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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
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<title>Constant Field Values (biojava 4.2.1 API)</title>
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<div class="header">
<h1 title="Constant Field Values" class="title">Constant Field Values</h1>
<h2 title="Contents">Contents</h2>
<ul>
<li><a href="#org.biojava">org.biojava.*</a></li>
</ul>
</div>
<div class="constantValuesContainer"><a name="org.biojava">
<!-- -->
</a>
<h2 title="org.biojava">org.biojava.*</h2>
<ul class="blockList">
<li class="blockList">
<table class="constantsSummary" border="0" cellpadding="3" cellspacing="0" summary="Constant Field Values table, listing constant fields, and values">
<caption><span>org.biojava.nbio.aaproperties.profeat.convertor.<a href="org/biojava/nbio/aaproperties/profeat/convertor/Convertor.html" title="class in org.biojava.nbio.aaproperties.profeat.convertor">Convertor</a></span><span class="tabEnd"> </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.biojava.nbio.aaproperties.profeat.convertor.Convertor.group1">
<!-- -->
</a><code>public static final char</code></td>
<td><code><a href="org/biojava/nbio/aaproperties/profeat/convertor/Convertor.html#group1">group1</a></code></td>
<td class="colLast"><code>49</code></td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a name="org.biojava.nbio.aaproperties.profeat.convertor.Convertor.group2">
<!-- -->
</a><code>public static final char</code></td>
<td><code><a href="org/biojava/nbio/aaproperties/profeat/convertor/Convertor.html#group2">group2</a></code></td>
<td class="colLast"><code>50</code></td>
</tr>
<tr class="altColor">
<td class="colFirst"><a name="org.biojava.nbio.aaproperties.profeat.convertor.Convertor.group3">
<!-- -->
</a><code>public static final char</code></td>
<td><code><a href="org/biojava/nbio/aaproperties/profeat/convertor/Convertor.html#group3">group3</a></code></td>
<td class="colLast"><code>51</code></td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a name="org.biojava.nbio.aaproperties.profeat.convertor.Convertor.unknownGroup">
<!-- -->
</a><code>public static final char</code></td>
<td><code><a href="org/biojava/nbio/aaproperties/profeat/convertor/Convertor.html#unknownGroup">unknownGroup</a></code></td>
<td class="colLast"><code>48</code></td>
</tr>
</tbody>
</table>
</li>
</ul>
<ul class="blockList">
<li class="blockList">
<table class="constantsSummary" border="0" cellpadding="3" cellspacing="0" summary="Constant Field Values table, listing constant fields, and values">
<caption><span>org.biojava.nbio.alignment.io.<a href="org/biojava/nbio/alignment/io/StockholmFileParser.html" title="class in org.biojava.nbio.alignment.io">StockholmFileParser</a></span><span class="tabEnd"> </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.biojava.nbio.alignment.io.StockholmFileParser.INFINITY">
<!-- -->
</a><code>public static final int</code></td>
<td><code><a href="org/biojava/nbio/alignment/io/StockholmFileParser.html#INFINITY">INFINITY</a></code></td>
<td class="colLast"><code>-1</code></td>
</tr>
</tbody>
</table>
</li>
<li class="blockList">
<table class="constantsSummary" border="0" cellpadding="3" cellspacing="0" summary="Constant Field Values table, listing constant fields, and values">
<caption><span>org.biojava.nbio.alignment.io.<a href="org/biojava/nbio/alignment/io/StockholmStructure.html" title="class in org.biojava.nbio.alignment.io">StockholmStructure</a></span><span class="tabEnd"> </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.biojava.nbio.alignment.io.StockholmStructure.PFAM">
<!-- -->
</a><code>public static final <a href="http://docs.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/biojava/nbio/alignment/io/StockholmStructure.html#PFAM">PFAM</a></code></td>
<td class="colLast"><code>"PFAM"</code></td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a name="org.biojava.nbio.alignment.io.StockholmStructure.RFAM">
<!-- -->
</a><code>public static final <a href="http://docs.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/biojava/nbio/alignment/io/StockholmStructure.html#RFAM">RFAM</a></code></td>
<td class="colLast"><code>"RFAM"</code></td>
</tr>
</tbody>
</table>
</li>
<li class="blockList">
<table class="constantsSummary" border="0" cellpadding="3" cellspacing="0" summary="Constant Field Values table, listing constant fields, and values">
<caption><span>org.biojava.nbio.alignment.io.<a href="org/biojava/nbio/alignment/io/StockholmStructure.DatabaseReference.html" title="class in org.biojava.nbio.alignment.io">StockholmStructure.DatabaseReference</a></span><span class="tabEnd"> </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.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference.EXPERT">
<!-- -->
</a><code>public static final <a href="http://docs.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/biojava/nbio/alignment/io/StockholmStructure.DatabaseReference.html#EXPERT">EXPERT</a></code></td>
<td class="colLast"><code>"EXPERT"</code></td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a name="org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference.HOMSTRAD">
<!-- -->
</a><code>public static final <a href="http://docs.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/biojava/nbio/alignment/io/StockholmStructure.DatabaseReference.html#HOMSTRAD">HOMSTRAD</a></code></td>
<td class="colLast"><code>"HOMSTRAD"</code></td>
</tr>
<tr class="altColor">
<td class="colFirst"><a name="org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference.INTERPRO">
<!-- -->
</a><code>public static final <a href="http://docs.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/biojava/nbio/alignment/io/StockholmStructure.DatabaseReference.html#INTERPRO">INTERPRO</a></code></td>
<td class="colLast"><code>"INTERPRO"</code></td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a name="org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference.LOAD">
<!-- -->
</a><code>public static final <a href="http://docs.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/biojava/nbio/alignment/io/StockholmStructure.DatabaseReference.html#LOAD">LOAD</a></code></td>
<td class="colLast"><code>"LOAD"</code></td>
</tr>
<tr class="altColor">
<td class="colFirst"><a name="org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference.MIM">
<!-- -->
</a><code>public static final <a href="http://docs.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/biojava/nbio/alignment/io/StockholmStructure.DatabaseReference.html#MIM">MIM</a></code></td>
<td class="colLast"><code>"MIM"</code></td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a name="org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference.PDB">
<!-- -->
</a><code>public static final <a href="http://docs.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/biojava/nbio/alignment/io/StockholmStructure.DatabaseReference.html#PDB">PDB</a></code></td>
<td class="colLast"><code>"PDB"</code></td>
</tr>
<tr class="altColor">
<td class="colFirst"><a name="org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference.PFAMB">
<!-- -->
</a><code>public static final <a href="http://docs.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/biojava/nbio/alignment/io/StockholmStructure.DatabaseReference.html#PFAMB">PFAMB</a></code></td>
<td class="colLast"><code>"PFAMB"</code></td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a name="org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference.PRINTS">
<!-- -->
</a><code>public static final <a href="http://docs.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/biojava/nbio/alignment/io/StockholmStructure.DatabaseReference.html#PRINTS">PRINTS</a></code></td>
<td class="colLast"><code>"PRINTS"</code></td>
</tr>
<tr class="altColor">
<td class="colFirst"><a name="org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference.PROSITE">
<!-- -->
</a><code>public static final <a href="http://docs.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/biojava/nbio/alignment/io/StockholmStructure.DatabaseReference.html#PROSITE">PROSITE</a></code></td>
<td class="colLast"><code>"PROSITE"</code></td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a name="org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference.PROSITE_PROFILE">
<!-- -->
</a><code>public static final <a href="http://docs.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/biojava/nbio/alignment/io/StockholmStructure.DatabaseReference.html#PROSITE_PROFILE">PROSITE_PROFILE</a></code></td>
<td class="colLast"><code>"PROSITE_PROFILE"</code></td>
</tr>
<tr class="altColor">
<td class="colFirst"><a name="org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference.SCOP">
<!-- -->
</a><code>public static final <a href="http://docs.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/biojava/nbio/alignment/io/StockholmStructure.DatabaseReference.html#SCOP">SCOP</a></code></td>
<td class="colLast"><code>"SCOP"</code></td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a name="org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference.SMART">
<!-- -->
</a><code>public static final <a href="http://docs.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/biojava/nbio/alignment/io/StockholmStructure.DatabaseReference.html#SMART">SMART</a></code></td>
<td class="colLast"><code>"SMART"</code></td>
</tr>
<tr class="altColor">
<td class="colFirst"><a name="org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference.URL">
<!-- -->
</a><code>public static final <a href="http://docs.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/biojava/nbio/alignment/io/StockholmStructure.DatabaseReference.html#URL">URL</a></code></td>
<td class="colLast"><code>"URL"</code></td>
</tr>
</tbody>
</table>
</li>
</ul>
<ul class="blockList">
<li class="blockList">
<table class="constantsSummary" border="0" cellpadding="3" cellspacing="0" summary="Constant Field Values table, listing constant fields, and values">
<caption><span>org.biojava.nbio.core.exceptions.<a href="org/biojava/nbio/core/exceptions/Messages.html" title="class in org.biojava.nbio.core.exceptions">Messages</a></span><span class="tabEnd"> </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.biojava.nbio.core.exceptions.Messages.ENDOFFILE">
<!-- -->
</a><code>public static final <a href="http://docs.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/biojava/nbio/core/exceptions/Messages.html#ENDOFFILE">ENDOFFILE</a></code></td>
<td class="colLast"><code>"end of file"</code></td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a name="org.biojava.nbio.core.exceptions.Messages.SECTIONKEYNULL">
<!-- -->
</a><code>public static final <a href="http://docs.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/biojava/nbio/core/exceptions/Messages.html#SECTIONKEYNULL">SECTIONKEYNULL</a></code></td>
<td class="colLast"><code>"section key is null"</code></td>
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</tbody>
</table>
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</ul>
<ul class="blockList">
<li class="blockList">
<table class="constantsSummary" border="0" cellpadding="3" cellspacing="0" summary="Constant Field Values table, listing constant fields, and values">
<caption><span>org.biojava.nbio.core.sequence.io.<a href="org/biojava/nbio/core/sequence/io/GenbankSequenceParser.html" title="class in org.biojava.nbio.core.sequence.io">GenbankSequenceParser</a><<a href="org/biojava/nbio/core/sequence/io/GenbankSequenceParser.html" title="type parameter in GenbankSequenceParser">S</a> extends <a href="org/biojava/nbio/core/sequence/template/AbstractSequence.html" title="class in org.biojava.nbio.core.sequence.template">AbstractSequence</a><<a href="org/biojava/nbio/core/sequence/io/GenbankSequenceParser.html" title="type parameter in GenbankSequenceParser">C</a>>,<a href="org/biojava/nbio/core/sequence/io/GenbankSequenceParser.html" title="type parameter in GenbankSequenceParser">C</a> extends <a href="org/biojava/nbio/core/sequence/template/Compound.html" title="interface in org.biojava.nbio.core.sequence.template">Compound</a>></span><span class="tabEnd"> </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.biojava.nbio.core.sequence.io.GenbankSequenceParser.ACCESSION_TAG">
<!-- -->
</a><code>protected static final <a href="http://docs.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/biojava/nbio/core/sequence/io/GenbankSequenceParser.html#ACCESSION_TAG">ACCESSION_TAG</a></code></td>
<td class="colLast"><code>"ACCESSION"</code></td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a name="org.biojava.nbio.core.sequence.io.GenbankSequenceParser.AUTHORS_TAG">
<!-- -->
</a><code>protected static final <a href="http://docs.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/biojava/nbio/core/sequence/io/GenbankSequenceParser.html#AUTHORS_TAG">AUTHORS_TAG</a></code></td>
<td class="colLast"><code>"AUTHORS"</code></td>
</tr>
<tr class="altColor">
<td class="colFirst"><a name="org.biojava.nbio.core.sequence.io.GenbankSequenceParser.BASE_COUNT_TAG">
<!-- -->
</a><code>protected static final <a href="http://docs.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/biojava/nbio/core/sequence/io/GenbankSequenceParser.html#BASE_COUNT_TAG">BASE_COUNT_TAG</a></code></td>
<td class="colLast"><code>"BASE"</code></td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a name="org.biojava.nbio.core.sequence.io.GenbankSequenceParser.BASE_COUNT_TAG_FULL">
<!-- -->
</a><code>protected static final <a href="http://docs.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/biojava/nbio/core/sequence/io/GenbankSequenceParser.html#BASE_COUNT_TAG_FULL">BASE_COUNT_TAG_FULL</a></code></td>
<td class="colLast"><code>"BASE COUNT"</code></td>
</tr>
<tr class="altColor">
<td class="colFirst"><a name="org.biojava.nbio.core.sequence.io.GenbankSequenceParser.COMMENT_TAG">
<!-- -->
</a><code>protected static final <a href="http://docs.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/biojava/nbio/core/sequence/io/GenbankSequenceParser.html#COMMENT_TAG">COMMENT_TAG</a></code></td>
<td class="colLast"><code>"COMMENT"</code></td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a name="org.biojava.nbio.core.sequence.io.GenbankSequenceParser.CONSORTIUM_TAG">
<!-- -->
</a><code>protected static final <a href="http://docs.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/biojava/nbio/core/sequence/io/GenbankSequenceParser.html#CONSORTIUM_TAG">CONSORTIUM_TAG</a></code></td>
<td class="colLast"><code>"CONSRTM"</code></td>
</tr>
<tr class="altColor">
<td class="colFirst"><a name="org.biojava.nbio.core.sequence.io.GenbankSequenceParser.DEFINITION_TAG">
<!-- -->
</a><code>protected static final <a href="http://docs.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/biojava/nbio/core/sequence/io/GenbankSequenceParser.html#DEFINITION_TAG">DEFINITION_TAG</a></code></td>
<td class="colLast"><code>"DEFINITION"</code></td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a name="org.biojava.nbio.core.sequence.io.GenbankSequenceParser.END_SEQUENCE_TAG">
<!-- -->
</a><code>protected static final <a href="http://docs.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/biojava/nbio/core/sequence/io/GenbankSequenceParser.html#END_SEQUENCE_TAG">END_SEQUENCE_TAG</a></code></td>
<td class="colLast"><code>"//"</code></td>
</tr>
<tr class="altColor">
<td class="colFirst"><a name="org.biojava.nbio.core.sequence.io.GenbankSequenceParser.FEATURE_TAG">
<!-- -->
</a><code>protected static final <a href="http://docs.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/biojava/nbio/core/sequence/io/GenbankSequenceParser.html#FEATURE_TAG">FEATURE_TAG</a></code></td>
<td class="colLast"><code>"FEATURES"</code></td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a name="org.biojava.nbio.core.sequence.io.GenbankSequenceParser.GENBANK_FORMAT">
<!-- -->
</a><code>public static final <a href="http://docs.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/biojava/nbio/core/sequence/io/GenbankSequenceParser.html#GENBANK_FORMAT">GENBANK_FORMAT</a></code></td>
<td class="colLast"><code>"GENBANK"</code></td>
</tr>
<tr class="altColor">
<td class="colFirst"><a name="org.biojava.nbio.core.sequence.io.GenbankSequenceParser.JOURNAL_TAG">
<!-- -->
</a><code>protected static final <a href="http://docs.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/biojava/nbio/core/sequence/io/GenbankSequenceParser.html#JOURNAL_TAG">JOURNAL_TAG</a></code></td>
<td class="colLast"><code>"JOURNAL"</code></td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a name="org.biojava.nbio.core.sequence.io.GenbankSequenceParser.KEYWORDS_TAG">
<!-- -->
</a><code>protected static final <a href="http://docs.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/biojava/nbio/core/sequence/io/GenbankSequenceParser.html#KEYWORDS_TAG">KEYWORDS_TAG</a></code></td>
<td class="colLast"><code>"KEYWORDS"</code></td>
</tr>
<tr class="altColor">
<td class="colFirst"><a name="org.biojava.nbio.core.sequence.io.GenbankSequenceParser.LOCUS_TAG">
<!-- -->
</a><code>protected static final <a href="http://docs.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/biojava/nbio/core/sequence/io/GenbankSequenceParser.html#LOCUS_TAG">LOCUS_TAG</a></code></td>
<td class="colLast"><code>"LOCUS"</code></td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a name="org.biojava.nbio.core.sequence.io.GenbankSequenceParser.MEDLINE_TAG">
<!-- -->
</a><code>protected static final <a href="http://docs.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/biojava/nbio/core/sequence/io/GenbankSequenceParser.html#MEDLINE_TAG">MEDLINE_TAG</a></code></td>
<td class="colLast"><code>"MEDLINE"</code></td>
</tr>
<tr class="altColor">
<td class="colFirst"><a name="org.biojava.nbio.core.sequence.io.GenbankSequenceParser.ORGANISM_TAG">
<!-- -->
</a><code>protected static final <a href="http://docs.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/biojava/nbio/core/sequence/io/GenbankSequenceParser.html#ORGANISM_TAG">ORGANISM_TAG</a></code></td>
<td class="colLast"><code>"ORGANISM"</code></td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a name="org.biojava.nbio.core.sequence.io.GenbankSequenceParser.PUBMED_TAG">
<!-- -->
</a><code>protected static final <a href="http://docs.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/biojava/nbio/core/sequence/io/GenbankSequenceParser.html#PUBMED_TAG">PUBMED_TAG</a></code></td>
<td class="colLast"><code>"PUBMED"</code></td>
</tr>
<tr class="altColor">
<td class="colFirst"><a name="org.biojava.nbio.core.sequence.io.GenbankSequenceParser.REFERENCE_TAG">
<!-- -->
</a><code>protected static final <a href="http://docs.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/biojava/nbio/core/sequence/io/GenbankSequenceParser.html#REFERENCE_TAG">REFERENCE_TAG</a></code></td>
<td class="colLast"><code>"REFERENCE"</code></td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a name="org.biojava.nbio.core.sequence.io.GenbankSequenceParser.REMARK_TAG">
<!-- -->
</a><code>protected static final <a href="http://docs.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/biojava/nbio/core/sequence/io/GenbankSequenceParser.html#REMARK_TAG">REMARK_TAG</a></code></td>
<td class="colLast"><code>"REMARK"</code></td>
</tr>
<tr class="altColor">
<td class="colFirst"><a name="org.biojava.nbio.core.sequence.io.GenbankSequenceParser.SOURCE_TAG">
<!-- -->
</a><code>protected static final <a href="http://docs.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/biojava/nbio/core/sequence/io/GenbankSequenceParser.html#SOURCE_TAG">SOURCE_TAG</a></code></td>
<td class="colLast"><code>"SOURCE"</code></td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a name="org.biojava.nbio.core.sequence.io.GenbankSequenceParser.START_SEQUENCE_TAG">
<!-- -->
</a><code>protected static final <a href="http://docs.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/biojava/nbio/core/sequence/io/GenbankSequenceParser.html#START_SEQUENCE_TAG">START_SEQUENCE_TAG</a></code></td>
<td class="colLast"><code>"ORIGIN"</code></td>
</tr>
<tr class="altColor">
<td class="colFirst"><a name="org.biojava.nbio.core.sequence.io.GenbankSequenceParser.TITLE_TAG">
<!-- -->
</a><code>protected static final <a href="http://docs.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/biojava/nbio/core/sequence/io/GenbankSequenceParser.html#TITLE_TAG">TITLE_TAG</a></code></td>
<td class="colLast"><code>"TITLE"</code></td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a name="org.biojava.nbio.core.sequence.io.GenbankSequenceParser.VERSION_TAG">
<!-- -->
</a><code>protected static final <a href="http://docs.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/biojava/nbio/core/sequence/io/GenbankSequenceParser.html#VERSION_TAG">VERSION_TAG</a></code></td>
<td class="colLast"><code>"VERSION"</code></td>
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<table class="constantsSummary" border="0" cellpadding="3" cellspacing="0" summary="Constant Field Values table, listing constant fields, and values">
<caption><span>org.biojava.nbio.core.sequence.io.<a href="org/biojava/nbio/core/sequence/io/GenbankWriterHelper.html" title="class in org.biojava.nbio.core.sequence.io">GenbankWriterHelper</a></span><span class="tabEnd"> </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.biojava.nbio.core.sequence.io.GenbankWriterHelper.CIRCULAR_DNA">
<!-- -->
</a><code>public static final <a href="http://docs.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/biojava/nbio/core/sequence/io/GenbankWriterHelper.html#CIRCULAR_DNA">CIRCULAR_DNA</a></code></td>
<td class="colLast"><code>"circular"</code></td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a name="org.biojava.nbio.core.sequence.io.GenbankWriterHelper.LINEAR_DNA">
<!-- -->
</a><code>public static final <a href="http://docs.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/biojava/nbio/core/sequence/io/GenbankWriterHelper.html#LINEAR_DNA">LINEAR_DNA</a></code></td>
<td class="colLast"><code>"linear"</code></td>
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</tbody>
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</li>
<li class="blockList">
<table class="constantsSummary" border="0" cellpadding="3" cellspacing="0" summary="Constant Field Values table, listing constant fields, and values">
<caption><span>org.biojava.nbio.core.sequence.io.<a href="org/biojava/nbio/core/sequence/io/GenericInsdcHeaderFormat.html" title="class in org.biojava.nbio.core.sequence.io">GenericInsdcHeaderFormat</a><<a href="org/biojava/nbio/core/sequence/io/GenericInsdcHeaderFormat.html" title="type parameter in GenericInsdcHeaderFormat">S</a> extends <a href="org/biojava/nbio/core/sequence/template/AbstractSequence.html" title="class in org.biojava.nbio.core.sequence.template">AbstractSequence</a><<a href="org/biojava/nbio/core/sequence/io/GenericInsdcHeaderFormat.html" title="type parameter in GenericInsdcHeaderFormat">C</a>>,<a href="org/biojava/nbio/core/sequence/io/GenericInsdcHeaderFormat.html" title="type parameter in GenericInsdcHeaderFormat">C</a> extends <a href="org/biojava/nbio/core/sequence/template/Compound.html" title="interface in org.biojava.nbio.core.sequence.template">Compound</a>></span><span class="tabEnd"> </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.biojava.nbio.core.sequence.io.GenericInsdcHeaderFormat.MAX_WIDTH">
<!-- -->
</a><code>protected static final int</code></td>
<td><code><a href="org/biojava/nbio/core/sequence/io/GenericInsdcHeaderFormat.html#MAX_WIDTH">MAX_WIDTH</a></code></td>
<td class="colLast"><code>80</code></td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a name="org.biojava.nbio.core.sequence.io.GenericInsdcHeaderFormat.QUALIFIER_INDENT">
<!-- -->
</a><code>protected static final int</code></td>
<td><code><a href="org/biojava/nbio/core/sequence/io/GenericInsdcHeaderFormat.html#QUALIFIER_INDENT">QUALIFIER_INDENT</a></code></td>
<td class="colLast"><code>21</code></td>
</tr>
<tr class="altColor">
<td class="colFirst"><a name="org.biojava.nbio.core.sequence.io.GenericInsdcHeaderFormat.QUALIFIER_INDENT_STR">
<!-- -->
</a><code>protected static final <a href="http://docs.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/biojava/nbio/core/sequence/io/GenericInsdcHeaderFormat.html#QUALIFIER_INDENT_STR">QUALIFIER_INDENT_STR</a></code></td>
<td class="colLast"><code>" "</code></td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a name="org.biojava.nbio.core.sequence.io.GenericInsdcHeaderFormat.QUALIFIER_INDENT_TMP">
<!-- -->
</a><code>protected static final <a href="http://docs.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/biojava/nbio/core/sequence/io/GenericInsdcHeaderFormat.html#QUALIFIER_INDENT_TMP">QUALIFIER_INDENT_TMP</a></code></td>
<td class="colLast"><code>" %s "</code></td>
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<li class="blockList">
<table class="constantsSummary" border="0" cellpadding="3" cellspacing="0" summary="Constant Field Values table, listing constant fields, and values">
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<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.biojava.nbio.core.sequence.io.IUPACParser.IUPAC_LOCATION">
<!-- -->
</a><code>public static final <a href="http://docs.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/biojava/nbio/core/sequence/io/IUPACParser.html#IUPAC_LOCATION">IUPAC_LOCATION</a></code></td>
<td class="colLast"><code>"org/biojava/nbio/core/sequence/iupac.txt"</code></td>
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<ul class="blockList">
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<table class="constantsSummary" border="0" cellpadding="3" cellspacing="0" summary="Constant Field Values table, listing constant fields, and values">
<caption><span>org.biojava.nbio.core.sequence.io.template.<a href="org/biojava/nbio/core/sequence/io/template/GenbankHeaderFormatInterface.html" title="interface in org.biojava.nbio.core.sequence.io.template">GenbankHeaderFormatInterface</a><<a href="org/biojava/nbio/core/sequence/io/template/GenbankHeaderFormatInterface.html" title="type parameter in GenbankHeaderFormatInterface">S</a> extends <a href="org/biojava/nbio/core/sequence/template/Sequence.html" title="interface in org.biojava.nbio.core.sequence.template">Sequence</a><?>,<a href="org/biojava/nbio/core/sequence/io/template/GenbankHeaderFormatInterface.html" title="type parameter in GenbankHeaderFormatInterface">C</a> extends <a href="org/biojava/nbio/core/sequence/template/Compound.html" title="interface in org.biojava.nbio.core.sequence.template">Compound</a>></span><span class="tabEnd"> </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.biojava.nbio.core.sequence.io.template.GenbankHeaderFormatInterface.UNKNOWN_DNA">
<!-- -->
</a><code>public static final <a href="http://docs.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/biojava/nbio/core/sequence/io/template/GenbankHeaderFormatInterface.html#UNKNOWN_DNA">UNKNOWN_DNA</a></code></td>
<td class="colLast"><code>"UNK"</code></td>
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<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.biojava.nbio.core.sequence.location.InsdcParser.locationSplitPattern">
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</a><code>protected static final <a href="http://docs.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/biojava/nbio/core/sequence/location/InsdcParser.html#locationSplitPattern">locationSplitPattern</a></code></td>
<td class="colLast"><code>",(?=([^\\(|\\)]+\\([^\\(|\\)]+\\))[^\\(|\\)]+)"</code></td>
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<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.biojava.nbio.core.sequence.storage.BitSequenceReader.BitArrayWorker.BYTES_PER_INT">
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</a><code>public static final int</code></td>
<td><code><a href="org/biojava/nbio/core/sequence/storage/BitSequenceReader.BitArrayWorker.html#BYTES_PER_INT">BYTES_PER_INT</a></code></td>
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<tr>
<th class="colFirst" scope="col">Modifier and Type</th>
<th scope="col">Constant Field</th>
<th class="colLast" scope="col">Value</th>
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<tbody>
<tr class="altColor">
<td class="colFirst"><a name="org.biojava.nbio.core.util.Hashcoder.PRIME">
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</a><code>public static final int</code></td>
<td><code><a href="org/biojava/nbio/core/util/Hashcoder.html#PRIME">PRIME</a></code></td>
<td class="colLast"><code>79</code></td>
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<tr class="rowColor">
<td class="colFirst"><a name="org.biojava.nbio.core.util.Hashcoder.SEED">
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</a><code>public static final int</code></td>
<td><code><a href="org/biojava/nbio/core/util/Hashcoder.html#SEED">SEED</a></code></td>
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<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.biojava.nbio.core.util.InputStreamProvider.CACHE_PROPERTY">
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</a><code>public static final <a href="http://docs.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/biojava/nbio/core/util/InputStreamProvider.html#CACHE_PROPERTY">CACHE_PROPERTY</a></code></td>
<td class="colLast"><code>"biojava.cache.files"</code></td>
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<tr class="rowColor">
<td class="colFirst"><a name="org.biojava.nbio.core.util.InputStreamProvider.GZIP_MAGIC">
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</a><code>public static final int</code></td>
<td><code><a href="org/biojava/nbio/core/util/InputStreamProvider.html#GZIP_MAGIC">GZIP_MAGIC</a></code></td>
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<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.biojava.nbio.core.util.SequenceTools.NUCLEOTIDE_LETTERS">
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</a><code>protected static final <a href="http://docs.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/biojava/nbio/core/util/SequenceTools.html#NUCLEOTIDE_LETTERS">NUCLEOTIDE_LETTERS</a></code></td>
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<tr>
<th class="colFirst" scope="col">Modifier and Type</th>
<th scope="col">Constant Field</th>
<th class="colLast" scope="col">Value</th>
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<tbody>
<tr class="altColor">
<td class="colFirst"><a name="org.biojava.nbio.core.util.SoftHashMap.DEFAULT_LIMIT">
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</a><code>public static final int</code></td>
<td><code><a href="org/biojava/nbio/core/util/SoftHashMap.html#DEFAULT_LIMIT">DEFAULT_LIMIT</a></code></td>
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<tr>
<th class="colFirst" scope="col">Modifier and Type</th>
<th scope="col">Constant Field</th>
<th class="colLast" scope="col">Value</th>
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<tbody>
<tr class="altColor">
<td class="colFirst"><a name="org.biojava.nbio.genome.parsers.cytoband.CytobandParser.DEFAULT_LOCATION">
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</a><code>public static final <a href="http://docs.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/biojava/nbio/genome/parsers/cytoband/CytobandParser.html#DEFAULT_LOCATION">DEFAULT_LOCATION</a></code></td>
<td class="colLast"><code>"http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/cytoBand.txt.gz"</code></td>
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<tr>
<th class="colFirst" scope="col">Modifier and Type</th>
<th scope="col">Constant Field</th>
<th class="colLast" scope="col">Value</th>
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<tbody>
<tr class="altColor">
<td class="colFirst"><a name="org.biojava.nbio.genome.parsers.genename.GeneChromosomePositionParser.DEFAULT_MAPPING_URL">
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</a><code>public static final <a href="http://docs.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/biojava/nbio/genome/parsers/genename/GeneChromosomePositionParser.html#DEFAULT_MAPPING_URL">DEFAULT_MAPPING_URL</a></code></td>
<td class="colLast"><code>"http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/refFlat.txt.gz"</code></td>
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<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.biojava.nbio.genome.parsers.genename.GeneNamesParser.DEFAULT_GENENAMES_URL">
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</a><code>public static final <a href="http://docs.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/biojava/nbio/genome/parsers/genename/GeneNamesParser.html#DEFAULT_GENENAMES_URL">DEFAULT_GENENAMES_URL</a></code></td>
<td class="colLast"><code>"http://www.genenames.org/cgi-bin/download?title=HGNC+output+data&hgnc_dbtag=on&col=gd_app_sym&col=gd_app_name&col=gd_status&col=gd_prev_sym&col=gd_prev_name&col=gd_aliases&col=gd_pub_chrom_map&col=gd_pub_acc_ids&col=md_mim_id&col=gd_pub_refseq_ids&col=md_ensembl_id&col=md_prot_id&col=gd_hgnc_id&status=Approved&status_opt=2&where=((gd_pub_chrom_map%20not%20like%20%27%patch%%27%20and%20gd_pub_chrom_map%20not%20like%20%27%ALT_REF%%27)%20or%20gd_pub_chrom_map%20IS%20NULL)%20and%20gd_locus_group%20%3d%20%27protein-coding%20gene%27&order_by=gd_app_sym_sort&format=text&limit=&submit=submit&.cgifields=&.cgifields=chr&.cgifields=status&.cgifields=hgnc_dbtag"</code></td>
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<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.biojava.nbio.ontology.Synonym.BROAD_SYNONYM">
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</a><code>public static final int</code></td>
<td><code><a href="org/biojava/nbio/ontology/Synonym.html#BROAD_SYNONYM">BROAD_SYNONYM</a></code></td>
<td class="colLast"><code>3</code></td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a name="org.biojava.nbio.ontology.Synonym.EXACT_SYNONYM">
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</a><code>public static final int</code></td>
<td><code><a href="org/biojava/nbio/ontology/Synonym.html#EXACT_SYNONYM">EXACT_SYNONYM</a></code></td>
<td class="colLast"><code>1</code></td>
</tr>
<tr class="altColor">
<td class="colFirst"><a name="org.biojava.nbio.ontology.Synonym.NARROW_SYNONYM">
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</a><code>public static final int</code></td>
<td><code><a href="org/biojava/nbio/ontology/Synonym.html#NARROW_SYNONYM">NARROW_SYNONYM</a></code></td>
<td class="colLast"><code>2</code></td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a name="org.biojava.nbio.ontology.Synonym.RELATED_SYNONYM">
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</a><code>public static final int</code></td>
<td><code><a href="org/biojava/nbio/ontology/Synonym.html#RELATED_SYNONYM">RELATED_SYNONYM</a></code></td>
<td class="colLast"><code>0</code></td>
</tr>
<tr class="altColor">
<td class="colFirst"><a name="org.biojava.nbio.ontology.Synonym.UNKNOWN_SCOPE">
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</a><code>public static final int</code></td>
<td><code><a href="org/biojava/nbio/ontology/Synonym.html#UNKNOWN_SCOPE">UNKNOWN_SCOPE</a></code></td>
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<caption><span>org.biojava.nbio.ontology.obo.<a href="org/biojava/nbio/ontology/obo/OboFileHandler.html" title="class in org.biojava.nbio.ontology.obo">OboFileHandler</a></span><span class="tabEnd"> </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.biojava.nbio.ontology.obo.OboFileHandler.ALT_ID">
<!-- -->
</a><code>public static final <a href="http://docs.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/biojava/nbio/ontology/obo/OboFileHandler.html#ALT_ID">ALT_ID</a></code></td>
<td class="colLast"><code>"alt_id"</code></td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a name="org.biojava.nbio.ontology.obo.OboFileHandler.BROAD_SYNONYM">
<!-- -->
</a><code>public static final <a href="http://docs.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/biojava/nbio/ontology/obo/OboFileHandler.html#BROAD_SYNONYM">BROAD_SYNONYM</a></code></td>
<td class="colLast"><code>"broad_synonym"</code></td>
</tr>
<tr class="altColor">
<td class="colFirst"><a name="org.biojava.nbio.ontology.obo.OboFileHandler.COMMENT">
<!-- -->
</a><code>public static final <a href="http://docs.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/biojava/nbio/ontology/obo/OboFileHandler.html#COMMENT">COMMENT</a></code></td>
<td class="colLast"><code>"comment"</code></td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a name="org.biojava.nbio.ontology.obo.OboFileHandler.DEF">
<!-- -->
</a><code>public static final <a href="http://docs.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/biojava/nbio/ontology/obo/OboFileHandler.html#DEF">DEF</a></code></td>
<td class="colLast"><code>"def"</code></td>
</tr>
<tr class="altColor">
<td class="colFirst"><a name="org.biojava.nbio.ontology.obo.OboFileHandler.DISJOINT_FROM">
<!-- -->
</a><code>public static final <a href="http://docs.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/biojava/nbio/ontology/obo/OboFileHandler.html#DISJOINT_FROM">DISJOINT_FROM</a></code></td>
<td class="colLast"><code>"disjoint_from"</code></td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a name="org.biojava.nbio.ontology.obo.OboFileHandler.EXACT_SYNONYM">
<!-- -->
</a><code>public static final <a href="http://docs.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/biojava/nbio/ontology/obo/OboFileHandler.html#EXACT_SYNONYM">EXACT_SYNONYM</a></code></td>
<td class="colLast"><code>"exact_synonym"</code></td>
</tr>
<tr class="altColor">
<td class="colFirst"><a name="org.biojava.nbio.ontology.obo.OboFileHandler.ID_KEY">
<!-- -->
</a><code>public static final <a href="http://docs.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/biojava/nbio/ontology/obo/OboFileHandler.html#ID_KEY">ID_KEY</a></code></td>
<td class="colLast"><code>"id"</code></td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a name="org.biojava.nbio.ontology.obo.OboFileHandler.INTERSECTION_OF">
<!-- -->
</a><code>public static final <a href="http://docs.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/biojava/nbio/ontology/obo/OboFileHandler.html#INTERSECTION_OF">INTERSECTION_OF</a></code></td>
<td class="colLast"><code>"intersection_of"</code></td>
</tr>
<tr class="altColor">
<td class="colFirst"><a name="org.biojava.nbio.ontology.obo.OboFileHandler.IS_A">
<!-- -->
</a><code>public static final <a href="http://docs.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/biojava/nbio/ontology/obo/OboFileHandler.html#IS_A">IS_A</a></code></td>
<td class="colLast"><code>"is_a"</code></td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a name="org.biojava.nbio.ontology.obo.OboFileHandler.IS_OBSOLETE">
<!-- -->
</a><code>public static final <a href="http://docs.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/biojava/nbio/ontology/obo/OboFileHandler.html#IS_OBSOLETE">IS_OBSOLETE</a></code></td>
<td class="colLast"><code>"is_obsolete"</code></td>
</tr>
<tr class="altColor">
<td class="colFirst"><a name="org.biojava.nbio.ontology.obo.OboFileHandler.NAME">
<!-- -->
</a><code>public static final <a href="http://docs.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/biojava/nbio/ontology/obo/OboFileHandler.html#NAME">NAME</a></code></td>
<td class="colLast"><code>"name"</code></td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a name="org.biojava.nbio.ontology.obo.OboFileHandler.NARROW_SYNONYM">
<!-- -->
</a><code>public static final <a href="http://docs.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/biojava/nbio/ontology/obo/OboFileHandler.html#NARROW_SYNONYM">NARROW_SYNONYM</a></code></td>
<td class="colLast"><code>"narrow_synonym"</code></td>
</tr>
<tr class="altColor">
<td class="colFirst"><a name="org.biojava.nbio.ontology.obo.OboFileHandler.ONTOLOGY">
<!-- -->
</a><code>public static final <a href="http://docs.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/biojava/nbio/ontology/obo/OboFileHandler.html#ONTOLOGY">ONTOLOGY</a></code></td>
<td class="colLast"><code>"ontologys"</code></td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a name="org.biojava.nbio.ontology.obo.OboFileHandler.REL_SYNONYM">
<!-- -->
</a><code>public static final <a href="http://docs.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/biojava/nbio/ontology/obo/OboFileHandler.html#REL_SYNONYM">REL_SYNONYM</a></code></td>
<td class="colLast"><code>"related_synonym"</code></td>
</tr>
<tr class="altColor">
<td class="colFirst"><a name="org.biojava.nbio.ontology.obo.OboFileHandler.RELATIONSHIP">
<!-- -->
</a><code>public static final <a href="http://docs.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/biojava/nbio/ontology/obo/OboFileHandler.html#RELATIONSHIP">RELATIONSHIP</a></code></td>
<td class="colLast"><code>"relationship"</code></td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a name="org.biojava.nbio.ontology.obo.OboFileHandler.SUBSET">
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</a><code>public static final <a href="http://docs.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/biojava/nbio/ontology/obo/OboFileHandler.html#SUBSET">SUBSET</a></code></td>
<td class="colLast"><code>"subset"</code></td>
</tr>
<tr class="altColor">
<td class="colFirst"><a name="org.biojava.nbio.ontology.obo.OboFileHandler.SYNONYM">
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</a><code>public static final <a href="http://docs.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/biojava/nbio/ontology/obo/OboFileHandler.html#SYNONYM">SYNONYM</a></code></td>
<td class="colLast"><code>"synonym"</code></td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a name="org.biojava.nbio.ontology.obo.OboFileHandler.TERM">
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</a><code>public static final <a href="http://docs.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/biojava/nbio/ontology/obo/OboFileHandler.html#TERM">TERM</a></code></td>
<td class="colLast"><code>"Term"</code></td>
</tr>
<tr class="altColor">
<td class="colFirst"><a name="org.biojava.nbio.ontology.obo.OboFileHandler.TYPEDEF">
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</a><code>public static final <a href="http://docs.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/biojava/nbio/ontology/obo/OboFileHandler.html#TYPEDEF">TYPEDEF</a></code></td>
<td class="colLast"><code>"Typedef"</code></td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a name="org.biojava.nbio.ontology.obo.OboFileHandler.XREF_ANALOG">
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</a><code>public static final <a href="http://docs.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/biojava/nbio/ontology/obo/OboFileHandler.html#XREF_ANALOG">XREF_ANALOG</a></code></td>
<td class="colLast"><code>"xref_analog"</code></td>
</tr>
</tbody>
</table>
</li>
</ul>
<ul class="blockList">
<li class="blockList">
<table class="constantsSummary" border="0" cellpadding="3" cellspacing="0" summary="Constant Field Values table, listing constant fields, and values">
<caption><span>org.biojava.nbio.phosphosite.<a href="org/biojava/nbio/phosphosite/Dataset.html" title="class in org.biojava.nbio.phosphosite">Dataset</a></span><span class="tabEnd"> </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.biojava.nbio.phosphosite.Dataset.ACETYLATION">
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</a><code>public static final <a href="http://docs.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/biojava/nbio/phosphosite/Dataset.html#ACETYLATION">ACETYLATION</a></code></td>
<td class="colLast"><code>"http://www.phosphosite.org/downloads/Acetylation_site_dataset.gz"</code></td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a name="org.biojava.nbio.phosphosite.Dataset.DISEASE_ASSOC">
<!-- -->
</a><code>public static final <a href="http://docs.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/biojava/nbio/phosphosite/Dataset.html#DISEASE_ASSOC">DISEASE_ASSOC</a></code></td>
<td class="colLast"><code>"http://www.phosphosite.org/downloads/Disease-associated_sites.gz"</code></td>
</tr>
<tr class="altColor">