updated javadocs

draeger-lab · Jul 26, 2024 · 4e237f2 · 4e237f2
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diff --git a/docs/allclasses-index.html b/docs/allclasses-index.html
diff --git a/docs/constant-values.html b/docs/constant-values.html
@@ -123,6 +123,22 @@ <h2 title="edu.ucsd.*">edu.ucsd.*</h2>
 </ul>
 <ul class="block-list">
 <li>
+<div class="caption"><span>edu.ucsd.sbrg.io.<a href="edu/ucsd/sbrg/io/CombineArchive.html" title="class in edu.ucsd.sbrg.io">CombineArchive</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.io.CombineArchive.COMBINE_SPECIFICATION">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/io/CombineArchive.html#COMBINE_SPECIFICATION">COMBINE_SPECIFICATION</a></code></div>
+<div class="col-last even-row-color"><code>"https://identifiers.org/combine.specifications/sbml"</code></div>
+<div class="col-first odd-row-color"><code id="edu.ucsd.sbrg.io.CombineArchive.RDF_MEDIATYPE">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/io/CombineArchive.html#RDF_MEDIATYPE">RDF_MEDIATYPE</a></code></div>
+<div class="col-last odd-row-color"><code>"https://purl.org/NET/mediatypes/application/rdf+xml"</code></div>
+</div>
+</li>
+</ul>
+<ul class="block-list">
+<li>
 <div class="caption"><span>edu.ucsd.sbrg.parameters.<a href="edu/ucsd/sbrg/parameters/FluxObjectivesPolishingParameters.html" title="class in edu.ucsd.sbrg.parameters">FluxObjectivesPolishingParameters</a></span></div>
 <div class="summary-table three-column-summary">
 <div class="table-header col-first">Modifier and Type</div>

diff --git a/docs/edu/ucsd/sbrg/ModelPolisherCLILauncher.html b/docs/edu/ucsd/sbrg/ModelPolisherCLILauncher.html
@@ -111,7 +111,7 @@ <h1 title="Class ModelPolisherCLILauncher" class="title">Class ModelPolisherCLIL
  - HTML tag correction in SBML files.
  - SBML document validation and conversion.
  - Annotation of models using external databases.
- - Output management including file writing, COMBINE archive creation, and compression.
+ - Output management including file writing, COMBINE archive creation, and outputType.
  <p>
  This class also handles error logging and provides detailed logging of the processing steps.</div>
 <dl class="notes">

diff --git a/...brg/ModelPolisherOptions.Compression.html → ...sbrg/ModelPolisherOptions.OutputType.html b/...brg/ModelPolisherOptions.Compression.html → ...sbrg/ModelPolisherOptions.OutputType.html
@@ -2,10 +2,10 @@
 <html lang="en">
 <head>
 <!-- Generated by javadoc (21) -->
-<title>ModelPolisherOptions.Compression (ModelPolisher 2.1 API)</title>
+<title>ModelPolisherOptions.OutputType (ModelPolisher 2.1 API)</title>
 <meta name="viewport" content="width=device-width, initial-scale=1">
 <meta http-equiv="Content-Type" content="text/html; charset=utf-8">
-<meta name="description" content="declaration: package: edu.ucsd.sbrg, interface: ModelPolisherOptions, enum: Compression">
+<meta name="description" content="declaration: package: edu.ucsd.sbrg, interface: ModelPolisherOptions, enum: OutputType">
 <meta name="generator" content="javadoc/ClassWriterImpl">
 <link rel="stylesheet" type="text/css" href="../../../stylesheet.css" title="Style">
 <link rel="stylesheet" type="text/css" href="../../../script-dir/jquery-ui.min.css" title="Style">
@@ -82,25 +82,25 @@
 <!-- ======== START OF CLASS DATA ======== -->
 <div class="header">
 <div class="sub-title"><span class="package-label-in-type">Package</span>&nbsp;<a href="package-summary.html">edu.ucsd.sbrg</a></div>
-<h1 title="Enum Class ModelPolisherOptions.Compression" class="title">Enum Class ModelPolisherOptions.Compression</h1>
+<h1 title="Enum Class ModelPolisherOptions.OutputType" class="title">Enum Class ModelPolisherOptions.OutputType</h1>
 </div>
 <div class="inheritance" title="Inheritance Tree"><a href="https://docs.oracle.com/en/java/javase/21/docs/api/java.base/java/lang/Object.html" title="class or interface in java.lang" class="external-link">java.lang.Object</a>
-<div class="inheritance"><a href="https://docs.oracle.com/en/java/javase/21/docs/api/java.base/java/lang/Enum.html" title="class or interface in java.lang" class="external-link">java.lang.Enum</a>&lt;<a href="ModelPolisherOptions.Compression.html" title="enum class in edu.ucsd.sbrg">ModelPolisherOptions.Compression</a>&gt;
-<div class="inheritance">edu.ucsd.sbrg.ModelPolisherOptions.Compression</div>
+<div class="inheritance"><a href="https://docs.oracle.com/en/java/javase/21/docs/api/java.base/java/lang/Enum.html" title="class or interface in java.lang" class="external-link">java.lang.Enum</a>&lt;<a href="ModelPolisherOptions.OutputType.html" title="enum class in edu.ucsd.sbrg">ModelPolisherOptions.OutputType</a>&gt;
+<div class="inheritance">edu.ucsd.sbrg.ModelPolisherOptions.OutputType</div>
 </div>
 </div>
 <section class="class-description" id="class-description">
 <dl class="notes">
 <dt>All Implemented Interfaces:</dt>
-<dd><code><a href="https://docs.oracle.com/en/java/javase/21/docs/api/java.base/java/io/Serializable.html" title="class or interface in java.io" class="external-link">Serializable</a></code>, <code><a href="https://docs.oracle.com/en/java/javase/21/docs/api/java.base/java/lang/Comparable.html" title="class or interface in java.lang" class="external-link">Comparable</a>&lt;<a href="ModelPolisherOptions.Compression.html" title="enum class in edu.ucsd.sbrg">ModelPolisherOptions.Compression</a>&gt;</code>, <code><a href="https://docs.oracle.com/en/java/javase/21/docs/api/java.base/java/lang/constant/Constable.html" title="class or interface in java.lang.constant" class="external-link">Constable</a></code></dd>
+<dd><code><a href="https://docs.oracle.com/en/java/javase/21/docs/api/java.base/java/io/Serializable.html" title="class or interface in java.io" class="external-link">Serializable</a></code>, <code><a href="https://docs.oracle.com/en/java/javase/21/docs/api/java.base/java/lang/Comparable.html" title="class or interface in java.lang" class="external-link">Comparable</a>&lt;<a href="ModelPolisherOptions.OutputType.html" title="enum class in edu.ucsd.sbrg">ModelPolisherOptions.OutputType</a>&gt;</code>, <code><a href="https://docs.oracle.com/en/java/javase/21/docs/api/java.base/java/lang/constant/Constable.html" title="class or interface in java.lang.constant" class="external-link">Constable</a></code></dd>
 </dl>
 <dl class="notes">
 <dt>Enclosing interface:</dt>
 <dd><code><a href="ModelPolisherOptions.html" title="interface in edu.ucsd.sbrg">ModelPolisherOptions</a></code></dd>
 </dl>
 <hr>
-<div class="type-signature"><span class="modifiers">public static enum </span><span class="element-name type-name-label">ModelPolisherOptions.Compression</span>
-<span class="extends-implements">extends <a href="https://docs.oracle.com/en/java/javase/21/docs/api/java.base/java/lang/Enum.html" title="class or interface in java.lang" class="external-link">Enum</a>&lt;<a href="ModelPolisherOptions.Compression.html" title="enum class in edu.ucsd.sbrg">ModelPolisherOptions.Compression</a>&gt;</span></div>
+<div class="type-signature"><span class="modifiers">public static enum </span><span class="element-name type-name-label">ModelPolisherOptions.OutputType</span>
+<span class="extends-implements">extends <a href="https://docs.oracle.com/en/java/javase/21/docs/api/java.base/java/lang/Enum.html" title="class or interface in java.lang" class="external-link">Enum</a>&lt;<a href="ModelPolisherOptions.OutputType.html" title="enum class in edu.ucsd.sbrg">ModelPolisherOptions.OutputType</a>&gt;</span></div>
 </section>
 <section class="summary">
 <ul class="summary-list">
@@ -121,11 +121,11 @@ <h2>Enum Constant Summary</h2>
 <div class="summary-table two-column-summary">
 <div class="table-header col-first">Enum Constant</div>
 <div class="table-header col-last">Description</div>
-<div class="col-first even-row-color"><code><a href="#GZIP" class="member-name-link">GZIP</a></code></div>
+<div class="col-first even-row-color"><code><a href="#COMBINE" class="member-name-link">COMBINE</a></code></div>
 <div class="col-last even-row-color">&nbsp;</div>
-<div class="col-first odd-row-color"><code><a href="#NONE" class="member-name-link">NONE</a></code></div>
+<div class="col-first odd-row-color"><code><a href="#JSON" class="member-name-link">JSON</a></code></div>
 <div class="col-last odd-row-color">&nbsp;</div>
-<div class="col-first even-row-color"><code><a href="#ZIP" class="member-name-link">ZIP</a></code></div>
+<div class="col-first even-row-color"><code><a href="#SBML" class="member-name-link">SBML</a></code></div>
 <div class="col-last even-row-color">&nbsp;</div>
 </div>
 </section>
@@ -144,12 +144,12 @@ <h2>Method Summary</h2>
 <div class="col-first even-row-color method-summary-table method-summary-table-tab2 method-summary-table-tab4"><code><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 method-summary-table method-summary-table-tab2 method-summary-table-tab4"><code><a href="#getFileExtension()" class="member-name-link">getFileExtension</a>()</code></div>
 <div class="col-last even-row-color method-summary-table method-summary-table-tab2 method-summary-table-tab4">&nbsp;</div>
-<div class="col-first odd-row-color method-summary-table method-summary-table-tab1 method-summary-table-tab4"><code>static <a href="ModelPolisherOptions.Compression.html" title="enum class in edu.ucsd.sbrg">ModelPolisherOptions.Compression</a></code></div>
+<div class="col-first odd-row-color method-summary-table method-summary-table-tab1 method-summary-table-tab4"><code>static <a href="ModelPolisherOptions.OutputType.html" title="enum class in edu.ucsd.sbrg">ModelPolisherOptions.OutputType</a></code></div>
 <div class="col-second odd-row-color method-summary-table method-summary-table-tab1 method-summary-table-tab4"><code><a href="#valueOf(java.lang.String)" class="member-name-link">valueOf</a><wbr>(<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>&nbsp;name)</code></div>
 <div class="col-last odd-row-color method-summary-table method-summary-table-tab1 method-summary-table-tab4">
 <div class="block">Returns the enum constant of this class with the specified name.</div>
 </div>
-<div class="col-first even-row-color method-summary-table method-summary-table-tab1 method-summary-table-tab4"><code>static <a href="ModelPolisherOptions.Compression.html" title="enum class in edu.ucsd.sbrg">ModelPolisherOptions.Compression</a>[]</code></div>
+<div class="col-first even-row-color method-summary-table method-summary-table-tab1 method-summary-table-tab4"><code>static <a href="ModelPolisherOptions.OutputType.html" title="enum class in edu.ucsd.sbrg">ModelPolisherOptions.OutputType</a>[]</code></div>
 <div class="col-second even-row-color method-summary-table method-summary-table-tab1 method-summary-table-tab4"><code><a href="#values()" class="member-name-link">values</a>()</code></div>
 <div class="col-last even-row-color method-summary-table method-summary-table-tab1 method-summary-table-tab4">
 <div class="block">Returns an array containing the constants of this enum class, in
@@ -176,21 +176,21 @@ <h3 id="methods-inherited-from-class-java.lang.Object">Methods inherited from cl
 <h2>Enum Constant Details</h2>
 <ul class="member-list">
 <li>
-<section class="detail" id="GZIP">
-<h3>GZIP</h3>
-<div class="member-signature"><span class="modifiers">public static final</span>&nbsp;<span class="return-type"><a href="ModelPolisherOptions.Compression.html" title="enum class in edu.ucsd.sbrg">ModelPolisherOptions.Compression</a></span>&nbsp;<span class="element-name">GZIP</span></div>
+<section class="detail" id="SBML">
+<h3>SBML</h3>
+<div class="member-signature"><span class="modifiers">public static final</span>&nbsp;<span class="return-type"><a href="ModelPolisherOptions.OutputType.html" title="enum class in edu.ucsd.sbrg">ModelPolisherOptions.OutputType</a></span>&nbsp;<span class="element-name">SBML</span></div>
 </section>
 </li>
 <li>
-<section class="detail" id="NONE">
-<h3>NONE</h3>
-<div class="member-signature"><span class="modifiers">public static final</span>&nbsp;<span class="return-type"><a href="ModelPolisherOptions.Compression.html" title="enum class in edu.ucsd.sbrg">ModelPolisherOptions.Compression</a></span>&nbsp;<span class="element-name">NONE</span></div>
+<section class="detail" id="JSON">
+<h3>JSON</h3>
+<div class="member-signature"><span class="modifiers">public static final</span>&nbsp;<span class="return-type"><a href="ModelPolisherOptions.OutputType.html" title="enum class in edu.ucsd.sbrg">ModelPolisherOptions.OutputType</a></span>&nbsp;<span class="element-name">JSON</span></div>
 </section>
 </li>
 <li>
-<section class="detail" id="ZIP">
-<h3>ZIP</h3>
-<div class="member-signature"><span class="modifiers">public static final</span>&nbsp;<span class="return-type"><a href="ModelPolisherOptions.Compression.html" title="enum class in edu.ucsd.sbrg">ModelPolisherOptions.Compression</a></span>&nbsp;<span class="element-name">ZIP</span></div>
+<section class="detail" id="COMBINE">
+<h3>COMBINE</h3>
+<div class="member-signature"><span class="modifiers">public static final</span>&nbsp;<span class="return-type"><a href="ModelPolisherOptions.OutputType.html" title="enum class in edu.ucsd.sbrg">ModelPolisherOptions.OutputType</a></span>&nbsp;<span class="element-name">COMBINE</span></div>
 </section>
 </li>
 </ul>
@@ -204,7 +204,7 @@ <h2>Method Details</h2>
 <li>
 <section class="detail" id="values()">
 <h3>values</h3>
-<div class="member-signature"><span class="modifiers">public static</span>&nbsp;<span class="return-type"><a href="ModelPolisherOptions.Compression.html" title="enum class in edu.ucsd.sbrg">ModelPolisherOptions.Compression</a>[]</span>&nbsp;<span class="element-name">values</span>()</div>
+<div class="member-signature"><span class="modifiers">public static</span>&nbsp;<span class="return-type"><a href="ModelPolisherOptions.OutputType.html" title="enum class in edu.ucsd.sbrg">ModelPolisherOptions.OutputType</a>[]</span>&nbsp;<span class="element-name">values</span>()</div>
 <div class="block">Returns an array containing the constants of this enum class, in
 the order they are declared.</div>
 <dl class="notes">
@@ -216,7 +216,7 @@ <h3>values</h3>
 <li>
 <section class="detail" id="valueOf(java.lang.String)">
 <h3>valueOf</h3>
-<div class="member-signature"><span class="modifiers">public static</span>&nbsp;<span class="return-type"><a href="ModelPolisherOptions.Compression.html" title="enum class in edu.ucsd.sbrg">ModelPolisherOptions.Compression</a></span>&nbsp;<span class="element-name">valueOf</span><wbr><span class="parameters">(<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>&nbsp;name)</span></div>
+<div class="member-signature"><span class="modifiers">public static</span>&nbsp;<span class="return-type"><a href="ModelPolisherOptions.OutputType.html" title="enum class in edu.ucsd.sbrg">ModelPolisherOptions.OutputType</a></span>&nbsp;<span class="element-name">valueOf</span><wbr><span class="parameters">(<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>&nbsp;name)</span></div>
 <div class="block">Returns the enum constant of this class with the specified name.
 The string must match <i>exactly</i> an identifier used to declare an
 enum constant in this class.  (Extraneous whitespace characters are