Updated JavaDocs

SynBioDex · May 19, 2016 · 1e671f5 · 1e671f5
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diff --git a/docs/javadocs/allclasses-frame.html b/docs/javadocs/allclasses-frame.html
@@ -2,16 +2,53 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (version 1.7.0_60) on Wed May 18 16:41:09 MDT 2016 -->
+<!-- Generated by javadoc (version 1.7.0_60) on Thu May 19 15:21:28 MDT 2016 -->
 <title>All Classes</title>
-<meta name="date" content="2016-05-18">
+<meta name="date" content="2016-05-19">
 <link rel="stylesheet" type="text/css" href="stylesheet.css" title="Style">
 </head>
 <body>
 <h1 class="bar">All Classes</h1>
 <div class="indexContainer">
 <ul>
+<li><a href="org/sbolstandard/core2/AccessType.html" title="enum in org.sbolstandard.core2" target="classFrame">AccessType</a></li>
+<li><a href="org/sbolstandard/core2/Annotation.html" title="class in org.sbolstandard.core2" target="classFrame">Annotation</a></li>
+<li><a href="org/sbolstandard/core2/Collection.html" title="class in org.sbolstandard.core2" target="classFrame">Collection</a></li>
+<li><a href="org/sbolstandard/core2/Component.html" title="class in org.sbolstandard.core2" target="classFrame">Component</a></li>
+<li><a href="org/sbolstandard/core2/ComponentDefinition.html" title="class in org.sbolstandard.core2" target="classFrame">ComponentDefinition</a></li>
+<li><a href="org/sbolstandard/core2/ComponentInstance.html" title="class in org.sbolstandard.core2" target="classFrame">ComponentInstance</a></li>
+<li><a href="org/sbolstandard/core2/Cut.html" title="class in org.sbolstandard.core2" target="classFrame">Cut</a></li>
+<li><a href="org/sbolstandard/core2/DirectionType.html" title="enum in org.sbolstandard.core2" target="classFrame">DirectionType</a></li>
+<li><a href="org/sbolstandard/core2/EDAMOntology.html" title="class in org.sbolstandard.core2" target="classFrame">EDAMOntology</a></li>
+<li><a href="org/sbolstandard/core2/FunctionalComponent.html" title="class in org.sbolstandard.core2" target="classFrame">FunctionalComponent</a></li>
+<li><a href="org/sbolstandard/core2/GenericLocation.html" title="class in org.sbolstandard.core2" target="classFrame">GenericLocation</a></li>
+<li><a href="org/sbolstandard/core2/GenericTopLevel.html" title="class in org.sbolstandard.core2" target="classFrame">GenericTopLevel</a></li>
+<li><a href="org/sbolstandard/core2/Identified.html" title="class in org.sbolstandard.core2" target="classFrame">Identified</a></li>
+<li><a href="org/sbolstandard/core2/Interaction.html" title="class in org.sbolstandard.core2" target="classFrame">Interaction</a></li>
+<li><a href="org/sbolstandard/core2/Location.html" title="class in org.sbolstandard.core2" target="classFrame">Location</a></li>
+<li><a href="org/sbolstandard/core2/MapsTo.html" title="class in org.sbolstandard.core2" target="classFrame">MapsTo</a></li>
+<li><a href="org/sbolstandard/core2/Model.html" title="class in org.sbolstandard.core2" target="classFrame">Model</a></li>
+<li><a href="org/sbolstandard/core2/Module.html" title="class in org.sbolstandard.core2" target="classFrame">Module</a></li>
 <li><a href="org/sbolstandard/core2/ModuleDefinition.html" title="class in org.sbolstandard.core2" target="classFrame">ModuleDefinition</a></li>
+<li><a href="org/sbolstandard/core2/OrientationType.html" title="enum in org.sbolstandard.core2" target="classFrame">OrientationType</a></li>
+<li><a href="org/sbolstandard/core2/Participation.html" title="class in org.sbolstandard.core2" target="classFrame">Participation</a></li>
+<li><a href="org/sbolstandard/core2/Range.html" title="class in org.sbolstandard.core2" target="classFrame">Range</a></li>
+<li><a href="org/sbolstandard/core2/RefinementType.html" title="enum in org.sbolstandard.core2" target="classFrame">RefinementType</a></li>
+<li><a href="org/sbolstandard/core2/RestrictionType.html" title="enum in org.sbolstandard.core2" target="classFrame">RestrictionType</a></li>
+<li><a href="org/sbolstandard/core2/RoleIntegrationType.html" title="enum in org.sbolstandard.core2" target="classFrame">RoleIntegrationType</a></li>
+<li><a href="org/sbolstandard/core2/SBOLConversionException.html" title="class in org.sbolstandard.core2" target="classFrame">SBOLConversionException</a></li>
+<li><a href="org/sbolstandard/core2/SBOLDocument.html" title="class in org.sbolstandard.core2" target="classFrame">SBOLDocument</a></li>
+<li><a href="org/sbolstandard/core2/SBOLFactory.html" title="class in org.sbolstandard.core2" target="classFrame">SBOLFactory</a></li>
+<li><a href="org/sbolstandard/core2/SBOLReader.html" title="class in org.sbolstandard.core2" target="classFrame">SBOLReader</a></li>
+<li><a href="org/sbolstandard/core2/SBOLValidate.html" title="class in org.sbolstandard.core2" target="classFrame">SBOLValidate</a></li>
+<li><a href="org/sbolstandard/core2/SBOLValidationException.html" title="class in org.sbolstandard.core2" target="classFrame">SBOLValidationException</a></li>
+<li><a href="org/sbolstandard/core2/SBOLWriter.html" title="class in org.sbolstandard.core2" target="classFrame">SBOLWriter</a></li>
+<li><a href="org/sbolstandard/core2/Sequence.html" title="class in org.sbolstandard.core2" target="classFrame">Sequence</a></li>
+<li><a href="org/sbolstandard/core2/SequenceAnnotation.html" title="class in org.sbolstandard.core2" target="classFrame">SequenceAnnotation</a></li>
+<li><a href="org/sbolstandard/core2/SequenceConstraint.html" title="class in org.sbolstandard.core2" target="classFrame">SequenceConstraint</a></li>
+<li><a href="org/sbolstandard/core2/SequenceOntology.html" title="class in org.sbolstandard.core2" target="classFrame">SequenceOntology</a></li>
+<li><a href="org/sbolstandard/core2/SystemsBiologyOntology.html" title="class in org.sbolstandard.core2" target="classFrame">SystemsBiologyOntology</a></li>
+<li><a href="org/sbolstandard/core2/TopLevel.html" title="class in org.sbolstandard.core2" target="classFrame">TopLevel</a></li>
 </ul>
 </div>
 </body>

diff --git a/docs/javadocs/allclasses-noframe.html b/docs/javadocs/allclasses-noframe.html
@@ -2,16 +2,53 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (version 1.7.0_60) on Wed May 18 16:41:09 MDT 2016 -->
+<!-- Generated by javadoc (version 1.7.0_60) on Thu May 19 15:21:28 MDT 2016 -->
 <title>All Classes</title>
-<meta name="date" content="2016-05-18">
+<meta name="date" content="2016-05-19">
 <link rel="stylesheet" type="text/css" href="stylesheet.css" title="Style">
 </head>
 <body>
 <h1 class="bar">All Classes</h1>
 <div class="indexContainer">
 <ul>
+<li><a href="org/sbolstandard/core2/AccessType.html" title="enum in org.sbolstandard.core2">AccessType</a></li>
+<li><a href="org/sbolstandard/core2/Annotation.html" title="class in org.sbolstandard.core2">Annotation</a></li>
+<li><a href="org/sbolstandard/core2/Collection.html" title="class in org.sbolstandard.core2">Collection</a></li>
+<li><a href="org/sbolstandard/core2/Component.html" title="class in org.sbolstandard.core2">Component</a></li>
+<li><a href="org/sbolstandard/core2/ComponentDefinition.html" title="class in org.sbolstandard.core2">ComponentDefinition</a></li>
+<li><a href="org/sbolstandard/core2/ComponentInstance.html" title="class in org.sbolstandard.core2">ComponentInstance</a></li>
+<li><a href="org/sbolstandard/core2/Cut.html" title="class in org.sbolstandard.core2">Cut</a></li>
+<li><a href="org/sbolstandard/core2/DirectionType.html" title="enum in org.sbolstandard.core2">DirectionType</a></li>
+<li><a href="org/sbolstandard/core2/EDAMOntology.html" title="class in org.sbolstandard.core2">EDAMOntology</a></li>
+<li><a href="org/sbolstandard/core2/FunctionalComponent.html" title="class in org.sbolstandard.core2">FunctionalComponent</a></li>
+<li><a href="org/sbolstandard/core2/GenericLocation.html" title="class in org.sbolstandard.core2">GenericLocation</a></li>
+<li><a href="org/sbolstandard/core2/GenericTopLevel.html" title="class in org.sbolstandard.core2">GenericTopLevel</a></li>
+<li><a href="org/sbolstandard/core2/Identified.html" title="class in org.sbolstandard.core2">Identified</a></li>
+<li><a href="org/sbolstandard/core2/Interaction.html" title="class in org.sbolstandard.core2">Interaction</a></li>
+<li><a href="org/sbolstandard/core2/Location.html" title="class in org.sbolstandard.core2">Location</a></li>
+<li><a href="org/sbolstandard/core2/MapsTo.html" title="class in org.sbolstandard.core2">MapsTo</a></li>
+<li><a href="org/sbolstandard/core2/Model.html" title="class in org.sbolstandard.core2">Model</a></li>
+<li><a href="org/sbolstandard/core2/Module.html" title="class in org.sbolstandard.core2">Module</a></li>
 <li><a href="org/sbolstandard/core2/ModuleDefinition.html" title="class in org.sbolstandard.core2">ModuleDefinition</a></li>
+<li><a href="org/sbolstandard/core2/OrientationType.html" title="enum in org.sbolstandard.core2">OrientationType</a></li>
+<li><a href="org/sbolstandard/core2/Participation.html" title="class in org.sbolstandard.core2">Participation</a></li>
+<li><a href="org/sbolstandard/core2/Range.html" title="class in org.sbolstandard.core2">Range</a></li>
+<li><a href="org/sbolstandard/core2/RefinementType.html" title="enum in org.sbolstandard.core2">RefinementType</a></li>
+<li><a href="org/sbolstandard/core2/RestrictionType.html" title="enum in org.sbolstandard.core2">RestrictionType</a></li>
+<li><a href="org/sbolstandard/core2/RoleIntegrationType.html" title="enum in org.sbolstandard.core2">RoleIntegrationType</a></li>
+<li><a href="org/sbolstandard/core2/SBOLConversionException.html" title="class in org.sbolstandard.core2">SBOLConversionException</a></li>
+<li><a href="org/sbolstandard/core2/SBOLDocument.html" title="class in org.sbolstandard.core2">SBOLDocument</a></li>
+<li><a href="org/sbolstandard/core2/SBOLFactory.html" title="class in org.sbolstandard.core2">SBOLFactory</a></li>
+<li><a href="org/sbolstandard/core2/SBOLReader.html" title="class in org.sbolstandard.core2">SBOLReader</a></li>
+<li><a href="org/sbolstandard/core2/SBOLValidate.html" title="class in org.sbolstandard.core2">SBOLValidate</a></li>
+<li><a href="org/sbolstandard/core2/SBOLValidationException.html" title="class in org.sbolstandard.core2">SBOLValidationException</a></li>
+<li><a href="org/sbolstandard/core2/SBOLWriter.html" title="class in org.sbolstandard.core2">SBOLWriter</a></li>
+<li><a href="org/sbolstandard/core2/Sequence.html" title="class in org.sbolstandard.core2">Sequence</a></li>
+<li><a href="org/sbolstandard/core2/SequenceAnnotation.html" title="class in org.sbolstandard.core2">SequenceAnnotation</a></li>
+<li><a href="org/sbolstandard/core2/SequenceConstraint.html" title="class in org.sbolstandard.core2">SequenceConstraint</a></li>
+<li><a href="org/sbolstandard/core2/SequenceOntology.html" title="class in org.sbolstandard.core2">SequenceOntology</a></li>
+<li><a href="org/sbolstandard/core2/SystemsBiologyOntology.html" title="class in org.sbolstandard.core2">SystemsBiologyOntology</a></li>
+<li><a href="org/sbolstandard/core2/TopLevel.html" title="class in org.sbolstandard.core2">TopLevel</a></li>
 </ul>
 </div>
 </body>

diff --git a/docs/javadocs/constant-values.html b/docs/javadocs/constant-values.html
@@ -2,9 +2,9 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (version 1.7.0_60) on Wed May 18 16:41:09 MDT 2016 -->
+<!-- Generated by javadoc (version 1.7.0_60) on Thu May 19 15:21:27 MDT 2016 -->
 <title>Constant Field Values</title>
-<meta name="date" content="2016-05-18">
+<meta name="date" content="2016-05-19">
 <link rel="stylesheet" type="text/css" href="stylesheet.css" title="Style">
 </head>
 <body>
@@ -64,6 +64,150 @@
 <div class="header">
 <h1 title="Constant Field Values" class="title">Constant Field Values</h1>
 <h2 title="Contents">Contents</h2>
+<ul>
+<li><a href="#org.sbolstandard">org.sbolstandard.*</a></li>
+</ul>
+</div>
+<div class="constantValuesContainer"><a name="org.sbolstandard">
+<!--   -->
+</a>
+<h2 title="org.sbolstandard">org.sbolstandard.*</h2>
+<ul class="blockList">
+<li class="blockList">
+<table border="0" cellpadding="3" cellspacing="0" summary="Constant Field Values table, listing constant fields, and values">
+<caption><span>org.sbolstandard.core2.<a href="org/sbolstandard/core2/SBOLDocument.html" title="class in org.sbolstandard.core2">SBOLDocument</a></span><span class="tabEnd">&nbsp;</span></caption>
+<tr>
+<th class="colFirst" scope="col">Modifier and Type</th>
+<th scope="col">Constant Field</th>
+<th class="colLast" scope="col">Value</th>
+</tr>
+<tbody>
+<tr class="altColor">
+<td class="colFirst"><a name="org.sbolstandard.core2.SBOLDocument.FASTAformat">
+<!--   -->
+</a><code>public&nbsp;static&nbsp;final&nbsp;<a href="http://download.oracle.com/javase/7/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</a></code></td>
+<td><code><a href="org/sbolstandard/core2/SBOLDocument.html#FASTAformat">FASTAformat</a></code></td>
+<td class="colLast"><code>"FASTA"</code></td>
+</tr>
+<tr class="rowColor">
+<td class="colFirst"><a name="org.sbolstandard.core2.SBOLDocument.GENBANK">
+<!--   -->
+</a><code>public&nbsp;static&nbsp;final&nbsp;<a href="http://download.oracle.com/javase/7/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</a></code></td>
+<td><code><a href="org/sbolstandard/core2/SBOLDocument.html#GENBANK">GENBANK</a></code></td>
+<td class="colLast"><code>"GENBANK"</code></td>
+</tr>
+<tr class="altColor">
+<td class="colFirst"><a name="org.sbolstandard.core2.SBOLDocument.JSON">
+<!--   -->
+</a><code>public&nbsp;static&nbsp;final&nbsp;<a href="http://download.oracle.com/javase/7/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</a></code></td>
+<td><code><a href="org/sbolstandard/core2/SBOLDocument.html#JSON">JSON</a></code></td>
+<td class="colLast"><code>"JSON"</code></td>
+</tr>
+<tr class="rowColor">
+<td class="colFirst"><a name="org.sbolstandard.core2.SBOLDocument.RDF">
+<!--   -->
+</a><code>public&nbsp;static&nbsp;final&nbsp;<a href="http://download.oracle.com/javase/7/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</a></code></td>
+<td><code><a href="org/sbolstandard/core2/SBOLDocument.html#RDF">RDF</a></code></td>
+<td class="colLast"><code>"RDF"</code></td>
+</tr>
+<tr class="altColor">
+<td class="colFirst"><a name="org.sbolstandard.core2.SBOLDocument.RDFV1">
+<!--   -->
+</a><code>public&nbsp;static&nbsp;final&nbsp;<a href="http://download.oracle.com/javase/7/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</a></code></td>
+<td><code><a href="org/sbolstandard/core2/SBOLDocument.html#RDFV1">RDFV1</a></code></td>
+<td class="colLast"><code>"RDFV1"</code></td>
+</tr>
+<tr class="rowColor">
+<td class="colFirst"><a name="org.sbolstandard.core2.SBOLDocument.TURTLE">
+<!--   -->
+</a><code>public&nbsp;static&nbsp;final&nbsp;<a href="http://download.oracle.com/javase/7/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</a></code></td>
+<td><code><a href="org/sbolstandard/core2/SBOLDocument.html#TURTLE">TURTLE</a></code></td>
+<td class="colLast"><code>"TURTLE"</code></td>
+</tr>
+</tbody>
+</table>
+</li>
+<li class="blockList">
+<table border="0" cellpadding="3" cellspacing="0" summary="Constant Field Values table, listing constant fields, and values">
+<caption><span>org.sbolstandard.core2.<a href="org/sbolstandard/core2/SBOLReader.html" title="class in org.sbolstandard.core2">SBOLReader</a></span><span class="tabEnd">&nbsp;</span></caption>
+<tr>
+<th class="colFirst" scope="col">Modifier and Type</th>
+<th scope="col">Constant Field</th>
+<th class="colLast" scope="col">Value</th>
+</tr>
+<tbody>
+<tr class="altColor">
+<td class="colFirst"><a name="org.sbolstandard.core2.SBOLReader.SBOLVERSION1">
+<!--   -->
+</a><code>public&nbsp;static&nbsp;final&nbsp;<a href="http://download.oracle.com/javase/7/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</a></code></td>
+<td><code><a href="org/sbolstandard/core2/SBOLReader.html#SBOLVERSION1">SBOLVERSION1</a></code></td>
+<td class="colLast"><code>"v1"</code></td>
+</tr>
+<tr class="rowColor">
+<td class="colFirst"><a name="org.sbolstandard.core2.SBOLReader.SBOLVERSION2">
+<!--   -->
+</a><code>public&nbsp;static&nbsp;final&nbsp;<a href="http://download.oracle.com/javase/7/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</a></code></td>
+<td><code><a href="org/sbolstandard/core2/SBOLReader.html#SBOLVERSION2">SBOLVERSION2</a></code></td>
+<td class="colLast"><code>"v2"</code></td>
+</tr>
+</tbody>
+</table>
+</li>
+<li class="blockList">
+<table border="0" cellpadding="3" cellspacing="0" summary="Constant Field Values table, listing constant fields, and values">
+<caption><span>org.sbolstandard.core2.<a href="org/sbolstandard/core2/TopLevel.html" title="class in org.sbolstandard.core2">TopLevel</a></span><span class="tabEnd">&nbsp;</span></caption>
+<tr>
+<th class="colFirst" scope="col">Modifier and Type</th>
+<th scope="col">Constant Field</th>
+<th class="colLast" scope="col">Value</th>
+</tr>
+<tbody>
+<tr class="altColor">
+<td class="colFirst"><a name="org.sbolstandard.core2.TopLevel.COLLECTION">
+<!--   -->
+</a><code>public&nbsp;static&nbsp;final&nbsp;<a href="http://download.oracle.com/javase/7/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</a></code></td>
+<td><code><a href="org/sbolstandard/core2/TopLevel.html#COLLECTION">COLLECTION</a></code></td>
+<td class="colLast"><code>"col"</code></td>
+</tr>
+<tr class="rowColor">
+<td class="colFirst"><a name="org.sbolstandard.core2.TopLevel.COMPONENT_DEFINITION">
+<!--   -->
+</a><code>public&nbsp;static&nbsp;final&nbsp;<a href="http://download.oracle.com/javase/7/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</a></code></td>
+<td><code><a href="org/sbolstandard/core2/TopLevel.html#COMPONENT_DEFINITION">COMPONENT_DEFINITION</a></code></td>
+<td class="colLast"><code>"cd"</code></td>
+</tr>
+<tr class="altColor">
+<td class="colFirst"><a name="org.sbolstandard.core2.TopLevel.GENERIC_TOP_LEVEL">
+<!--   -->
+</a><code>public&nbsp;static&nbsp;final&nbsp;<a href="http://download.oracle.com/javase/7/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</a></code></td>
+<td><code><a href="org/sbolstandard/core2/TopLevel.html#GENERIC_TOP_LEVEL">GENERIC_TOP_LEVEL</a></code></td>
+<td class="colLast"><code>"gen"</code></td>
+</tr>
+<tr class="rowColor">
+<td class="colFirst"><a name="org.sbolstandard.core2.TopLevel.MODEL">
+<!--   -->
+</a><code>public&nbsp;static&nbsp;final&nbsp;<a href="http://download.oracle.com/javase/7/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</a></code></td>
+<td><code><a href="org/sbolstandard/core2/TopLevel.html#MODEL">MODEL</a></code></td>
+<td class="colLast"><code>"mod"</code></td>
+</tr>
+<tr class="altColor">
+<td class="colFirst"><a name="org.sbolstandard.core2.TopLevel.MODULE_DEFINITION">
+<!--   -->
+</a><code>public&nbsp;static&nbsp;final&nbsp;<a href="http://download.oracle.com/javase/7/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</a></code></td>
+<td><code><a href="org/sbolstandard/core2/TopLevel.html#MODULE_DEFINITION">MODULE_DEFINITION</a></code></td>
+<td class="colLast"><code>"md"</code></td>
+</tr>
+<tr class="rowColor">
+<td class="colFirst"><a name="org.sbolstandard.core2.TopLevel.SEQUENCE">
+<!--   -->
+</a><code>public&nbsp;static&nbsp;final&nbsp;<a href="http://download.oracle.com/javase/7/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</a></code></td>
+<td><code><a href="org/sbolstandard/core2/TopLevel.html#SEQUENCE">SEQUENCE</a></code></td>
+<td class="colLast"><code>"seq"</code></td>
+</tr>
+</tbody>
+</table>
+</li>
+</ul>
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 <!-- ======= START OF BOTTOM NAVBAR ====== -->
 <div class="bottomNav"><a name="navbar_bottom">

diff --git a/docs/javadocs/deprecated-list.html b/docs/javadocs/deprecated-list.html
@@ -2,9 +2,9 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (version 1.7.0_60) on Wed May 18 16:41:09 MDT 2016 -->
+<!-- Generated by javadoc (version 1.7.0_60) on Thu May 19 15:21:28 MDT 2016 -->
 <title>Deprecated List</title>
-<meta name="date" content="2016-05-18">
+<meta name="date" content="2016-05-19">
 <link rel="stylesheet" type="text/css" href="stylesheet.css" title="Style">
 </head>
 <body>