libsbgn.js
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SBGN-ML parsing and writing for JavaScript
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<title>libsbgn.js 0.1.3 | Documentation</title>
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<h3 class='mb0 no-anchor'>libsbgn.js</h3>
<div class='mb1'><code>0.1.3</code></div>
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<div id='toc'>
<ul class='list-reset h5 py1-ul'>
<li><a
href='#standard-sbgn'
class="h5 bold black caps">
Standard SBGN
</a>
</li>
<li><a
href='#libsbgn'
class="">
libsbgn
</a>
</li>
<li><a
href='#arc'
class=" toggle-sibling">
Arc
<span class='icon'>▸</span>
</a>
<div class='toggle-target display-none'>
<ul class='list-reset py1-ul pl1'>
<li class='h5'><span>Static members</span></li>
<li><a
href='#arcfromxml'
class='regular pre-open'>
.fromXML
</a></li>
<li><a
href='#arcfromobj'
class='regular pre-open'>
.fromObj
</a></li>
</ul>
<ul class='list-reset py1-ul pl1'>
<li class='h5'><span>Instance members</span></li>
<li><a
href='#arcsetstart'
class='regular pre-open'>
#setStart
</a></li>
<li><a
href='#arcsetend'
class='regular pre-open'>
#setEnd
</a></li>
<li><a
href='#arcaddnext'
class='regular pre-open'>
#addNext
</a></li>
<li><a
href='#arcaddglyph'
class='regular pre-open'>
#addGlyph
</a></li>
<li><a
href='#arcbuildjsobj'
class='regular pre-open'>
#buildJsObj
</a></li>
<li><a
href='#arctoxml'
class='regular pre-open'>
#toXML
</a></li>
</ul>
</div>
</li>
<li><a
href='#arcgroup'
class=" toggle-sibling">
Arcgroup
<span class='icon'>▸</span>
</a>
<div class='toggle-target display-none'>
<ul class='list-reset py1-ul pl1'>
<li class='h5'><span>Static members</span></li>
<li><a
href='#arcgroupfromxml'
class='regular pre-open'>
.fromXML
</a></li>
<li><a
href='#arcgroupfromobj'
class='regular pre-open'>
.fromObj
</a></li>
</ul>
<ul class='list-reset py1-ul pl1'>
<li class='h5'><span>Instance members</span></li>
<li><a
href='#arcgroupaddglyph'
class='regular pre-open'>
#addGlyph
</a></li>
<li><a
href='#arcgroupaddarc'
class='regular pre-open'>
#addArc
</a></li>
<li><a
href='#arcgroupbuildjsobj'
class='regular pre-open'>
#buildJsObj
</a></li>
<li><a
href='#arcgrouptoxml'
class='regular pre-open'>
#toXML
</a></li>
</ul>
</div>
</li>
<li><a
href='#bbox'
class=" toggle-sibling">
Bbox
<span class='icon'>▸</span>
</a>
<div class='toggle-target display-none'>
<ul class='list-reset py1-ul pl1'>
<li class='h5'><span>Static members</span></li>
<li><a
href='#bboxfromxml'
class='regular pre-open'>
.fromXML
</a></li>
<li><a
href='#bboxfromobj'
class='regular pre-open'>
.fromObj
</a></li>
</ul>
<ul class='list-reset py1-ul pl1'>
<li class='h5'><span>Instance members</span></li>
<li><a
href='#bboxbuildjsobj'
class='regular pre-open'>
#buildJsObj
</a></li>
<li><a
href='#bboxtoxml'
class='regular pre-open'>
#toXML
</a></li>
</ul>
</div>
</li>
<li><a
href='#callout'
class=" toggle-sibling">
Callout
<span class='icon'>▸</span>
</a>
<div class='toggle-target display-none'>
<ul class='list-reset py1-ul pl1'>
<li class='h5'><span>Static members</span></li>
<li><a
href='#calloutfromxml'
class='regular pre-open'>
.fromXML
</a></li>
<li><a
href='#calloutfromobj'
class='regular pre-open'>
.fromObj
</a></li>
</ul>
<ul class='list-reset py1-ul pl1'>
<li class='h5'><span>Instance members</span></li>
<li><a
href='#calloutsetpoint'
class='regular pre-open'>
#setPoint
</a></li>
<li><a
href='#calloutbuildjsobj'
class='regular pre-open'>
#buildJsObj
</a></li>
<li><a
href='#callouttoxml'
class='regular pre-open'>
#toXML
</a></li>
</ul>
</div>
</li>
<li><a
href='#clone'
class=" toggle-sibling">
Clone
<span class='icon'>▸</span>
</a>
<div class='toggle-target display-none'>
<ul class='list-reset py1-ul pl1'>
<li class='h5'><span>Static members</span></li>
<li><a
href='#clonefromxml'
class='regular pre-open'>
.fromXML
</a></li>
<li><a
href='#clonefromobj'
class='regular pre-open'>
.fromObj
</a></li>
</ul>
<ul class='list-reset py1-ul pl1'>
<li class='h5'><span>Instance members</span></li>
<li><a
href='#clonesetlabel'
class='regular pre-open'>
#setLabel
</a></li>
<li><a
href='#clonebuildjsobj'
class='regular pre-open'>
#buildJsObj
</a></li>
<li><a
href='#clonetoxml'
class='regular pre-open'>
#toXML
</a></li>
</ul>
</div>
</li>
<li><a
href='#end'
class=" toggle-sibling">
End
<span class='icon'>▸</span>
</a>
<div class='toggle-target display-none'>
<ul class='list-reset py1-ul pl1'>
<li class='h5'><span>Static members</span></li>
<li><a
href='#endfromxml'
class='regular pre-open'>
.fromXML
</a></li>
<li><a
href='#endfromobj'
class='regular pre-open'>
.fromObj
</a></li>
</ul>
<ul class='list-reset py1-ul pl1'>
<li class='h5'><span>Instance members</span></li>
<li><a
href='#endbuildjsobj'
class='regular pre-open'>
#buildJsObj
</a></li>
<li><a
href='#endtoxml'
class='regular pre-open'>
#toXML
</a></li>
</ul>
</div>
</li>
<li><a
href='#entity'
class=" toggle-sibling">
Entity
<span class='icon'>▸</span>
</a>
<div class='toggle-target display-none'>
<ul class='list-reset py1-ul pl1'>
<li class='h5'><span>Static members</span></li>
<li><a
href='#entityfromxml'
class='regular pre-open'>
.fromXML
</a></li>
<li><a
href='#entityfromobj'
class='regular pre-open'>
.fromObj
</a></li>
</ul>
<ul class='list-reset py1-ul pl1'>
<li class='h5'><span>Instance members</span></li>
<li><a
href='#entitybuildjsobj'
class='regular pre-open'>
#buildJsObj
</a></li>
<li><a
href='#entitytoxml'
class='regular pre-open'>
#toXML
</a></li>
</ul>
</div>
</li>
<li><a
href='#extension'
class=" toggle-sibling">
Extension
<span class='icon'>▸</span>
</a>
<div class='toggle-target display-none'>
<ul class='list-reset py1-ul pl1'>
<li class='h5'><span>Static members</span></li>
<li><a
href='#extensionfromxml'
class='regular pre-open'>
.fromXML
</a></li>
<li><a
href='#extensionfromobj'
class='regular pre-open'>
.fromObj
</a></li>
</ul>
<ul class='list-reset py1-ul pl1'>
<li class='h5'><span>Instance members</span></li>
<li><a
href='#extensionadd'
class='regular pre-open'>
#add
</a></li>
<li><a
href='#extensionhas'
class='regular pre-open'>
#has
</a></li>
<li><a
href='#extensionget'
class='regular pre-open'>
#get
</a></li>
<li><a
href='#extensionbuildjsobj'
class='regular pre-open'>
#buildJsObj
</a></li>
<li><a
href='#extensiontoxml'
class='regular pre-open'>
#toXML
</a></li>
</ul>
</div>
</li>
<li><a
href='#glyph'
class=" toggle-sibling">
Glyph
<span class='icon'>▸</span>
</a>
<div class='toggle-target display-none'>
<ul class='list-reset py1-ul pl1'>
<li class='h5'><span>Static members</span></li>
<li><a
href='#glyphfromxml'
class='regular pre-open'>
.fromXML
</a></li>
<li><a
href='#glyphfromobj'
class='regular pre-open'>
.fromObj
</a></li>
</ul>
<ul class='list-reset py1-ul pl1'>
<li class='h5'><span>Instance members</span></li>
<li><a
href='#glyphsetlabel'
class='regular pre-open'>
#setLabel
</a></li>
<li><a
href='#glyphsetstate'
class='regular pre-open'>
#setState
</a></li>
<li><a
href='#glyphsetbbox'
class='regular pre-open'>
#setBbox
</a></li>
<li><a
href='#glyphsetclone'
class='regular pre-open'>
#setClone
</a></li>
<li><a
href='#glyphsetcallout'
class='regular pre-open'>
#setCallout
</a></li>
<li><a
href='#glyphsetentity'
class='regular pre-open'>
#setEntity
</a></li>
<li><a
href='#glyphaddglyphmember'
class='regular pre-open'>
#addGlyphMember
</a></li>
<li><a
href='#glyphaddport'
class='regular pre-open'>
#addPort
</a></li>
<li><a
href='#glyphbuildjsobj'
class='regular pre-open'>
#buildJsObj
</a></li>
<li><a
href='#glyphtoxml'
class='regular pre-open'>
#toXML
</a></li>
</ul>
</div>
</li>
<li><a
href='#label'
class=" toggle-sibling">
Label
<span class='icon'>▸</span>
</a>
<div class='toggle-target display-none'>
<ul class='list-reset py1-ul pl1'>
<li class='h5'><span>Static members</span></li>
<li><a
href='#labelfromxml'
class='regular pre-open'>
.fromXML
</a></li>
<li><a
href='#labelfromobj'
class='regular pre-open'>
.fromObj
</a></li>
</ul>
<ul class='list-reset py1-ul pl1'>
<li class='h5'><span>Instance members</span></li>
<li><a
href='#labelsetbbox'
class='regular pre-open'>
#setBbox
</a></li>
<li><a
href='#labelbuildjsobj'
class='regular pre-open'>
#buildJsObj
</a></li>
<li><a
href='#labeltoxml'
class='regular pre-open'>
#toXML
</a></li>
</ul>
</div>
</li>
<li><a
href='#map'
class=" toggle-sibling">
Map
<span class='icon'>▸</span>
</a>
<div class='toggle-target display-none'>
<ul class='list-reset py1-ul pl1'>
<li class='h5'><span>Static members</span></li>
<li><a
href='#mapfromxml'
class='regular pre-open'>
.fromXML
</a></li>
<li><a
href='#mapfromobj'
class='regular pre-open'>
.fromObj
</a></li>
</ul>
<ul class='list-reset py1-ul pl1'>
<li class='h5'><span>Instance members</span></li>
<li><a
href='#mapaddglyph'
class='regular pre-open'>
#addGlyph
</a></li>
<li><a
href='#mapaddarc'
class='regular pre-open'>
#addArc
</a></li>
<li><a
href='#mapsetbbox'
class='regular pre-open'>
#setBbox
</a></li>
<li><a
href='#mapaddarcgroup'
class='regular pre-open'>
#addArcgroup
</a></li>
<li><a
href='#mapgetglyphsbyclass'
class='regular pre-open'>
#getGlyphsByClass
</a></li>
<li><a
href='#mapbuildjsobj'
class='regular pre-open'>
#buildJsObj
</a></li>
<li><a
href='#maptoxml'
class='regular pre-open'>
#toXML
</a></li>
</ul>
</div>
</li>
<li><a
href='#next'
class=" toggle-sibling">
Next
<span class='icon'>▸</span>
</a>
<div class='toggle-target display-none'>
<ul class='list-reset py1-ul pl1'>
<li class='h5'><span>Static members</span></li>
<li><a
href='#nextfromxml'
class='regular pre-open'>
.fromXML
</a></li>
<li><a
href='#nextfromobj'
class='regular pre-open'>
.fromObj
</a></li>
</ul>
<ul class='list-reset py1-ul pl1'>
<li class='h5'><span>Instance members</span></li>
<li><a
href='#nextbuildjsobj'
class='regular pre-open'>
#buildJsObj
</a></li>
<li><a
href='#nexttoxml'
class='regular pre-open'>
#toXML
</a></li>
</ul>
</div>
</li>
<li><a
href='#notes'
class=" toggle-sibling">
Notes
<span class='icon'>▸</span>
</a>
<div class='toggle-target display-none'>
<ul class='list-reset py1-ul pl1'>
<li class='h5'><span>Static members</span></li>
<li><a
href='#notesfromxml'
class='regular pre-open'>
.fromXML
</a></li>
<li><a
href='#notesfromobj'
class='regular pre-open'>
.fromObj
</a></li>
</ul>
<ul class='list-reset py1-ul pl1'>
<li class='h5'><span>Instance members</span></li>
<li><a
href='#notessetcontent'
class='regular pre-open'>
#setContent
</a></li>
<li><a
href='#notesappendcontent'
class='regular pre-open'>
#appendContent
</a></li>
<li><a
href='#notesbuildjsobj'
class='regular pre-open'>
#buildJsObj
</a></li>
<li><a
href='#notestoxml'
class='regular pre-open'>
#toXML
</a></li>
</ul>
</div>
</li>
<li><a
href='#point'
class=" toggle-sibling">
Point
<span class='icon'>▸</span>
</a>
<div class='toggle-target display-none'>
<ul class='list-reset py1-ul pl1'>
<li class='h5'><span>Static members</span></li>
<li><a
href='#pointfromxml'
class='regular pre-open'>
.fromXML
</a></li>
<li><a
href='#pointfromobj'
class='regular pre-open'>
.fromObj
</a></li>
</ul>
<ul class='list-reset py1-ul pl1'>
<li class='h5'><span>Instance members</span></li>
<li><a
href='#pointbuildjsobj'
class='regular pre-open'>
#buildJsObj
</a></li>
<li><a
href='#pointtoxml'
class='regular pre-open'>
#toXML
</a></li>
</ul>
</div>
</li>
<li><a
href='#port'
class=" toggle-sibling">
Port
<span class='icon'>▸</span>
</a>
<div class='toggle-target display-none'>
<ul class='list-reset py1-ul pl1'>
<li class='h5'><span>Static members</span></li>
<li><a
href='#portfromxml'
class='regular pre-open'>
.fromXML
</a></li>
<li><a
href='#portfromobj'
class='regular pre-open'>
.fromObj
</a></li>
</ul>
<ul class='list-reset py1-ul pl1'>
<li class='h5'><span>Instance members</span></li>
<li><a
href='#portbuildjsobj'
class='regular pre-open'>
#buildJsObj
</a></li>
<li><a
href='#porttoxml'
class='regular pre-open'>
#toXML
</a></li>
</ul>
</div>
</li>
<li><a
href='#sbgn'
class=" toggle-sibling">
Sbgn
<span class='icon'>▸</span>
</a>
<div class='toggle-target display-none'>
<ul class='list-reset py1-ul pl1'>
<li class='h5'><span>Static members</span></li>
<li><a
href='#sbgndoschematronvalidation'
class='regular pre-open'>
.doSchematronValidation
</a></li>
<li><a
href='#sbgnfromxml'
class='regular pre-open'>
.fromXML
</a></li>
<li><a
href='#sbgnfromobj'
class='regular pre-open'>
.fromObj
</a></li>
</ul>
<ul class='list-reset py1-ul pl1'>
<li class='h5'><span>Instance members</span></li>
<li><a
href='#sbgnaddmap'
class='regular pre-open'>
#addMap
</a></li>
<li><a
href='#sbgnbuildjsobj'
class='regular pre-open'>
#buildJsObj
</a></li>
<li><a
href='#sbgntoxml'
class='regular pre-open'>
#toXML
</a></li>
</ul>
</div>
</li>
<li><a
href='#sbgnbase'
class=" toggle-sibling">
SBGNBase
<span class='icon'>▸</span>
</a>
<div class='toggle-target display-none'>
<ul class='list-reset py1-ul pl1'>
<li class='h5'><span>Instance members</span></li>
<li><a
href='#sbgnbasesetextension'
class='regular pre-open'>
#setExtension
</a></li>
<li><a
href='#sbgnbasesetnotes'
class='regular pre-open'>
#setNotes
</a></li>
<li><a
href='#sbgnbasebasetojsobj'
class='regular pre-open'>
#baseToJsObj
</a></li>
<li><a
href='#sbgnbasebasefromobj'
class='regular pre-open'>
#baseFromObj
</a></li>
</ul>
</div>
</li>
<li><a
href='#start'
class=" toggle-sibling">
Start
<span class='icon'>▸</span>
</a>
<div class='toggle-target display-none'>
<ul class='list-reset py1-ul pl1'>
<li class='h5'><span>Static members</span></li>
<li><a
href='#startfromxml'
class='regular pre-open'>
.fromXML
</a></li>
<li><a
href='#startfromobj'
class='regular pre-open'>
.fromObj
</a></li>
</ul>
<ul class='list-reset py1-ul pl1'>
<li class='h5'><span>Instance members</span></li>
<li><a
href='#startbuildjsobj'
class='regular pre-open'>
#buildJsObj
</a></li>
<li><a
href='#starttoxml'
class='regular pre-open'>
#toXML
</a></li>
</ul>
</div>
</li>
<li><a
href='#state'
class=" toggle-sibling">
State
<span class='icon'>▸</span>
</a>
<div class='toggle-target display-none'>
<ul class='list-reset py1-ul pl1'>
<li class='h5'><span>Static members</span></li>
<li><a
href='#statefromxml'
class='regular pre-open'>
.fromXML
</a></li>
<li><a
href='#statefromobj'
class='regular pre-open'>
.fromObj
</a></li>
</ul>
<ul class='list-reset py1-ul pl1'>
<li class='h5'><span>Instance members</span></li>
<li><a
href='#statebuildjsobj'
class='regular pre-open'>
#buildJsObj
</a></li>
<li><a
href='#statetoxml'
class='regular pre-open'>
#toXML
</a></li>
</ul>
</div>
</li>
<li><a
href='#render-extension'
class="h5 bold black caps">
Render extension
</a>
</li>
<li><a
href='#libsbgnrender'
class="">
libsbgn.render
</a>
</li>
<li><a
href='#colordefinition'
class=" toggle-sibling">
ColorDefinition
<span class='icon'>▸</span>
</a>
<div class='toggle-target display-none'>
<ul class='list-reset py1-ul pl1'>
<li class='h5'><span>Static members</span></li>
<li><a
href='#colordefinitionfromxml'
class='regular pre-open'>
.fromXML
</a></li>
<li><a
href='#colordefinitionfromobj'
class='regular pre-open'>
.fromObj
</a></li>
</ul>
<ul class='list-reset py1-ul pl1'>
<li class='h5'><span>Instance members</span></li>
<li><a
href='#colordefinitionbuildjsobj'
class='regular pre-open'>
#buildJsObj
</a></li>
<li><a
href='#colordefinitiontoxml'
class='regular pre-open'>
#toXML
</a></li>
</ul>
</div>
</li>
<li><a
href='#listofcolordefinitions'
class=" toggle-sibling">
ListOfColorDefinitions
<span class='icon'>▸</span>
</a>
<div class='toggle-target display-none'>
<ul class='list-reset py1-ul pl1'>
<li class='h5'><span>Static members</span></li>
<li><a
href='#listofcolordefinitionsfromxml'
class='regular pre-open'>
.fromXML
</a></li>
<li><a
href='#listofcolordefinitionsfromobj'
class='regular pre-open'>
.fromObj
</a></li>
</ul>
<ul class='list-reset py1-ul pl1'>
<li class='h5'><span>Instance members</span></li>
<li><a
href='#listofcolordefinitionsaddcolordefinition'
class='regular pre-open'>
#addColorDefinition
</a></li>
<li><a
href='#listofcolordefinitionsgetcolorbyid'
class='regular pre-open'>
#getColorById
</a></li>
<li><a
href='#listofcolordefinitionsgetallcolors'
class='regular pre-open'>
#getAllColors
</a></li>
<li><a
href='#listofcolordefinitionsbuildjsobj'
class='regular pre-open'>
#buildJsObj
</a></li>
<li><a
href='#listofcolordefinitionstoxml'
class='regular pre-open'>
#toXML
</a></li>
</ul>
</div>
</li>
<li><a
href='#listofstyles'
class=" toggle-sibling">
ListOfStyles
<span class='icon'>▸</span>
</a>
<div class='toggle-target display-none'>
<ul class='list-reset py1-ul pl1'>
<li class='h5'><span>Static members</span></li>
<li><a
href='#listofstylesfromxml'
class='regular pre-open'>
.fromXML
</a></li>
<li><a
href='#listofstylesfromobj'
class='regular pre-open'>
.fromObj
</a></li>
</ul>
<ul class='list-reset py1-ul pl1'>
<li class='h5'><span>Instance members</span></li>
<li><a
href='#listofstylesaddstyle'
class='regular pre-open'>
#addStyle
</a></li>
<li><a
href='#listofstylesgetstylemap'
class='regular pre-open'>
#getStyleMap
</a></li>
<li><a
href='#listofstylesbuildjsobj'
class='regular pre-open'>
#buildJsObj
</a></li>
<li><a
href='#listofstylestoxml'
class='regular pre-open'>
#toXML
</a></li>
</ul>
</div>
</li>
<li><a
href='#rendergroup'
class=" toggle-sibling">
RenderGroup
<span class='icon'>▸</span>
</a>
<div class='toggle-target display-none'>
<ul class='list-reset py1-ul pl1'>
<li class='h5'><span>Static members</span></li>
<li><a
href='#rendergroupfromxml'
class='regular pre-open'>
.fromXML
</a></li>
<li><a
href='#rendergroupfromobj'
class='regular pre-open'>
.fromObj
</a></li>
</ul>
<ul class='list-reset py1-ul pl1'>
<li class='h5'><span>Instance members</span></li>
<li><a
href='#rendergroupbuildjsobj'
class='regular pre-open'>
#buildJsObj
</a></li>
<li><a
href='#rendergrouptoxml'
class='regular pre-open'>
#toXML
</a></li>
</ul>
</div>
</li>
<li><a
href='#renderinformation'
class=" toggle-sibling">
RenderInformation
<span class='icon'>▸</span>
</a>
<div class='toggle-target display-none'>
<ul class='list-reset py1-ul pl1'>
<li class='h5'><span>Static members</span></li>
<li><a
href='#renderinformationfromxml'
class='regular pre-open'>
.fromXML
</a></li>
<li><a
href='#renderinformationfromobj'
class='regular pre-open'>
.fromObj
</a></li>
</ul>
<ul class='list-reset py1-ul pl1'>
<li class='h5'><span>Instance members</span></li>
<li><a
href='#renderinformationsetlistofcolordefinitions'
class='regular pre-open'>
#setListOfColorDefinitions
</a></li>
<li><a
href='#renderinformationsetlistofstyles'
class='regular pre-open'>
#setListOfStyles
</a></li>
<li><a
href='#renderinformationbuildjsobj'
class='regular pre-open'>
#buildJsObj
</a></li>
<li><a
href='#renderinformationtoxml'
class='regular pre-open'>
#toXML
</a></li>
</ul>
</div>
</li>
<li><a
href='#style'
class=" toggle-sibling">
Style
<span class='icon'>▸</span>
</a>