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updated javadocs
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Schmoho committed Jul 22, 2024
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302 changes: 159 additions & 143 deletions docs/allclasses-index.html
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34 changes: 23 additions & 11 deletions docs/allpackages-index.html
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Expand Up @@ -57,27 +57,39 @@ <h1 title="All&amp;nbsp;Packages" class="title">All&nbsp;Packages</h1>
<div class="col-last even-row-color">&nbsp;</div>
<div class="col-first odd-row-color"><a href="edu/ucsd/sbrg/annotation/package-summary.html">edu.ucsd.sbrg.annotation</a></div>
<div class="col-last odd-row-color">&nbsp;</div>
<div class="col-first even-row-color"><a href="edu/ucsd/sbrg/db/package-summary.html">edu.ucsd.sbrg.db</a></div>
<div class="col-first even-row-color"><a href="edu/ucsd/sbrg/annotation/adb/package-summary.html">edu.ucsd.sbrg.annotation.adb</a></div>
<div class="col-last even-row-color">&nbsp;</div>
<div class="col-first odd-row-color"><a href="edu/ucsd/sbrg/db/adb/package-summary.html">edu.ucsd.sbrg.db.adb</a></div>
<div class="col-first odd-row-color"><a href="edu/ucsd/sbrg/annotation/bigg/package-summary.html">edu.ucsd.sbrg.annotation.bigg</a></div>
<div class="col-last odd-row-color">&nbsp;</div>
<div class="col-first even-row-color"><a href="edu/ucsd/sbrg/db/bigg/package-summary.html">edu.ucsd.sbrg.db.bigg</a></div>
<div class="col-first even-row-color"><a href="edu/ucsd/sbrg/annotation/bigg/fbc/package-summary.html">edu.ucsd.sbrg.annotation.bigg.fbc</a></div>
<div class="col-last even-row-color">&nbsp;</div>
<div class="col-first odd-row-color"><a href="edu/ucsd/sbrg/eco/package-summary.html">edu.ucsd.sbrg.eco</a></div>
<div class="col-first odd-row-color"><a href="edu/ucsd/sbrg/db/package-summary.html">edu.ucsd.sbrg.db</a></div>
<div class="col-last odd-row-color">&nbsp;</div>
<div class="col-first even-row-color"><a href="edu/ucsd/sbrg/io/package-summary.html">edu.ucsd.sbrg.io</a></div>
<div class="col-first even-row-color"><a href="edu/ucsd/sbrg/db/adb/package-summary.html">edu.ucsd.sbrg.db.adb</a></div>
<div class="col-last even-row-color">&nbsp;</div>
<div class="col-first odd-row-color"><a href="edu/ucsd/sbrg/miriam/package-summary.html">edu.ucsd.sbrg.miriam</a></div>
<div class="col-first odd-row-color"><a href="edu/ucsd/sbrg/db/bigg/package-summary.html">edu.ucsd.sbrg.db.bigg</a></div>
<div class="col-last odd-row-color">&nbsp;</div>
<div class="col-first even-row-color"><a href="edu/ucsd/sbrg/miriam/models/package-summary.html">edu.ucsd.sbrg.miriam.models</a></div>
<div class="col-first even-row-color"><a href="edu/ucsd/sbrg/eco/package-summary.html">edu.ucsd.sbrg.eco</a></div>
<div class="col-last even-row-color">&nbsp;</div>
<div class="col-first odd-row-color"><a href="edu/ucsd/sbrg/parsers/cobra/package-summary.html">edu.ucsd.sbrg.parsers.cobra</a></div>
<div class="col-first odd-row-color"><a href="edu/ucsd/sbrg/io/package-summary.html">edu.ucsd.sbrg.io</a></div>
<div class="col-last odd-row-color">&nbsp;</div>
<div class="col-first even-row-color"><a href="edu/ucsd/sbrg/parsers/json/package-summary.html">edu.ucsd.sbrg.parsers.json</a></div>
<div class="col-first even-row-color"><a href="edu/ucsd/sbrg/io/parsers/cobra/package-summary.html">edu.ucsd.sbrg.io.parsers.cobra</a></div>
<div class="col-last even-row-color">&nbsp;</div>
<div class="col-first odd-row-color"><a href="edu/ucsd/sbrg/parsers/json/models/package-summary.html">edu.ucsd.sbrg.parsers.json.models</a></div>
<div class="col-first odd-row-color"><a href="edu/ucsd/sbrg/io/parsers/json/package-summary.html">edu.ucsd.sbrg.io.parsers.json</a></div>
<div class="col-last odd-row-color">&nbsp;</div>
<div class="col-first even-row-color"><a href="edu/ucsd/sbrg/polishing/package-summary.html">edu.ucsd.sbrg.polishing</a></div>
<div class="col-first even-row-color"><a href="edu/ucsd/sbrg/io/parsers/json/mapping/package-summary.html">edu.ucsd.sbrg.io.parsers.json.mapping</a></div>
<div class="col-last even-row-color">&nbsp;</div>
<div class="col-first odd-row-color"><a href="edu/ucsd/sbrg/polishing/package-summary.html">edu.ucsd.sbrg.polishing</a></div>
<div class="col-last odd-row-color">&nbsp;</div>
<div class="col-first even-row-color"><a href="edu/ucsd/sbrg/polishing/fbc/package-summary.html">edu.ucsd.sbrg.polishing.fbc</a></div>
<div class="col-last even-row-color">&nbsp;</div>
<div class="col-first odd-row-color"><a href="edu/ucsd/sbrg/reporting/package-summary.html">edu.ucsd.sbrg.reporting</a></div>
<div class="col-last odd-row-color">&nbsp;</div>
<div class="col-first even-row-color"><a href="edu/ucsd/sbrg/resolver/package-summary.html">edu.ucsd.sbrg.resolver</a></div>
<div class="col-last even-row-color">&nbsp;</div>
<div class="col-first odd-row-color"><a href="edu/ucsd/sbrg/resolver/identifiersorg/package-summary.html">edu.ucsd.sbrg.resolver.identifiersorg</a></div>
<div class="col-last odd-row-color">&nbsp;</div>
<div class="col-first even-row-color"><a href="edu/ucsd/sbrg/resolver/identifiersorg/mapping/package-summary.html">edu.ucsd.sbrg.resolver.identifiersorg.mapping</a></div>
<div class="col-last even-row-color">&nbsp;</div>
<div class="col-first odd-row-color"><a href="edu/ucsd/sbrg/util/package-summary.html">edu.ucsd.sbrg.util</a></div>
<div class="col-last odd-row-color">&nbsp;</div>
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52 changes: 47 additions & 5 deletions docs/constant-values.html
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Expand Up @@ -59,6 +59,35 @@ <h2 title="Contents">Contents</h2>
<h2 title="edu.ucsd.*">edu.ucsd.*</h2>
<ul class="block-list">
<li>
<div class="caption"><span>edu.ucsd.sbrg.annotation.bigg.<a href="edu/ucsd/sbrg/annotation/bigg/BiGGModelAnnotator.html" title="class in edu.ucsd.sbrg.annotation.bigg">BiGGModelAnnotator</a></span></div>
<div class="summary-table three-column-summary">
<div class="table-header col-first">Modifier and Type</div>
<div class="table-header col-second">Constant Field</div>
<div class="table-header col-last">Value</div>
<div class="col-first even-row-color"><code id="edu.ucsd.sbrg.annotation.bigg.BiGGModelAnnotator.GENOME_ASSEMBLY_ID_PATTERN">public&nbsp;static&nbsp;final&nbsp;<a href="https://docs.oracle.com/en/java/javase/21/docs/api/java.base/java/lang/String.html" title="class or interface in java.lang" class="external-link">String</a></code></div>
<div class="col-second even-row-color"><code><a href="edu/ucsd/sbrg/annotation/bigg/BiGGModelAnnotator.html#GENOME_ASSEMBLY_ID_PATTERN">GENOME_ASSEMBLY_ID_PATTERN</a></code></div>
<div class="col-last even-row-color"><code>"^GC[AF]_[0-9]{9}\\.[0-9]+$"</code></div>
<div class="col-first odd-row-color"><code id="edu.ucsd.sbrg.annotation.bigg.BiGGModelAnnotator.REF_SEQ_ACCESSION_NUMBER_PATTERN">public&nbsp;static&nbsp;final&nbsp;<a href="https://docs.oracle.com/en/java/javase/21/docs/api/java.base/java/lang/String.html" title="class or interface in java.lang" class="external-link">String</a></code></div>
<div class="col-second odd-row-color"><code><a href="edu/ucsd/sbrg/annotation/bigg/BiGGModelAnnotator.html#REF_SEQ_ACCESSION_NUMBER_PATTERN">REF_SEQ_ACCESSION_NUMBER_PATTERN</a></code></div>
<div class="col-last odd-row-color"><code>"^(((AC|AP|NC|NG|NM|NP|NR|NT|NW|XM|XP|XR|YP|ZP)_\\d+)|(NZ_[A-Z]{2,4}\\d+))(\\.\\d+)?$"</code></div>
</div>
</li>
</ul>
<ul class="block-list">
<li>
<div class="caption"><span>edu.ucsd.sbrg.annotation.bigg.fbc.<a href="edu/ucsd/sbrg/annotation/bigg/fbc/BiGGGeneProductAnnotator.html" title="class in edu.ucsd.sbrg.annotation.bigg.fbc">BiGGGeneProductAnnotator</a></span></div>
<div class="summary-table three-column-summary">
<div class="table-header col-first">Modifier and Type</div>
<div class="table-header col-second">Constant Field</div>
<div class="table-header col-last">Value</div>
<div class="col-first even-row-color"><code id="edu.ucsd.sbrg.annotation.bigg.fbc.BiGGGeneProductAnnotator.BIGG_GENE_ID_PATTERN">public&nbsp;static&nbsp;final&nbsp;<a href="https://docs.oracle.com/en/java/javase/21/docs/api/java.base/java/lang/String.html" title="class or interface in java.lang" class="external-link">String</a></code></div>
<div class="col-second even-row-color"><code><a href="edu/ucsd/sbrg/annotation/bigg/fbc/BiGGGeneProductAnnotator.html#BIGG_GENE_ID_PATTERN">BIGG_GENE_ID_PATTERN</a></code></div>
<div class="col-last even-row-color"><code>"^(G_)?([a-zA-Z][a-zA-Z0-9_]+)(?:_([a-z][a-z0-9]?))?(?:_([A-Z][A-Z0-9]?))?$"</code></div>
</div>
</li>
</ul>
<ul class="block-list">
<li>
<div class="caption"><span>edu.ucsd.sbrg.db.adb.<a href="edu/ucsd/sbrg/db/adb/AnnotateDBContract.Constants.html" title="class in edu.ucsd.sbrg.db.adb">AnnotateDBContract.Constants</a></span></div>
<div class="summary-table three-column-summary">
<div class="table-header col-first">Modifier and Type</div>
Expand Down Expand Up @@ -94,22 +123,35 @@ <h2 title="edu.ucsd.*">edu.ucsd.*</h2>
</ul>
<ul class="block-list">
<li>
<div class="caption"><span>edu.ucsd.sbrg.polishing.<a href="edu/ucsd/sbrg/polishing/UnitPolishing.html" title="class in edu.ucsd.sbrg.polishing">UnitPolishing</a></span></div>
<div class="caption"><span>edu.ucsd.sbrg.polishing.<a href="edu/ucsd/sbrg/polishing/UnitPolisher.html" title="class in edu.ucsd.sbrg.polishing">UnitPolisher</a></span></div>
<div class="summary-table three-column-summary">
<div class="table-header col-first">Modifier and Type</div>
<div class="table-header col-second">Constant Field</div>
<div class="table-header col-last">Value</div>
<div class="col-first even-row-color"><code id="edu.ucsd.sbrg.polishing.UnitPolishing.GROWTH_UNIT_ID">public&nbsp;static&nbsp;final&nbsp;<a href="https://docs.oracle.com/en/java/javase/21/docs/api/java.base/java/lang/String.html" title="class or interface in java.lang" class="external-link">String</a></code></div>
<div class="col-second even-row-color"><code><a href="edu/ucsd/sbrg/polishing/UnitPolishing.html#GROWTH_UNIT_ID">GROWTH_UNIT_ID</a></code></div>
<div class="col-first even-row-color"><code id="edu.ucsd.sbrg.polishing.UnitPolisher.GROWTH_UNIT_ID">public&nbsp;static&nbsp;final&nbsp;<a href="https://docs.oracle.com/en/java/javase/21/docs/api/java.base/java/lang/String.html" title="class or interface in java.lang" class="external-link">String</a></code></div>
<div class="col-second even-row-color"><code><a href="edu/ucsd/sbrg/polishing/UnitPolisher.html#GROWTH_UNIT_ID">GROWTH_UNIT_ID</a></code></div>
<div class="col-last even-row-color"><code>"mmol_per_gDW_per_hr"</code></div>
<div class="col-first odd-row-color"><code id="edu.ucsd.sbrg.polishing.UnitPolishing.GROWTH_UNIT_NAME">public&nbsp;static&nbsp;final&nbsp;<a href="https://docs.oracle.com/en/java/javase/21/docs/api/java.base/java/lang/String.html" title="class or interface in java.lang" class="external-link">String</a></code></div>
<div class="col-second odd-row-color"><code><a href="edu/ucsd/sbrg/polishing/UnitPolishing.html#GROWTH_UNIT_NAME">GROWTH_UNIT_NAME</a></code></div>
<div class="col-first odd-row-color"><code id="edu.ucsd.sbrg.polishing.UnitPolisher.GROWTH_UNIT_NAME">public&nbsp;static&nbsp;final&nbsp;<a href="https://docs.oracle.com/en/java/javase/21/docs/api/java.base/java/lang/String.html" title="class or interface in java.lang" class="external-link">String</a></code></div>
<div class="col-second odd-row-color"><code><a href="edu/ucsd/sbrg/polishing/UnitPolisher.html#GROWTH_UNIT_NAME">GROWTH_UNIT_NAME</a></code></div>
<div class="col-last odd-row-color"><code>"Millimoles per gram (dry weight) per hour"</code></div>
</div>
</li>
</ul>
<ul class="block-list">
<li>
<div class="caption"><span>edu.ucsd.sbrg.resolver.identifiersorg.<a href="edu/ucsd/sbrg/resolver/identifiersorg/IdentifiersOrgURI.html" title="class in edu.ucsd.sbrg.resolver.identifiersorg">IdentifiersOrgURI</a></span></div>
<div class="summary-table three-column-summary">
<div class="table-header col-first">Modifier and Type</div>
<div class="table-header col-second">Constant Field</div>
<div class="table-header col-last">Value</div>
<div class="col-first even-row-color"><code id="edu.ucsd.sbrg.resolver.identifiersorg.IdentifiersOrgURI.IDENTIFIERS_ORG_ID_PATTERN">public&nbsp;static&nbsp;final&nbsp;<a href="https://docs.oracle.com/en/java/javase/21/docs/api/java.base/java/lang/String.html" title="class or interface in java.lang" class="external-link">String</a></code></div>
<div class="col-second even-row-color"><code><a href="edu/ucsd/sbrg/resolver/identifiersorg/IdentifiersOrgURI.html#IDENTIFIERS_ORG_ID_PATTERN">IDENTIFIERS_ORG_ID_PATTERN</a></code></div>
<div class="col-last even-row-color"><code>"(https?://)?(www\\.)?identifiers\\.org/(?&lt;prefix&gt;.*?)/(?&lt;id&gt;.*)"</code></div>
</div>
</li>
</ul>
<ul class="block-list">
<li>
<div class="caption"><span>edu.ucsd.sbrg.util.<a href="edu/ucsd/sbrg/util/SBMLUtils.html" title="class in edu.ucsd.sbrg.util">SBMLUtils</a></span></div>
<div class="summary-table three-column-summary">
<div class="table-header col-first">Modifier and Type</div>
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