknown description ()
— Function on jBio.Seq: unknown display_id ()
— Function on jBio.Seq: unknown display_name ()
— Function on jBio.Seq: unknown feature_count ()
— Function on jBio.Seq: unknown get_SeqFeatures ()
— Function on jBio.Seq: unknown get_all_SeqFeatures ()
— Function on jBio.Seq: unknown id ()
— Function on jBio.Seq: unknown is_circular ()
— Function on jBio.Seq: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.Seq: unknown llength ()
— Function on jBio.Seq: unknown namespace ()
— Function on jBio.Seq: unknown object_id ()
— Function on jBio.Seq: unknown primary_id ()
— Function on jBio.Seq: unknown primary_seq ()
— Function on jBio.Seq: unknown remove_SeqFeatures ()
— Function on jBio.Seq: unknown seq ()
— Function on jBio.Seq: unknown species ()
— Function on jBio.Seq: unknown subseq ()
— Function on jBio.Seq: unknown validate_seq ()
— Function on jBio.Seq: unknown version ()
— Function on jBio.Seq: unknown write_GFF ()

3.3.81 jBio.Seq.RichSeq

— Class: jBio.Seq.RichSeq : jBio.Root, jBio.SeqI.RichSeqI, jBio.Seq

Sequence.

“Module implementing a sequence created from a rich sequence database entry.” The properties promised by the methods of this class are not necessarily provided.

Definition at line 3047 of file jbio.js.

— Variable of jBio.Seq.RichSeq: String classname
— Variable of jBio.Seq.RichSeq: Array of String parents
— Function on jBio.Seq.RichSeq: unknown _add_annotation_value ()
— Function on jBio.Seq.RichSeq: unknown _add_flattened_SeqFeatures ()
— Function on jBio.Seq.RichSeq: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.Seq.RichSeq: unknown _get_annotation_values ()
— Function on jBio.Seq.RichSeq: unknown accession ()
— Function on jBio.Seq.RichSeq: unknown accession_number ()
— Function on jBio.Seq.RichSeq: unknown add_SeqFeature ()
— Function on jBio.Seq.RichSeq: unknown add_date ()
— Function on jBio.Seq.RichSeq: unknown add_keyword ()
— Function on jBio.Seq.RichSeq: unknown add_secondary_accession ()
— Function on jBio.Seq.RichSeq: unknown all_SeqFeatures ()
— Function on jBio.Seq.RichSeq: unknown alphabet ()
— Function on jBio.Seq.RichSeq: unknown annotation ()
— Function on jBio.Seq.RichSeq: unknown authority ()
— Function on jBio.Seq.RichSeq: unknown description ()
— Function on jBio.Seq.RichSeq: unknown display_id ()
— Function on jBio.Seq.RichSeq: unknown display_name ()
— Function on jBio.Seq.RichSeq: unknown division ()
— Function on jBio.Seq.RichSeq: unknown feature_count ()
— Function on jBio.Seq.RichSeq: unknown get_SeqFeatures ()
— Function on jBio.Seq.RichSeq: unknown get_all_SeqFeatures ()
— Function on jBio.Seq.RichSeq: unknown get_dates ()
— Function on jBio.Seq.RichSeq: unknown get_keywords ()
— Function on jBio.Seq.RichSeq: unknown get_secondary_accessions ()
— Function on jBio.Seq.RichSeq: unknown id ()
— Function on jBio.Seq.RichSeq: unknown is_circular ()
— Function on jBio.Seq.RichSeq: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.Seq.RichSeq: unknown llength ()
— Function on jBio.Seq.RichSeq: unknown molecule ()
— Function on jBio.Seq.RichSeq: unknown namespace ()
— Function on jBio.Seq.RichSeq: unknown object_id ()
— Function on jBio.Seq.RichSeq: unknown pid ()
— Function on jBio.Seq.RichSeq: unknown primary_id ()
— Function on jBio.Seq.RichSeq: unknown primary_seq ()
— Function on jBio.Seq.RichSeq: unknown remove_SeqFeatures ()
— Function on jBio.Seq.RichSeq: unknown seq ()
— Function on jBio.Seq.RichSeq: unknown seq_version ()
— Function on jBio.Seq.RichSeq: unknown species ()
— Function on jBio.Seq.RichSeq: unknown subseq ()
— Function on jBio.Seq.RichSeq: unknown validate_seq ()
— Function on jBio.Seq.RichSeq: unknown version ()
— Function on jBio.Seq.RichSeq: unknown write_GFF ()

3.3.82 jBio.Seq.RichSeq.UniProtKBXML

— Class: jBio.Seq.RichSeq.UniProtKBXML : jBio.Root, jBio.SeqI.RichSeqI, jBio.XMLelementI, jBio.Seqbase

Sequence in a UniProtKB XML document.

See also the UniProtKB XML schema.

Definition at line 3147 of file jbio.js.

— Variable of jBio.Seq.RichSeq.UniProtKBXML: String classname
— Variable of jBio.Seq.RichSeq.UniProtKBXML: Array of String parents
— Function on jBio.Seq.RichSeq.UniProtKBXML: unknown _add_flattened_SeqFeatures ()
— Function on jBio.Seq.RichSeq.UniProtKBXML: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.Seq.RichSeq.UniProtKBXML: unknown accession_number ()
— Function on jBio.Seq.RichSeq.UniProtKBXML: unknown add_SeqFeature ()
— Function on jBio.Seq.RichSeq.UniProtKBXML: unknown alphabet ()
— Function on jBio.Seq.RichSeq.UniProtKBXML: unknown annotation ()
— Function on jBio.Seq.RichSeq.UniProtKBXML: unknown authority ()
— Function on jBio.Seq.RichSeq.UniProtKBXML: unknown description ()
— Function on jBio.Seq.RichSeq.UniProtKBXML: unknown display_id ()
— Function on jBio.Seq.RichSeq.UniProtKBXML: unknown display_name ()
— Function on jBio.Seq.RichSeq.UniProtKBXML: unknown division ()
— Function on jBio.Seq.RichSeq.UniProtKBXML: unknown feature_count ()
— Function on jBio.Seq.RichSeq.UniProtKBXML: unknown getElementsByTagNameAndAttr ()
— Function on jBio.Seq.RichSeq.UniProtKBXML: unknown get_SeqFeatures ()
— Function on jBio.Seq.RichSeq.UniProtKBXML: unknown get_all_SeqFeatures ()
— Function on jBio.Seq.RichSeq.UniProtKBXML: unknown get_dates ()
— Function on jBio.Seq.RichSeq.UniProtKBXML: unknown get_keywords ()
— Function on jBio.Seq.RichSeq.UniProtKBXML: unknown get_secondary_accessions ()
— Function on jBio.Seq.RichSeq.UniProtKBXML: unknown is_circular ()
— Function on jBio.Seq.RichSeq.UniProtKBXML: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.Seq.RichSeq.UniProtKBXML: unknown llength ()
— Function on jBio.Seq.RichSeq.UniProtKBXML: unknown molecule ()
— Function on jBio.Seq.RichSeq.UniProtKBXML: unknown namespace ()
— Function on jBio.Seq.RichSeq.UniProtKBXML: unknown object_id ()
— Function on jBio.Seq.RichSeq.UniProtKBXML: unknown pid ()
— Function on jBio.Seq.RichSeq.UniProtKBXML: unknown primary_id ()
— Function on jBio.Seq.RichSeq.UniProtKBXML: unknown primary_seq ()
— Function on jBio.Seq.RichSeq.UniProtKBXML: unknown remove_SeqFeatures ()
— Function on jBio.Seq.RichSeq.UniProtKBXML: unknown seq ()
— Function on jBio.Seq.RichSeq.UniProtKBXML: unknown seq_version ()
— Function on jBio.Seq.RichSeq.UniProtKBXML: unknown species ()
— Function on jBio.Seq.RichSeq.UniProtKBXML: unknown subseq ()
— Function on jBio.Seq.RichSeq.UniProtKBXML: unknown validate_seq ()
— Function on jBio.Seq.RichSeq.UniProtKBXML: unknown version ()
— Function on jBio.Seq.RichSeq.UniProtKBXML: unknown write_GFF ()
— Function on jBio.Seq.RichSeq.UniProtKBXML: unknown xml_instance ()

3.3.83 jBio.Seq.SeqFactory

— Class: jBio.Seq.SeqFactory : jBio.Root, jBio.Factory.SequenceFactoryI

Sequence factory for jBio.PrimarySeqI or jBio.Seq.QualI implementing sequences.

Definition at line 3252 of file jbio.js.

— Variable of jBio.Seq.SeqFactory: String classname
— Variable of jBio.Seq.SeqFactory: Array of String parents
— Function on jBio.Seq.SeqFactory: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.Seq.SeqFactory: unknown craete_object ()
— Function on jBio.Seq.SeqFactory: unknown create_object ()
— Function on jBio.Seq.SeqFactory: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.Seq.SeqFactory: unknown type ()

3.3.84 jBio.Seq.SeqFastaSpeedFactory

— Class: jBio.Seq.SeqFastaSpeedFactory : jBio.Root, jBio.Factory.SequenceFactoryI

No-frills sequence factory for jBio.PrimarySeqI or jBio.Seq.QualI implementing sequences.

If the sequence to be created comes from a FASTA format file, this implementation may have a speed advantage.

Definition at line 3300 of file jbio.js.

— Variable of jBio.Seq.SeqFastaSpeedFactory: String classname
— Variable of jBio.Seq.SeqFastaSpeedFactory: Array of String parents
— Function on jBio.Seq.SeqFastaSpeedFactory: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.Seq.SeqFastaSpeedFactory: unknown craete_object ()
— Function on jBio.Seq.SeqFastaSpeedFactory: unknown create_object ()
— Function on jBio.Seq.SeqFastaSpeedFactory: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.Seq.SeqFastaSpeedFactory: unknown type ()

3.3.85 jBio.SeqFeature.Alignment.Ppxml

— Class: jBio.SeqFeature.Alignment.Ppxml : jBio.Root, jBio.SeqFeature.Generic_base, jBio.XMLelementI

Alignment feature in a PredictProtein XML document.

Definition at line 1889 of file jbio.js.

— Variable of jBio.SeqFeature.Alignment.Ppxml: String classname
— Variable of jBio.SeqFeature.Alignment.Ppxml: Array of String parents
— Function on jBio.SeqFeature.Alignment.Ppxml: unknown _add_flattened_SeqFeatures ()
— Function on jBio.SeqFeature.Alignment.Ppxml: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.SeqFeature.Alignment.Ppxml: unknown _testStrand ()

Private method for strand testing.

Definition at line 411 of file jbio.js.

— Function on jBio.SeqFeature.Alignment.Ppxml: unknown add_SeqFeature ()
— Function on jBio.SeqFeature.Alignment.Ppxml: unknown annotation ()
— Function on jBio.SeqFeature.Alignment.Ppxml: Boolean contains (jBio.RangeI __other, Object __p)

Tests whether the range contains another.

Parameters:
__other
Other range.
__p
Parameter hash:
String strand-testing
‘strong’: Match if strands are defined and match.

‘weak’: Match if either strand is 0 or strands match.

‘ignore’: Disregard strands.


Returns:
‘true’ if range contains the other, ‘false’ otherwise.
Definition at line 455 of file jbio.js.

— Function on jBio.SeqFeature.Alignment.Ppxml: unknown display_name ()
— Function on jBio.SeqFeature.Alignment.Ppxml: unknown end ()
— Function on jBio.SeqFeature.Alignment.Ppxml: unknown feature_count ()
— Function on jBio.SeqFeature.Alignment.Ppxml: unknown getElementsByTagNameAndAttr ()
— Function on jBio.SeqFeature.Alignment.Ppxml: unknown get_SeqFeatures ()
— Function on jBio.SeqFeature.Alignment.Ppxml: unknown get_all_SeqFeatures ()
— Function on jBio.SeqFeature.Alignment.Ppxml: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.SeqFeature.Alignment.Ppxml: size type llength ()

Get length of range: end()-start()+1.

Returns:
Current length: positive integer or ‘0’.
Definition at line 367 of file jbio.js.

— Function on jBio.SeqFeature.Alignment.Ppxml: unknown location ()
— Function on jBio.SeqFeature.Alignment.Ppxml: unknown primary_tag ()
— Function on jBio.SeqFeature.Alignment.Ppxml: unknown remove_SeqFeatures ()
— Function on jBio.SeqFeature.Alignment.Ppxml: unknown source_tag ()
— Function on jBio.SeqFeature.Alignment.Ppxml: unknown start ()
— Function on jBio.SeqFeature.Alignment.Ppxml: unknown strand ()
— Function on jBio.SeqFeature.Alignment.Ppxml: unknown xml_instance ()

3.3.86 jBio.SeqFeature.DisoReg.Ppxml

— Class: jBio.SeqFeature.DisoReg.Ppxml : jBio.Root, jBio.SeqFeature.Generic.UniProtKBXML

Disordered region feature in a PredictProtein XML document.

Definition at line 1797 of file jbio.js.

— Variable of jBio.SeqFeature.DisoReg.Ppxml: String classname
— Variable of jBio.SeqFeature.DisoReg.Ppxml: Array of String parents
— Function on jBio.SeqFeature.DisoReg.Ppxml: unknown _add_flattened_SeqFeatures ()
— Function on jBio.SeqFeature.DisoReg.Ppxml: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.SeqFeature.DisoReg.Ppxml: unknown _expand_region ()
— Function on jBio.SeqFeature.DisoReg.Ppxml: unknown _testStrand ()

Private method for strand testing.

Definition at line 411 of file jbio.js.

— Function on jBio.SeqFeature.DisoReg.Ppxml: unknown add_SeqFeature ()
— Function on jBio.SeqFeature.DisoReg.Ppxml: unknown annotation ()
— Function on jBio.SeqFeature.DisoReg.Ppxml: Boolean contains (jBio.RangeI __other, Object __p)

Tests whether the range contains another.

Parameters:
__other
Other range.
__p
Parameter hash:
String strand-testing
‘strong’: Match if strands are defined and match.

‘weak’: Match if either strand is 0 or strands match.

‘ignore’: Disregard strands.


Returns:
‘true’ if range contains the other, ‘false’ otherwise.
Definition at line 455 of file jbio.js.

— Function on jBio.SeqFeature.DisoReg.Ppxml: unknown display_name ()
— Function on jBio.SeqFeature.DisoReg.Ppxml: unknown end ()
— Function on jBio.SeqFeature.DisoReg.Ppxml: unknown feature_count ()
— Function on jBio.SeqFeature.DisoReg.Ppxml: unknown getElementsByTagNameAndAttr ()
— Function on jBio.SeqFeature.DisoReg.Ppxml: unknown get_SeqFeatures ()
— Function on jBio.SeqFeature.DisoReg.Ppxml: unknown get_all_SeqFeatures ()
— Function on jBio.SeqFeature.DisoReg.Ppxml: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.SeqFeature.DisoReg.Ppxml: size type llength ()

Get length of range: end()-start()+1.

Returns:
Current length: positive integer or ‘0’.
Definition at line 367 of file jbio.js.

— Function on jBio.SeqFeature.DisoReg.Ppxml: unknown location ()
— Function on jBio.SeqFeature.DisoReg.Ppxml: unknown primary_tag ()
— Function on jBio.SeqFeature.DisoReg.Ppxml: unknown remove_SeqFeatures ()
— Function on jBio.SeqFeature.DisoReg.Ppxml: unknown source_tag ()
— Function on jBio.SeqFeature.DisoReg.Ppxml: unknown start ()
— Function on jBio.SeqFeature.DisoReg.Ppxml: unknown strand ()
— Function on jBio.SeqFeature.DisoReg.Ppxml: unknown xml_instance ()

3.3.87 jBio.SeqFeature.Generic

— Class: jBio.SeqFeature.Generic : jBio.Root, jBio.SeqFeature.Generic_base

Generic sequence feature.

Definition at line 1643 of file jbio.js.

— Variable of jBio.SeqFeature.Generic: String classname
— Variable of jBio.SeqFeature.Generic: Array of String parents
— Function on jBio.SeqFeature.Generic: unknown _add_flattened_SeqFeatures ()
— Function on jBio.SeqFeature.Generic: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.SeqFeature.Generic: unknown _expand_region ()
— Function on jBio.SeqFeature.Generic: unknown _testStrand ()

Private method for strand testing.

Definition at line 411 of file jbio.js.

— Function on jBio.SeqFeature.Generic: unknown add_SeqFeature ()
— Function on jBio.SeqFeature.Generic: unknown annotation ()
— Function on jBio.SeqFeature.Generic: Boolean contains (jBio.RangeI __other, Object __p)

Tests whether the range contains another.

Parameters:
__other
Other range.
__p
Parameter hash:
String strand-testing
‘strong’: Match if strands are defined and match.

‘weak’: Match if either strand is 0 or strands match.

‘ignore’: Disregard strands.


Returns:
‘true’ if range contains the other, ‘false’ otherwise.
Definition at line 455 of file jbio.js.

— Function on jBio.SeqFeature.Generic: unknown display_name ()
— Function on jBio.SeqFeature.Generic: unknown end ()
— Function on jBio.SeqFeature.Generic: unknown feature_count ()
— Function on jBio.SeqFeature.Generic: unknown get_SeqFeatures ()
— Function on jBio.SeqFeature.Generic: unknown get_all_SeqFeatures ()
— Function on jBio.SeqFeature.Generic: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.SeqFeature.Generic: size type llength ()

Get length of range: end()-start()+1.

Returns:
Current length: positive integer or ‘0’.
Definition at line 367 of file jbio.js.

— Function on jBio.SeqFeature.Generic: unknown location ()
— Function on jBio.SeqFeature.Generic: unknown primary_tag ()
— Function on jBio.SeqFeature.Generic: unknown remove_SeqFeatures ()
— Function on jBio.SeqFeature.Generic: unknown source_tag ()
— Function on jBio.SeqFeature.Generic: unknown start ()
— Function on jBio.SeqFeature.Generic: unknown strand ()

3.3.88 jBio.SeqFeature.Generic.UniProtKBXML

— Class: jBio.SeqFeature.Generic.UniProtKBXML : jBio.Root, jBio.SeqFeature.Generic_base, jBio.XMLelementI

Generic sequence feature in a UniProtKB XML document.

See also the UniProtKB XML schema.

Definition at line 1724 of file jbio.js.

— Variable of jBio.SeqFeature.Generic.UniProtKBXML: String classname
— Variable of jBio.SeqFeature.Generic.UniProtKBXML: Array of String parents
— Function on jBio.SeqFeature.Generic.UniProtKBXML: unknown _add_flattened_SeqFeatures ()
— Function on jBio.SeqFeature.Generic.UniProtKBXML: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.SeqFeature.Generic.UniProtKBXML: unknown _expand_region ()
— Function on jBio.SeqFeature.Generic.UniProtKBXML: unknown _testStrand ()

Private method for strand testing.

Definition at line 411 of file jbio.js.

— Function on jBio.SeqFeature.Generic.UniProtKBXML: unknown add_SeqFeature ()
— Function on jBio.SeqFeature.Generic.UniProtKBXML: unknown annotation ()
— Function on jBio.SeqFeature.Generic.UniProtKBXML: Boolean contains (jBio.RangeI __other, Object __p)

Tests whether the range contains another.

Parameters:
__other
Other range.
__p
Parameter hash:
String strand-testing
‘strong’: Match if strands are defined and match.

‘weak’: Match if either strand is 0 or strands match.

‘ignore’: Disregard strands.


Returns:
‘true’ if range contains the other, ‘false’ otherwise.
Definition at line 455 of file jbio.js.

— Function on jBio.SeqFeature.Generic.UniProtKBXML: unknown display_name ()
— Function on jBio.SeqFeature.Generic.UniProtKBXML: unknown end ()
— Function on jBio.SeqFeature.Generic.UniProtKBXML: unknown feature_count ()
— Function on jBio.SeqFeature.Generic.UniProtKBXML: unknown getElementsByTagNameAndAttr ()
— Function on jBio.SeqFeature.Generic.UniProtKBXML: unknown get_SeqFeatures ()
— Function on jBio.SeqFeature.Generic.UniProtKBXML: unknown get_all_SeqFeatures ()
— Function on jBio.SeqFeature.Generic.UniProtKBXML: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.SeqFeature.Generic.UniProtKBXML: size type llength ()

Get length of range: end()-start()+1.

Returns:
Current length: positive integer or ‘0’.
Definition at line 367 of file jbio.js.

— Function on jBio.SeqFeature.Generic.UniProtKBXML: unknown location ()
— Function on jBio.SeqFeature.Generic.UniProtKBXML: unknown primary_tag ()
— Function on jBio.SeqFeature.Generic.UniProtKBXML: unknown remove_SeqFeatures ()
— Function on jBio.SeqFeature.Generic.UniProtKBXML: unknown source_tag ()
— Function on jBio.SeqFeature.Generic.UniProtKBXML: unknown start ()
— Function on jBio.SeqFeature.Generic.UniProtKBXML: unknown strand ()
— Function on jBio.SeqFeature.Generic.UniProtKBXML: unknown xml_instance ()

3.3.89 jBio.SeqFeature.GenericI

— Class: jBio.SeqFeature.GenericI : jBio.Root, jBio.SeqFeatureI, jBio.FeatureHolderI

Generic sequence feature.

Brings together its parents, jBio.SeqFeatureI and jBio.FeatureHolderI.

Definition at line 913 of file jbio.js.

— Variable of jBio.SeqFeature.GenericI: String classname
— Variable of jBio.SeqFeature.GenericI: Array of String parents
— Function on jBio.SeqFeature.GenericI: unknown _add_flattened_SeqFeatures ()
— Function on jBio.SeqFeature.GenericI: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.SeqFeature.GenericI: unknown _testStrand ()

Private method for strand testing.

Definition at line 411 of file jbio.js.

— Function on jBio.SeqFeature.GenericI: unknown add_SeqFeature ()
— Function on jBio.SeqFeature.GenericI: unknown annotation ()
— Function on jBio.SeqFeature.GenericI: Boolean contains (jBio.RangeI __other, Object __p)

Tests whether the range contains another.

Parameters:
__other
Other range.
__p
Parameter hash:
String strand-testing
‘strong’: Match if strands are defined and match.

‘weak’: Match if either strand is 0 or strands match.

‘ignore’: Disregard strands.


Returns:
‘true’ if range contains the other, ‘false’ otherwise.
Definition at line 455 of file jbio.js.

— Function on jBio.SeqFeature.GenericI: unknown display_name ()
— Function on jBio.SeqFeature.GenericI: positive integer end (positive integer __nv)

Get/set end of range.

Parameters:
__nv
New value. Optional.

Returns:
Current value.
Definition at line 358 of file jbio.js.

— Function on jBio.SeqFeature.GenericI: unknown feature_count ()
— Function on jBio.SeqFeature.GenericI: unknown get_SeqFeatures ()
— Function on jBio.SeqFeature.GenericI: unknown get_all_SeqFeatures ()
— Function on jBio.SeqFeature.GenericI: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.SeqFeature.GenericI: size type llength ()

Get length of range: end()-start()+1.

Returns:
Current length: positive integer or ‘0’.
Definition at line 367 of file jbio.js.

— Function on jBio.SeqFeature.GenericI: unknown location ()
— Function on jBio.SeqFeature.GenericI: unknown primary_tag ()
— Function on jBio.SeqFeature.GenericI: unknown remove_SeqFeatures ()
— Function on jBio.SeqFeature.GenericI: unknown source_tag ()
— Function on jBio.SeqFeature.GenericI: positive integer start (positive integer __nv)

Get/set start of range.

Parameters:
__nv
New value. Optional.

Returns:
Current value.
Definition at line 376 of file jbio.js.

— Function on jBio.SeqFeature.GenericI: Number strand (String __nv)

Get/set strand.

Parameters:
__nv
New value. Optional.

Returns:
Current numeric strand identifier.
Strand types are represented by three numerical values: ‘-1’, ‘0’ and ‘1’. These correspond to the ‘-’, ‘.’ (not applicable/not defined) and ‘+’ strands respectively. The symbols are also accepted when setting the value.

Definition at line 387 of file jbio.js.

3.3.90 jBio.SeqFeature.Generic_base

— Class: jBio.SeqFeature.Generic_base : jBio.Root, jBio.SeqFeature.GenericI

Generic sequence feature base for `real' classes.

Definition at line 1597 of file jbio.js.

— Variable of jBio.SeqFeature.Generic_base: String classname
— Variable of jBio.SeqFeature.Generic_base: Array of String parents
— Function on jBio.SeqFeature.Generic_base: unknown _add_flattened_SeqFeatures ()
— Function on jBio.SeqFeature.Generic_base: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.SeqFeature.Generic_base: unknown _testStrand ()

Private method for strand testing.

Definition at line 411 of file jbio.js.

— Function on jBio.SeqFeature.Generic_base: unknown add_SeqFeature ()
— Function on jBio.SeqFeature.Generic_base: unknown annotation ()
— Function on jBio.SeqFeature.Generic_base: Boolean contains (jBio.RangeI __other, Object __p)

Tests whether the range contains another.

Parameters:
__other
Other range.
__p
Parameter hash:
String strand-testing
‘strong’: Match if strands are defined and match.

‘weak’: Match if either strand is 0 or strands match.

‘ignore’: Disregard strands.


Returns:
‘true’ if range contains the other, ‘false’ otherwise.
Definition at line 455 of file jbio.js.

— Function on jBio.SeqFeature.Generic_base: unknown display_name ()
— Function on jBio.SeqFeature.Generic_base: unknown end ()
— Function on jBio.SeqFeature.Generic_base: unknown feature_count ()
— Function on jBio.SeqFeature.Generic_base: unknown get_SeqFeatures ()
— Function on jBio.SeqFeature.Generic_base: unknown get_all_SeqFeatures ()
— Function on jBio.SeqFeature.Generic_base: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.SeqFeature.Generic_base: size type llength ()

Get length of range: end()-start()+1.

Returns:
Current length: positive integer or ‘0’.
Definition at line 367 of file jbio.js.

— Function on jBio.SeqFeature.Generic_base: unknown location ()
— Function on jBio.SeqFeature.Generic_base: unknown primary_tag ()
— Function on jBio.SeqFeature.Generic_base: unknown remove_SeqFeatures ()
— Function on jBio.SeqFeature.Generic_base: unknown source_tag ()
— Function on jBio.SeqFeature.Generic_base: unknown start ()
— Function on jBio.SeqFeature.Generic_base: unknown strand ()

3.3.91 jBio.SeqFeature.SolvAcc.Ppxml

— Class: jBio.SeqFeature.SolvAcc.Ppxml : jBio.Root, jBio.SeqFeature.Generic.UniProtKBXML

Solvent accessibility feature in a PredictProtein XML document.

Definition at line 1840 of file jbio.js.

— Variable of jBio.SeqFeature.SolvAcc.Ppxml: String classname
— Variable of jBio.SeqFeature.SolvAcc.Ppxml: Array of String parents
— Function on jBio.SeqFeature.SolvAcc.Ppxml: unknown _add_flattened_SeqFeatures ()
— Function on jBio.SeqFeature.SolvAcc.Ppxml: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.SeqFeature.SolvAcc.Ppxml: unknown _expand_region ()
— Function on jBio.SeqFeature.SolvAcc.Ppxml: unknown _testStrand ()

Private method for strand testing.

Definition at line 411 of file jbio.js.

— Function on jBio.SeqFeature.SolvAcc.Ppxml: unknown add_SeqFeature ()
— Function on jBio.SeqFeature.SolvAcc.Ppxml: unknown annotation ()
— Function on jBio.SeqFeature.SolvAcc.Ppxml: Boolean contains (jBio.RangeI __other, Object __p)

Tests whether the range contains another.

Parameters:
__other
Other range.
__p
Parameter hash:
String strand-testing
‘strong’: Match if strands are defined and match.

‘weak’: Match if either strand is 0 or strands match.

‘ignore’: Disregard strands.


Returns:
‘true’ if range contains the other, ‘false’ otherwise.
Definition at line 455 of file jbio.js.

— Function on jBio.SeqFeature.SolvAcc.Ppxml: unknown display_name ()
— Function on jBio.SeqFeature.SolvAcc.Ppxml: unknown end ()
— Function on jBio.SeqFeature.SolvAcc.Ppxml: unknown feature_count ()
— Function on jBio.SeqFeature.SolvAcc.Ppxml: unknown getElementsByTagNameAndAttr ()
— Function on jBio.SeqFeature.SolvAcc.Ppxml: unknown get_SeqFeatures ()
— Function on jBio.SeqFeature.SolvAcc.Ppxml: unknown get_all_SeqFeatures ()
— Function on jBio.SeqFeature.SolvAcc.Ppxml: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.SeqFeature.SolvAcc.Ppxml: size type llength ()

Get length of range: end()-start()+1.

Returns:
Current length: positive integer or ‘0’.
Definition at line 367 of file jbio.js.

— Function on jBio.SeqFeature.SolvAcc.Ppxml: unknown location ()
— Function on jBio.SeqFeature.SolvAcc.Ppxml: unknown primary_tag ()
— Function on jBio.SeqFeature.SolvAcc.Ppxml: unknown remove_SeqFeatures ()
— Function on jBio.SeqFeature.SolvAcc.Ppxml: unknown source_tag ()
— Function on jBio.SeqFeature.SolvAcc.Ppxml: unknown start ()
— Function on jBio.SeqFeature.SolvAcc.Ppxml: unknown strand ()
— Function on jBio.SeqFeature.SolvAcc.Ppxml: unknown xml_instance ()

3.3.92 jBio.SeqFeatureI

— Class: jBio.SeqFeatureI : jBio.Root, jBio.AnnotatableI, jBio.RangeI

Sequence feature.

Pure abstract class.

Definition at line 812 of file jbio.js.

— Variable of jBio.SeqFeatureI: String classname
— Variable of jBio.SeqFeatureI: Array of String parents
— Function on jBio.SeqFeatureI: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.SeqFeatureI: unknown _testStrand ()

Private method for strand testing.

Definition at line 411 of file jbio.js.

— Function on jBio.SeqFeatureI: unknown annotation ()
— Function on jBio.SeqFeatureI: Boolean contains (jBio.RangeI __other, Object __p)

Tests whether the range contains another.

Parameters:
__other
Other range.
__p
Parameter hash:
String strand-testing
‘strong’: Match if strands are defined and match.

‘weak’: Match if either strand is 0 or strands match.

‘ignore’: Disregard strands.


Returns:
‘true’ if range contains the other, ‘false’ otherwise.
Definition at line 455 of file jbio.js.

— Function on jBio.SeqFeatureI: unknown display_name ()
— Function on jBio.SeqFeatureI: positive integer end (positive integer __nv)

Get/set end of range.

Parameters:
__nv
New value. Optional.

Returns:
Current value.
Definition at line 358 of file jbio.js.

— Function on jBio.SeqFeatureI: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.SeqFeatureI: size type llength ()

Get length of range: end()-start()+1.

Returns:
Current length: positive integer or ‘0’.
Definition at line 367 of file jbio.js.

— Function on jBio.SeqFeatureI: unknown location ()
— Function on jBio.SeqFeatureI: unknown primary_tag ()
— Function on jBio.SeqFeatureI: unknown source_tag ()
— Function on jBio.SeqFeatureI: positive integer start (positive integer __nv)

Get/set start of range.

Parameters:
__nv
New value. Optional.

Returns:
Current value.
Definition at line 376 of file jbio.js.

— Function on jBio.SeqFeatureI: Number strand (String __nv)

Get/set strand.

Parameters:
__nv
New value. Optional.

Returns:
Current numeric strand identifier.
Strand types are represented by three numerical values: ‘-1’, ‘0’ and ‘1’. These correspond to the ‘-’, ‘.’ (not applicable/not defined) and ‘+’ strands respectively. The symbols are also accepted when setting the value.

Definition at line 387 of file jbio.js.

3.3.93 jBio.SeqI

— Class: jBio.SeqI : jBio.Root, jBio.PrimarySeqI, jBio.AnnotatableI, jBio.DescribableI, jBio.FeatureHolderI, jBio.IdentifiableI

Sequence with features.

This class is used to define the interface.

Definition at line 1143 of file jbio.js.

— Variable of jBio.SeqI: String classname
— Variable of jBio.SeqI: Array of String parents
— Function on jBio.SeqI: unknown _add_flattened_SeqFeatures ()
— Function on jBio.SeqI: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.SeqI: unknown accession_number ()
— Function on jBio.SeqI: unknown add_SeqFeature ()
— Function on jBio.SeqI: unknown alphabet ()
— Function on jBio.SeqI: unknown annotation ()
— Function on jBio.SeqI: unknown authority ()
— Function on jBio.SeqI: unknown description ()
— Function on jBio.SeqI: unknown display_id ()
— Function on jBio.SeqI: unknown display_name ()
— Function on jBio.SeqI: unknown feature_count ()
— Function on jBio.SeqI: unknown get_SeqFeatures ()
— Function on jBio.SeqI: unknown get_all_SeqFeatures ()
— Function on jBio.SeqI: unknown is_circular ()
— Function on jBio.SeqI: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.SeqI: unknown llength ()
— Function on jBio.SeqI: unknown namespace ()
— Function on jBio.SeqI: unknown object_id ()
— Function on jBio.SeqI: unknown primary_id ()
— Function on jBio.SeqI: unknown primary_seq ()
— Function on jBio.SeqI: unknown remove_SeqFeatures ()
— Function on jBio.SeqI: unknown seq ()
— Function on jBio.SeqI: unknown species ()
— Function on jBio.SeqI: unknown subseq ()
— Function on jBio.SeqI: unknown validate_seq ()
— Function on jBio.SeqI: unknown version ()
— Function on jBio.SeqI: unknown write_GFF ()

3.3.94 jBio.SeqI.RichSeqI

— Class: jBio.SeqI.RichSeqI : jBio.Root, jBio.SeqI

Sequence with features and more methods.

Definition at line 1177 of file jbio.js.

— Variable of jBio.SeqI.RichSeqI: String classname
— Variable of jBio.SeqI.RichSeqI: Array of String parents
— Function on jBio.SeqI.RichSeqI: unknown _add_flattened_SeqFeatures ()
— Function on jBio.SeqI.RichSeqI: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.SeqI.RichSeqI: unknown accession_number ()
— Function on jBio.SeqI.RichSeqI: unknown add_SeqFeature ()
— Function on jBio.SeqI.RichSeqI: unknown alphabet ()
— Function on jBio.SeqI.RichSeqI: unknown annotation ()
— Function on jBio.SeqI.RichSeqI: unknown authority ()
— Function on jBio.SeqI.RichSeqI: unknown description ()
— Function on jBio.SeqI.RichSeqI: unknown display_id ()
— Function on jBio.SeqI.RichSeqI: unknown display_name ()
— Function on jBio.SeqI.RichSeqI: unknown division ()
— Function on jBio.SeqI.RichSeqI: unknown feature_count ()
— Function on jBio.SeqI.RichSeqI: unknown get_SeqFeatures ()
— Function on jBio.SeqI.RichSeqI: unknown get_all_SeqFeatures ()
— Function on jBio.SeqI.RichSeqI: unknown get_dates ()
— Function on jBio.SeqI.RichSeqI: unknown get_keywords ()
— Function on jBio.SeqI.RichSeqI: unknown get_secondary_accessions ()
— Function on jBio.SeqI.RichSeqI: unknown is_circular ()
— Function on jBio.SeqI.RichSeqI: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.SeqI.RichSeqI: unknown llength ()
— Function on jBio.SeqI.RichSeqI: unknown molecule ()
— Function on jBio.SeqI.RichSeqI: unknown namespace ()
— Function on jBio.SeqI.RichSeqI: unknown object_id ()
— Function on jBio.SeqI.RichSeqI: unknown pid ()
— Function on jBio.SeqI.RichSeqI: unknown primary_id ()
— Function on jBio.SeqI.RichSeqI: unknown primary_seq ()
— Function on jBio.SeqI.RichSeqI: unknown remove_SeqFeatures ()
— Function on jBio.SeqI.RichSeqI: unknown seq ()
— Function on jBio.SeqI.RichSeqI: unknown seq_version ()
— Function on jBio.SeqI.RichSeqI: unknown species ()
— Function on jBio.SeqI.RichSeqI: unknown subseq ()
— Function on jBio.SeqI.RichSeqI: unknown validate_seq ()
— Function on jBio.SeqI.RichSeqI: unknown version ()
— Function on jBio.SeqI.RichSeqI: unknown write_GFF ()

3.3.95 jBio.SeqIO.Ppxml

— Class: jBio.SeqIO.Ppxml : jBio.Root, jBio.SeqIO.UniProtKBXML

PredictProtein XML format IO handler.

Read only.

Definition at line 3676 of file jbio.js.

— Variable of jBio.SeqIO.Ppxml: String classname
— Variable of jBio.SeqIO.Ppxml: Array of String parents
— Function on jBio.SeqIO.Ppxml: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.SeqIO.Ppxml: unknown _readbuffer ()
— Function on jBio.SeqIO.Ppxml: unknown _readline ()
— Function on jBio.SeqIO.Ppxml: unknown _root_element ()
— Function on jBio.SeqIO.Ppxml: unknown alphabet ()
— Function on jBio.SeqIO.Ppxml: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.SeqIO.Ppxml: unknown location_factory ()
— Function on jBio.SeqIO.Ppxml: unknown next_seq ()
— Function on jBio.SeqIO.Ppxml: unknown object_factory ()
— Function on jBio.SeqIO.Ppxml: unknown open ()
— Function on jBio.SeqIO.Ppxml: unknown sequence_builder ()
— Function on jBio.SeqIO.Ppxml: unknown sequence_factory ()
— Function on jBio.SeqIO.Ppxml: unknown write_seq ()

3.3.96 jBio.SeqIO.UniProtKBXML

— Class: jBio.SeqIO.UniProtKBXML : jBio.Root, jBio.Root.SeqIO

UniProtKB XML format IO handler.

Read only.

Definition at line 3607 of file jbio.js.

— Variable of jBio.SeqIO.UniProtKBXML: String classname
— Variable of jBio.SeqIO.UniProtKBXML: Array of String parents
— Function on jBio.SeqIO.UniProtKBXML: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.SeqIO.UniProtKBXML: unknown _readbuffer ()
— Function on jBio.SeqIO.UniProtKBXML: unknown _readline ()
— Function on jBio.SeqIO.UniProtKBXML: unknown _root_element ()
— Function on jBio.SeqIO.UniProtKBXML: unknown alphabet ()
— Function on jBio.SeqIO.UniProtKBXML: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.SeqIO.UniProtKBXML: unknown location_factory ()
— Function on jBio.SeqIO.UniProtKBXML: unknown next_seq ()
— Function on jBio.SeqIO.UniProtKBXML: unknown object_factory ()
— Function on jBio.SeqIO.UniProtKBXML: unknown open ()
— Function on jBio.SeqIO.UniProtKBXML: unknown sequence_builder ()
— Function on jBio.SeqIO.UniProtKBXML: unknown sequence_factory ()
— Function on jBio.SeqIO.UniProtKBXML: unknown write_seq ()

3.3.97 jBio.SeqIO.fasta

— Class: jBio.SeqIO.fasta : jBio.Root, jBio.Root.SeqIO

FASTA format IO handler.

Read only.

Definition at line 3536 of file jbio.js.

— Variable of jBio.SeqIO.fasta: String classname
— Variable of jBio.SeqIO.fasta: Array of String parents
— Function on jBio.SeqIO.fasta: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.SeqIO.fasta: unknown _readbuffer ()
— Function on jBio.SeqIO.fasta: unknown _readline ()
— Function on jBio.SeqIO.fasta: unknown alphabet ()
— Function on jBio.SeqIO.fasta: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.SeqIO.fasta: unknown location_factory ()
— Function on jBio.SeqIO.fasta: unknown next_seq ()
— Function on jBio.SeqIO.fasta: unknown object_factory ()
— Function on jBio.SeqIO.fasta: unknown open ()
— Function on jBio.SeqIO.fasta: unknown sequence_builder ()
— Function on jBio.SeqIO.fasta: unknown sequence_factory ()
— Function on jBio.SeqIO.fasta: unknown write_seq ()

3.3.98 jBio.Seqbase

— Class: jBio.Seqbase : jBio.Root, jBio.SeqI

Class providing common implementation of certain methods for derived sequence classes such as jBio.Seq.

Definition at line 2854 of file jbio.js.

— Variable of jBio.Seqbase: String classname
— Variable of jBio.Seqbase: Array of String parents
— Function on jBio.Seqbase: unknown _add_flattened_SeqFeatures ()
— Function on jBio.Seqbase: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.Seqbase: unknown accession_number ()
— Function on jBio.Seqbase: unknown add_SeqFeature ()
— Function on jBio.Seqbase: unknown alphabet ()
— Function on jBio.Seqbase: unknown annotation ()
— Function on jBio.Seqbase: unknown authority ()
— Function on jBio.Seqbase: unknown description ()
— Function on jBio.Seqbase: unknown display_id ()
— Function on jBio.Seqbase: unknown display_name ()
— Function on jBio.Seqbase: unknown feature_count ()
— Function on jBio.Seqbase: unknown get_SeqFeatures ()
— Function on jBio.Seqbase: unknown get_all_SeqFeatures ()
— Function on jBio.Seqbase: unknown is_circular ()
— Function on jBio.Seqbase: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.Seqbase: unknown llength ()
— Function on jBio.Seqbase: unknown namespace ()
— Function on jBio.Seqbase: unknown object_id ()
— Function on jBio.Seqbase: unknown primary_id ()
— Function on jBio.Seqbase: unknown primary_seq ()
— Function on jBio.Seqbase: unknown remove_SeqFeatures ()
— Function on jBio.Seqbase: unknown seq ()
— Function on jBio.Seqbase: unknown species ()
— Function on jBio.Seqbase: unknown subseq ()
— Function on jBio.Seqbase: unknown validate_seq ()
— Function on jBio.Seqbase: unknown version ()
— Function on jBio.Seqbase: unknown write_GFF ()

3.3.99 jBio.XMLelementI

— Class: jBio.XMLelementI : jBio.Root

XML element representation with additional methods.

Definition at line 1214 of file jbio.js.

— Variable of jBio.XMLelementI: String classname
— Variable of jBio.XMLelementI: Array of String parents
— Function on jBio.XMLelementI: Array of String _add_parents (Array of String __typenames)

Add parents to class.

Parameters:
__typenames
Class names in an array.

Returns:
The value of __typenames.
Multiple inheritance aid. Attributes and methods of latter parents override former ones. Also sets parents attribute to __typenames, automatically adding jBio.Root to the list, so do not specify that. Give each parent only once.

Definition at line 148 of file jbio.js.

— Function on jBio.XMLelementI: unknown getElementsByTagNameAndAttr ()
— Function on jBio.XMLelementI: Boolean isa (String __typename)

Instance type checking.

Parameters:
__typename
Class name.

Returns:
true if instance is a __typename, false otherwise. 
          if( ! someinstance.isa('jBio.RangeI') ) alert('Big trouble!');

Definition at line 134 of file jbio.js.

— Function on jBio.XMLelementI: unknown xml_instance ()

4 Results and discussion

5 Acknowledgements

6 References

?. Stajich JE, Block D, Boulez K, Brenner SE, Chervitz SA, Dagdigian C, Fuellen G, Gilbert JG, Korf I, Lapp H, Lehväslaiho H, Matsalla C, Mungall CJ, Osborne BI, Pocock MR, Schattner P, Senger M, Stein LD, Stupka E, Wilkinson MD, Birney E. The Bioperl toolkit: Perl modules for the life sciences. Genome Res. 2002;12(10):1611-8.

?. UniProt Consortium. The Universal Protein Resource (UniProt). Nucleic Acids Res. 2007 Jan;35(Database issue):D193-7. Epub 2006 Nov 16.

Appendix A GNU Free Documentation License

Version 1.2, November 2002
Copyright © 2000,2001,2002 Free Software Foundation, Inc.
51 Franklin St, Fifth Floor, Boston, MA  02110-1301, USA

Everyone is permitted to copy and distribute verbatim copies
of this license document, but changing it is not allowed.
  1. PREAMBLE

    The purpose of this License is to make a manual, textbook, or other functional and useful document free in the sense of freedom: to assure everyone the effective freedom to copy and redistribute it, with or without modifying it, either commercially or noncommercially. Secondarily, this License preserves for the author and publisher a way to get credit for their work, while not being considered responsible for modifications made by others.

    This License is a kind of “copyleft”, which means that derivative works of the document must themselves be free in the same sense. It complements the GNU General Public License, which is a copyleft license designed for free software.

    We have designed this License in order to use it for manuals for free software, because free software needs free documentation: a free program should come with manuals providing the same freedoms that the software does. But this License is not limited to software manuals; it can be used for any textual work, regardless of subject matter or whether it is published as a printed book. We recommend this License principally for works whose purpose is instruction or reference.

  2. APPLICABILITY AND DEFINITIONS

    This License applies to any manual or other work, in any medium, that contains a notice placed by the copyright holder saying it can be distributed under the terms of this License. Such a notice grants a world-wide, royalty-free license, unlimited in duration, to use that work under the conditions stated herein. The “Document”, below, refers to any such manual or work. Any member of the public is a licensee, and is addressed as “you”. You accept the license if you copy, modify or distribute the work in a way requiring permission under copyright law.

    A “Modified Version” of the Document means any work containing the Document or a portion of it, either copied verbatim, or with modifications and/or translated into another language.

    A “Secondary Section” is a named appendix or a front-matter section of the Document that deals exclusively with the relationship of the publishers or authors of the Document to the Document's overall subject (or to related matters) and contains nothing that could fall directly within that overall subject. (Thus, if the Document is in part a textbook of mathematics, a Secondary Section may not explain any mathematics.) The relationship could be a matter of historical connection with the subject or with related matters, or of legal, commercial, philosophical, ethical or political position regarding them.

    The “Invariant Sections” are certain Secondary Sections whose titles are designated, as being those of Invariant Sections, in the notice that says that the Document is released under this License. If a section does not fit the above definition of Secondary then it is not allowed to be designated as Invariant. The Document may contain zero Invariant Sections. If the Document does not identify any Invariant Sections then there are none.

    The “Cover Texts” are certain short passages of text that are listed, as Front-Cover Texts or Back-Cover Texts, in the notice that says that the Document is released under this License. A Front-Cover Text may be at most 5 words, and a Back-Cover Text may be at most 25 words.

    A “Transparent” copy of the Document means a machine-readable copy, represented in a format whose specification is available to the general public, that is suitable for revising the document straightforwardly with generic text editors or (for images composed of pixels) generic paint programs or (for drawings) some widely available drawing editor, and that is suitable for input to text formatters or for automatic translation to a variety of formats suitable for input to text formatters. A copy made in an otherwise Transparent file format whose markup, or absence of markup, has been arranged to thwart or discourage subsequent modification by readers is not Transparent. An image format is not Transparent if used for any substantial amount of text. A copy that is not “Transparent” is called “Opaque”.

    Examples of suitable formats for Transparent copies include plain ascii without markup, Texinfo input format, LaTeX input format, SGML or XML using a publicly available DTD, and standard-conforming simple HTML, PostScript or PDF designed for human modification. Examples of transparent image formats include PNG, XCF and JPG. Opaque formats include proprietary formats that can be read and edited only by proprietary word processors, SGML or XML for which the DTD and/or processing tools are not generally available, and the machine-generated HTML, PostScript or PDF produced by some word processors for output purposes only.

    The “Title Page” means, for a printed book, the title page itself, plus such following pages as are needed to hold, legibly, the material this License requires to appear in the title page. For works in formats which do not have any title page as such, “Title Page” means the text near the most prominent appearance of the work's title, preceding the beginning of the body of the text.

    A section “Entitled XYZ” means a named subunit of the Document whose title either is precisely XYZ or contains XYZ in parentheses following text that translates XYZ in another language. (Here XYZ stands for a specific section name mentioned below, such as “Acknowledgements”, “Dedications”, “Endorsements”, or “History”.) To “Preserve the Title” of such a section when you modify the Document means that it remains a section “Entitled XYZ” according to this definition.

    The Document may include Warranty Disclaimers next to the notice which states that this License applies to the Document. These Warranty Disclaimers are considered to be included by reference in this License, but only as regards disclaiming warranties: any other implication that these Warranty Disclaimers may have is void and has no effect on the meaning of this License.

  3. VERBATIM COPYING

    You may copy and distribute the Document in any medium, either commercially or noncommercially, provided that this License, the copyright notices, and the license notice saying this License applies to the Document are reproduced in all copies, and that you add no other conditions whatsoever to those of this License. You may not use technical measures to obstruct or control the reading or further copying of the copies you make or distribute. However, you may accept compensation in exchange for copies. If you distribute a large enough number of copies you must also follow the conditions in section 3.

    You may also lend copies, under the same conditions stated above, and you may publicly display copies.

  4. COPYING IN QUANTITY

    If you publish printed copies (or copies in media that commonly have printed covers) of the Document, numbering more than 100, and the Document's license notice requires Cover Texts, you must enclose the copies in covers that carry, clearly and legibly, all these Cover Texts: Front-Cover Texts on the front cover, and Back-Cover Texts on the back cover. Both covers must also clearly and legibly identify you as the publisher of these copies. The front cover must present the full title with all words of the title equally prominent and visible. You may add other material on the covers in addition. Copying with changes limited to the covers, as long as they preserve the title of the Document and satisfy these conditions, can be treated as verbatim copying in other respects.

    If the required texts for either cover are too voluminous to fit legibly, you should put the first ones listed (as many as fit reasonably) on the actual cover, and continue the rest onto adjacent pages.

    If you publish or distribute Opaque copies of the Document numbering more than 100, you must either include a machine-readable Transparent copy along with each Opaque copy, or state in or with each Opaque copy a computer-network location from which the general network-using public has access to download using public-standard network protocols a complete Transparent copy of the Document, free of added material. If you use the latter option, you must take reasonably prudent steps, when you begin distribution of Opaque copies in quantity, to ensure that this Transparent copy will remain thus accessible at the stated location until at least one year after the last time you distribute an Opaque copy (directly or through your agents or retailers) of that edition to the public.

    It is requested, but not required, that you contact the authors of the Document well before redistributing any large number of copies, to give them a chance to provide you with an updated version of the Document.

  5. MODIFICATIONS

    You may copy and distribute a Modified Version of the Document under the conditions of sections 2 and 3 above, provided that you release the Modified Version under precisely this License, with the Modified Version filling the role of the Document, thus licensing distribution and modification of the Modified Version to whoever possesses a copy of it. In addition, you must do these things in the Modified Version:

    1. Use in the Title Page (and on the covers, if any) a title distinct from that of the Document, and from those of previous versions (which should, if there were any, be listed in the History section of the Document). You may use the same title as a previous version if the original publisher of that version gives permission.
    2. List on the Title Page, as authors, one or more persons or entities responsible for authorship of the modifications in the Modified Version, together with at least five of the principal authors of the Document (all of its principal authors, if it has fewer than five), unless they release you from this requirement.
    3. State on the Title page the name of the publisher of the Modified Version, as the publisher.
    4. Preserve all the copyright notices of the Document.
    5. Add an appropriate copyright notice for your modifications adjacent to the other copyright notices.
    6. Include, immediately after the copyright notices, a license notice giving the public permission to use the Modified Version under the terms of this License, in the form shown in the Addendum below.
    7. Preserve in that license notice the full lists of Invariant Sections and required Cover Texts given in the Document's license notice.
    8. Include an unaltered copy of this License.
    9. Preserve the section Entitled “History”, Preserve its Title, and add to it an item stating at least the title, year, new authors, and publisher of the Modified Version as given on the Title Page. If there is no section Entitled “History” in the Document, create one stating the title, year, authors, and publisher of the Document as given on its Title Page, then add an item describing the Modified Version as stated in the previous sentence.
    10. Preserve the network location, if any, given in the Document for public access to a Transparent copy of the Document, and likewise the network locations given in the Document for previous versions it was based on. These may be placed in the “History” section. You may omit a network location for a work that was published at least four years before the Document itself, or if the original publisher of the version it refers to gives permission.
    11. For any section Entitled “Acknowledgements” or “Dedications”, Preserve the Title of the section, and preserve in the section all the substance and tone of each of the contributor acknowledgements and/or dedications given therein.
    12. Preserve all the Invariant Sections of the Document, unaltered in their text and in their titles. Section numbers or the equivalent are not considered part of the section titles.
    13. Delete any section Entitled “Endorsements”. Such a section may not be included in the Modified Version.
    14. Do not retitle any existing section to be Entitled “Endorsements” or to conflict in title with any Invariant Section.
    15. Preserve any Warranty Disclaimers.

    If the Modified Version includes new front-matter sections or appendices that qualify as Secondary Sections and contain no material copied from the Document, you may at your option designate some or all of these sections as invariant. To do this, add their titles to the list of Invariant Sections in the Modified Version's license notice. These titles must be distinct from any other section titles.

    You may add a section Entitled “Endorsements”, provided it contains nothing but endorsements of your Modified Version by various parties—for example, statements of peer review or that the text has been approved by an organization as the authoritative definition of a standard.

    You may add a passage of up to five words as a Front-Cover Text, and a passage of up to 25 words as a Back-Cover Text, to the end of the list of Cover Texts in the Modified Version. Only one passage of Front-Cover Text and one of Back-Cover Text may be added by (or through arrangements made by) any one entity. If the Document already includes a cover text for the same cover, previously added by you or by arrangement made by the same entity you are acting on behalf of, you may not add another; but you may replace the old one, on explicit permission from the previous publisher that added the old one.

    The author(s) and publisher(s) of the Document do not by this License give permission to use their names for publicity for or to assert or imply endorsement of any Modified Version.

  6. COMBINING DOCUMENTS

    You may combine the Document with other documents released under this License, under the terms defined in section 4 above for modified versions, provided that you include in the combination all of the Invariant Sections of all of the original documents, unmodified, and list them all as Invariant Sections of your combined work in its license notice, and that you preserve all their Warranty Disclaimers.

    The combined work need only contain one copy of this License, and multiple identical Invariant Sections may be replaced with a single copy. If there are multiple Invariant Sections with the same name but different contents, make the title of each such section unique by adding at the end of it, in parentheses, the name of the original author or publisher of that section if known, or else a unique number. Make the same adjustment to the section titles in the list of Invariant Sections in the license notice of the combined work.

    In the combination, you must combine any sections Entitled “History” in the various original documents, forming one section Entitled “History”; likewise combine any sections Entitled “Acknowledgements”, and any sections Entitled “Dedications”. You must delete all sections Entitled “Endorsements.”

  7. COLLECTIONS OF DOCUMENTS

    You may make a collection consisting of the Document and other documents released under this License, and replace the individual copies of this License in the various documents with a single copy that is included in the collection, provided that you follow the rules of this License for verbatim copying of each of the documents in all other respects.

    You may extract a single document from such a collection, and distribute it individually under this License, provided you insert a copy of this License into the extracted document, and follow this License in all other respects regarding verbatim copying of that document.

  8. AGGREGATION WITH INDEPENDENT WORKS

    A compilation of the Document or its derivatives with other separate and independent documents or works, in or on a volume of a storage or distribution medium, is called an “aggregate” if the copyright resulting from the compilation is not used to limit the legal rights of the compilation's users beyond what the individual works permit. When the Document is included in an aggregate, this License does not apply to the other works in the aggregate which are not themselves derivative works of the Document.

    If the Cover Text requirement of section 3 is applicable to these copies of the Document, then if the Document is less than one half of the entire aggregate, the Document's Cover Texts may be placed on covers that bracket the Document within the aggregate, or the electronic equivalent of covers if the Document is in electronic form. Otherwise they must appear on printed covers that bracket the whole aggregate.

  9. TRANSLATION

    Translation is considered a kind of modification, so you may distribute translations of the Document under the terms of section 4. Replacing Invariant Sections with translations requires special permission from their copyright holders, but you may include translations of some or all Invariant Sections in addition to the original versions of these Invariant Sections. You may include a translation of this License, and all the license notices in the Document, and any Warranty Disclaimers, provided that you also include the original English version of this License and the original versions of those notices and disclaimers. In case of a disagreement between the translation and the original version of this License or a notice or disclaimer, the original version will prevail.

    If a section in the Document is Entitled “Acknowledgements”, “Dedications”, or “History”, the requirement (section 4) to Preserve its Title (section 1) will typically require changing the actual title.

  10. TERMINATION

    You may not copy, modify, sublicense, or distribute the Document except as expressly provided for under this License. Any other attempt to copy, modify, sublicense or distribute the Document is void, and will automatically terminate your rights under this License. However, parties who have received copies, or rights, from you under this License will not have their licenses terminated so long as such parties remain in full compliance.

  11. FUTURE REVISIONS OF THIS LICENSE

    The Free Software Foundation may publish new, revised versions of the GNU Free Documentation License from time to time. Such new versions will be similar in spirit to the present version, but may differ in detail to address new problems or concerns. See http://www.gnu.org/copyleft/.

    Each version of the License is given a distinguishing version number. If the Document specifies that a particular numbered version of this License “or any later version” applies to it, you have the option of following the terms and conditions either of that specified version or of any later version that has been published (not as a draft) by the Free Software Foundation. If the Document does not specify a version number of this License, you may choose any version ever published (not as a draft) by the Free Software Foundation.

Index