- Updated JavaDoc to v2.3.

Integrative-Transcriptomics · Mar 28, 2024 · f8940b7 · f8940b7
1 parent 03cced8
commit f8940b7
Show file tree

Hide file tree

Showing 92 changed files with 5,263 additions and 1,843 deletions.
diff --git a/doc/allclasses-index.html b/doc/allclasses-index.html
diff --git a/doc/allpackages-index.html b/doc/allpackages-index.html
@@ -1,11 +1,11 @@
 <!DOCTYPE HTML>
 <html lang="de">
 <head>
-<!-- Generated by javadoc (17) on Thu Aug 24 09:55:44 CEST 2023 -->
+<!-- Generated by javadoc (17) on Thu Mar 28 15:21:43 CET 2024 -->
 <title>All Packages</title>
 <meta name="viewport" content="width=device-width, initial-scale=1">
 <meta http-equiv="Content-Type" content="text/html; charset=utf-8">
-<meta name="dc.created" content="2023-08-24">
+<meta name="dc.created" content="2024-03-28">
 <meta name="description" content="package index">
 <meta name="generator" content="javadoc/AllPackagesIndexWriter">
 <link rel="stylesheet" type="text/css" href="stylesheet.css" title="Style">
@@ -70,12 +70,8 @@ <h1 title="All&amp;nbsp;Packages" class="title">All&nbsp;Packages</h1>
 <div class="col-last odd-row-color">
 <div class="block">Comprises the main class of MUSIAL.</div>
 </div>
-<div class="col-first even-row-color"><a href="runnables/package-summary.html">runnables</a></div>
+<div class="col-first even-row-color"><a href="utility/package-summary.html">utility</a></div>
 <div class="col-last even-row-color">
-<div class="block">Comprises classes that implement the <a href="https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/lang/Runnable.html" title="class or interface in java.lang" class="external-link"><code>Runnable</code></a> interface and are used to execute multithreaded tasks.</div>
-</div>
-<div class="col-first odd-row-color"><a href="utility/package-summary.html">utility</a></div>
-<div class="col-last odd-row-color">
 <div class="block">Comprises classes that mainly implement static methods, which are used by MUSIAL modules.</div>
 </div>
 </div>

diff --git a/doc/cli/BuildConfiguration.html b/doc/cli/BuildConfiguration.html
diff --git a/doc/cli/CLIParametersUpdateVDict.html b/doc/cli/CLIParametersUpdateVDict.html
@@ -364,7 +364,7 @@ <h3>features</h3>
 <div class="block"><code>ConcurrentSkipListMap</code> of <code>String</code>, <code>File</code> pairs. Each key specifies one feature on the
  passed reference `FASTA` to be analyzed. Each assigned value points to an optional `PDB` file per feature and
  induces the analysis variants allocated to the protein structure; values are expected to be `null` or `""` if
- variant to protein structure allocation shall not be run.</div>
+ variantInformation to protein structure allocation shall not be run.</div>
 </section>
 </li>
 <li>

diff --git a/doc/cli/CLIParser.html b/doc/cli/CLIParser.html
@@ -1,11 +1,11 @@
 <!DOCTYPE HTML>
 <html lang="de">
 <head>
-<!-- Generated by javadoc (17) on Thu Aug 24 09:55:44 CEST 2023 -->
+<!-- Generated by javadoc (17) on Thu Mar 28 15:21:43 CET 2024 -->
 <title>CLIParser</title>
 <meta name="viewport" content="width=device-width, initial-scale=1">
 <meta http-equiv="Content-Type" content="text/html; charset=utf-8">
-<meta name="dc.created" content="2023-08-24">
+<meta name="dc.created" content="2024-03-28">
 <meta name="description" content="declaration: package: cli, class: CLIParser">
 <meta name="generator" content="javadoc/ClassWriterImpl">
 <link rel="stylesheet" type="text/css" href="../stylesheet.css" title="Style">

diff --git a/doc/cli/package-summary.html b/doc/cli/package-summary.html
@@ -1,11 +1,11 @@
 <!DOCTYPE HTML>
 <html lang="de">
 <head>
-<!-- Generated by javadoc (17) on Thu Aug 24 09:55:44 CEST 2023 -->
+<!-- Generated by javadoc (17) on Thu Mar 28 15:21:43 CET 2024 -->
 <title>cli</title>
 <meta name="viewport" content="width=device-width, initial-scale=1">
 <meta http-equiv="Content-Type" content="text/html; charset=utf-8">
-<meta name="dc.created" content="2023-08-24">
+<meta name="dc.created" content="2024-03-28">
 <meta name="description" content="declaration: package: cli">
 <meta name="generator" content="javadoc/PackageWriterImpl">
 <link rel="stylesheet" type="text/css" href="../stylesheet.css" title="Style">
@@ -73,7 +73,7 @@ <h1 title="Package cli" class="title">Package cli</h1>
 <div class="table-header col-last">Description</div>
 <div class="col-first even-row-color class-summary class-summary-tab2"><a href="BuildConfiguration.html" title="class in cli">BuildConfiguration</a></div>
 <div class="col-last even-row-color class-summary class-summary-tab2">
-<div class="block">Parse parameters for the `build` task from a <a href="https://docs.oracle.com/en/java/javase/17/docs/api/java.base/java/util/HashMap.html" title="class or interface in java.util" class="external-link"><code>HashMap</code></a>.</div>
+<div class="block">Parse parameters for `build` task.</div>
 </div>
 <div class="col-first odd-row-color class-summary class-summary-tab2"><a href="CLIParser.html" title="class in cli">CLIParser</a></div>
 <div class="col-last odd-row-color class-summary class-summary-tab2">

diff --git a/doc/cli/package-tree.html b/doc/cli/package-tree.html
@@ -1,11 +1,11 @@
 <!DOCTYPE HTML>
 <html lang="de">
 <head>
-<!-- Generated by javadoc (17) on Thu Aug 24 09:55:44 CEST 2023 -->
+<!-- Generated by javadoc (17) on Thu Mar 28 15:21:43 CET 2024 -->
 <title>cli Class Hierarchy</title>
 <meta name="viewport" content="width=device-width, initial-scale=1">
 <meta http-equiv="Content-Type" content="text/html; charset=utf-8">
-<meta name="dc.created" content="2023-08-24">
+<meta name="dc.created" content="2024-03-28">
 <meta name="description" content="tree: package: cli">
 <meta name="generator" content="javadoc/PackageTreeWriter">
 <link rel="stylesheet" type="text/css" href="../stylesheet.css" title="Style">

diff --git a/doc/components/Bio.GLOBAL_SEQUENCE_ALIGNMENT_MARGIN_GAP_MODES.html b/doc/components/Bio.GLOBAL_SEQUENCE_ALIGNMENT_MARGIN_GAP_MODES.html
@@ -77,7 +77,7 @@ <h1 title="Enum Bio.GLOBAL_SEQUENCE_ALIGNMENT_MARGIN_GAP_MODES" class="title">En
 </div>
 <div class="inheritance" title="Inheritance Tree">java.lang.Object
 <div class="inheritance">java.lang.Enum&lt;<a href="Bio.GLOBAL_SEQUENCE_ALIGNMENT_MARGIN_GAP_MODES.html" title="enum in utility">Bio.GLOBAL_SEQUENCE_ALIGNMENT_MARGIN_GAP_MODES</a>&gt;
-<div class="inheritance">utility.Bio.GLOBAL_SEQUENCE_ALIGNMENT_MARGIN_GAP_MODES</div>
+<div class="inheritance">utility.SequenceOperations.GLOBAL_SEQUENCE_ALIGNMENT_MARGIN_GAP_MODES</div>
 </div>
 </div>
 <section class="description">

diff --git a/doc/components/Bio.html b/doc/components/Bio.html
@@ -76,7 +76,7 @@
 <h1 title="Class Bio" class="title">Class Bio</h1>
 </div>
 <div class="inheritance" title="Inheritance Tree">java.lang.Object
-<div class="inheritance">utility.Bio</div>
+<div class="inheritance">utility.SequenceOperations</div>
 </div>
 <section class="description">
 <hr>
@@ -283,7 +283,7 @@ <h2>Method Summary</h2>
 <td class="col-last">
 <div class="block">Invokes the <a href="#globalSequenceAlignment(java.lang.String,java.lang.String,java.util.HashMap,int%5B%5D%5B%5D,int,int,components.Bio.GLOBAL_SEQUENCE_ALIGNMENT_MARGIN_GAP_MODES,components.Bio.GLOBAL_SEQUENCE_ALIGNMENT_MARGIN_GAP_MODES)"><code>globalSequenceAlignment(java.lang.String,
     java.lang.String, java.util.HashMap&lt;java.lang.Character, java.lang.Integer&gt;, int[][], int, int,
-    utility.Bio.GLOBAL_SEQUENCE_ALIGNMENT_MARGIN_GAP_MODES, utility.Bio.GLOBAL_SEQUENCE_ALIGNMENT_MARGIN_GAP_MODES)</code></a> method with pre-specified parameters for amino-acid sequence
+    utility.SequenceOperations.GLOBAL_SEQUENCE_ALIGNMENT_MARGIN_GAP_MODES, utility.SequenceOperations.GLOBAL_SEQUENCE_ALIGNMENT_MARGIN_GAP_MODES)</code></a> method with pre-specified parameters for amino-acid sequence
  alignment.</div>
 </td>
 </tr>
@@ -296,7 +296,7 @@ <h2>Method Summary</h2>
 <td class="col-last">
 <div class="block">Invokes the <a href="#globalSequenceAlignment(java.lang.String,java.lang.String,java.util.HashMap,int%5B%5D%5B%5D,int,int,components.Bio.GLOBAL_SEQUENCE_ALIGNMENT_MARGIN_GAP_MODES,components.Bio.GLOBAL_SEQUENCE_ALIGNMENT_MARGIN_GAP_MODES)"><code>globalSequenceAlignment(java.lang.String,
     java.lang.String, java.util.HashMap&lt;java.lang.Character, java.lang.Integer&gt;, int[][], int, int,
-    utility.Bio.GLOBAL_SEQUENCE_ALIGNMENT_MARGIN_GAP_MODES, utility.Bio.GLOBAL_SEQUENCE_ALIGNMENT_MARGIN_GAP_MODES)</code></a> method with pre-specified parameters for nucleotide sequence
+    utility.SequenceOperations.GLOBAL_SEQUENCE_ALIGNMENT_MARGIN_GAP_MODES, utility.SequenceOperations.GLOBAL_SEQUENCE_ALIGNMENT_MARGIN_GAP_MODES)</code></a> method with pre-specified parameters for nucleotide sequence
  alignment.</div>
 </td>
 </tr>
@@ -637,7 +637,7 @@ <h3>globalNucleotideSequenceAlignment</h3>
 <a href="Bio.GLOBAL_SEQUENCE_ALIGNMENT_MARGIN_GAP_MODES.html" title="enum in utility">Bio.GLOBAL_SEQUENCE_ALIGNMENT_MARGIN_GAP_MODES</a>&nbsp;right_mode)</span></div>
 <div class="block">Invokes the <a href="#globalSequenceAlignment(java.lang.String,java.lang.String,java.util.HashMap,int%5B%5D%5B%5D,int,int,components.Bio.GLOBAL_SEQUENCE_ALIGNMENT_MARGIN_GAP_MODES,components.Bio.GLOBAL_SEQUENCE_ALIGNMENT_MARGIN_GAP_MODES)"><code>globalSequenceAlignment(java.lang.String,
     java.lang.String, java.util.HashMap&lt;java.lang.Character, java.lang.Integer&gt;, int[][], int, int,
-    utility.Bio.GLOBAL_SEQUENCE_ALIGNMENT_MARGIN_GAP_MODES, utility.Bio.GLOBAL_SEQUENCE_ALIGNMENT_MARGIN_GAP_MODES)</code></a> method with pre-specified parameters for nucleotide sequence
+    utility.SequenceOperations.GLOBAL_SEQUENCE_ALIGNMENT_MARGIN_GAP_MODES, utility.SequenceOperations.GLOBAL_SEQUENCE_ALIGNMENT_MARGIN_GAP_MODES)</code></a> method with pre-specified parameters for nucleotide sequence
  alignment.
  <p>
  - Uses a simple substitution matrix that scores matches with 1 and mismatches with -1.
@@ -664,7 +664,7 @@ <h3>globalAminoAcidSequenceAlignment</h3>
 <a href="Bio.GLOBAL_SEQUENCE_ALIGNMENT_MARGIN_GAP_MODES.html" title="enum in utility">Bio.GLOBAL_SEQUENCE_ALIGNMENT_MARGIN_GAP_MODES</a>&nbsp;right_mode)</span></div>
 <div class="block">Invokes the <a href="#globalSequenceAlignment(java.lang.String,java.lang.String,java.util.HashMap,int%5B%5D%5B%5D,int,int,components.Bio.GLOBAL_SEQUENCE_ALIGNMENT_MARGIN_GAP_MODES,components.Bio.GLOBAL_SEQUENCE_ALIGNMENT_MARGIN_GAP_MODES)"><code>globalSequenceAlignment(java.lang.String,
     java.lang.String, java.util.HashMap&lt;java.lang.Character, java.lang.Integer&gt;, int[][], int, int,
-    utility.Bio.GLOBAL_SEQUENCE_ALIGNMENT_MARGIN_GAP_MODES, utility.Bio.GLOBAL_SEQUENCE_ALIGNMENT_MARGIN_GAP_MODES)</code></a> method with pre-specified parameters for amino-acid sequence
+    utility.SequenceOperations.GLOBAL_SEQUENCE_ALIGNMENT_MARGIN_GAP_MODES, utility.SequenceOperations.GLOBAL_SEQUENCE_ALIGNMENT_MARGIN_GAP_MODES)</code></a> method with pre-specified parameters for amino-acid sequence
  alignment.
  <p>
  - Uses the PAM120 substitution matrix.</div>
@@ -715,7 +715,7 @@ <h3>getVariantsOfAlignedSequences</h3>
 java.lang.String&nbsp;querySequence)</span></div>
 <div class="block">Computes variants from two aligned sequences.
  <p>
- Variants are extracted wrt. the query versus the target sequence and formatted as p@r@a, where p is the variant
+ Variants are extracted wrt. the query versus the target sequence and formatted as p@r@a, where p is the variantInformation
  position, r is the reference content and a is the single alternate alleles content..</div>
 <dl class="notes">
 <dt>Parameters:</dt>
@@ -737,10 +737,10 @@ <h3>inferProteoform</h3>
  musialStorage.
  <p>
  - The computed variants maps keys are formatted as `x+y`, where x is the 1-based indexed position in the
- reference sequence at which the variant occurs and y is the 1-based indexed number of inserted positions after
+ reference sequence at which the variantInformation occurs and y is the 1-based indexed number of inserted positions after
  this position.
  - The computed variants maps values are the respective single letter code amino-acid contents of the variants
- including the content at the variant position.</div>
+ including the content at the variantInformation position.</div>
 <dl class="notes">
 <dt>Parameters:</dt>
 <dd><code>musialStorage</code> - <a href="../datastructure/VariantsDictionary.html" title="class in datastructure"><code>VariantsDictionary</code></a> instance which content is used to infer proteoform information.</dd>
@@ -749,7 +749,7 @@ <h3>inferProteoform</h3>
 <dd><code>sId</code> - <code>String</code> specifying the <a href="../datastructure/SampleEntry.html#name"><code>SampleEntry.name</code></a> of the sample of
                            which the proteoform should be inferred.</dd>
 <dt>Returns:</dt>
-<dd><code>ConcurrentSkipListMap</code> mapping positions to variant contents.</dd>
+<dd><code>ConcurrentSkipListMap</code> mapping positions to variantInformation contents.</dd>
 <dt>Throws:</dt>
 <dd><code><a href="../exceptions/MusialBioException.html" title="class in exceptions">MusialBioException</a></code> - If any translation procedure of nucleotide sequences fails.</dd>
 </dl>

diff --git a/doc/components/IO.html b/doc/components/IO.html
@@ -484,9 +484,9 @@ <h3>writeVcf</h3>
 <dl class="notes">
 <dt>Parameters:</dt>
 <dd><code>outputFile</code> - <code>File</code> object pointing to the output vcf file.</dd>
-<dd><code>variants</code> - <code>NavigableSet</code> containing variant information, cf. method description.</dd>
+<dd><code>variants</code> - <code>NavigableSet</code> containing variantInformation information, cf. method description.</dd>
 <dd><code>chrom</code> - <code>String</code> representing the value to use for the chromosome field of the vcf format for
-                   each variant.</dd>
+                   each variantInformation.</dd>
 </dl>
 </section>
 </li>

diff --git a/doc/components/SnpEffAnnotator.html b/doc/components/SnpEffAnnotator.html
@@ -76,7 +76,7 @@
 <h1 title="Class SnpEffAnnotator" class="title">Class SnpEffAnnotator</h1>
 </div>
 <div class="inheritance" title="Inheritance Tree">java.lang.Object
-<div class="inheritance">runnables.SnpEffAnnotator</div>
+<div class="inheritance">utility.SnpEffAnnotator</div>
 </div>
 <section class="description">
 <hr>

diff --git a/doc/components/VariantsDictionaryFactory.html b/doc/components/VariantsDictionaryFactory.html
@@ -76,7 +76,7 @@
 <h1 title="Class VariantsDictionaryFactory" class="title">Class VariantsDictionaryFactory</h1>
 </div>
 <div class="inheritance" title="Inheritance Tree">java.lang.Object
-<div class="inheritance">utility.MusialStorageFactory</div>
+<div class="inheritance">datastructure.MusialStorageFactory</div>
 </div>
 <section class="description">
 <hr>