added JavaDoc

README.md

@@ -192,7 +192,7 @@ java -cp YWWTools.jar --tool slda --model slda --vocab <vocab-file> --corpus <co
 - Jointly models topics and document labels. Support multi-class classification.
 - Extends [LDA](#lda_cmd).
 - Semi-optional arguments
-	- `--label <label-file>` [optional in test]: Label file. Each line contains corresponding document's numeric label.
+	- `--label <label-file>` [optional in test]: Label file. Each line contains corresponding document's numeric label. If a document label is not available, leave the corresponding line empty.
 - Optional arguments
 	- `--sigma <sigma-value>`: Variance for the Gaussian generation of response variable in SLDA (default: 1.0). Must be a positive real number.
 	- `--nu <nu-value>`: Variance of normal priors for weight vectors in SLDA and its extensions (default: 1.0). Must be a positive real number.

doc/allclasses-frame.html

@@ -15,9 +15,7 @@ <h1 class="bar">All&nbsp;Classes</h1>
 <li><a href="yang/weiwei/lda/slda/bs_lda/BSLDA.html" title="class in yang.weiwei.lda.slda.bs_lda" target="classFrame">BSLDA</a></li>
 <li><a href="yang/weiwei/lda/slda/bs_lda/BSLDAFunction.html" title="class in yang.weiwei.lda.slda.bs_lda" target="classFrame">BSLDAFunction</a></li>
 <li><a href="yang/weiwei/lda/slda/bs_lda/BSLDASyn.html" title="class in yang.weiwei.lda.slda.bs_lda" target="classFrame">BSLDASyn</a></li>
-<li><a href="yang/weiwei/cfg/Cfg.html" title="class in yang.weiwei.cfg" target="classFrame">Cfg</a></li>
 <li><a href="yang/weiwei/util/format/CorpusConverter.html" title="class in yang.weiwei.util.format" target="classFrame">CorpusConverter</a></li>
-<li><a href="yang/weiwei/tools/EmptyTool.html" title="class in yang.weiwei.tools" target="classFrame">EmptyTool</a></li>
 <li><a href="yang/weiwei/preprocess/FileMerger.html" title="class in yang.weiwei.preprocess" target="classFrame">FileMerger</a></li>
 <li><a href="yang/weiwei/util/format/Fourmat.html" title="class in yang.weiwei.util.format" target="classFrame">Fourmat</a></li>
 <li><a href="yang/weiwei/ICTCLAS/ICTCLAS.html" title="class in yang.weiwei.ICTCLAS" target="classFrame">ICTCLAS</a></li>
@@ -65,31 +63,6 @@ <h1 class="bar">All&nbsp;Classes</h1>
 <li><a href="yang/weiwei/lda/st_lda/STLDASyn.html" title="class in yang.weiwei.lda.st_lda" target="classFrame">STLDASyn</a></li>
 <li><a href="yang/weiwei/preprocess/StopList.html" title="class in yang.weiwei.preprocess" target="classFrame">StopList</a></li>
 <li><a href="yang/weiwei/preprocess/Tokenizer.html" title="class in yang.weiwei.preprocess" target="classFrame">Tokenizer</a></li>
-<li><a href="yang/weiwei/tools/lda/ToolBPLDA.html" title="class in yang.weiwei.tools.lda" target="classFrame">ToolBPLDA</a></li>
-<li><a href="yang/weiwei/tools/lda/ToolBSLDA.html" title="class in yang.weiwei.tools.lda" target="classFrame">ToolBSLDA</a></li>
-<li><a href="yang/weiwei/tools/ToolCorpusConverter.html" title="class in yang.weiwei.tools" target="classFrame">ToolCorpusConverter</a></li>
-<li><a href="yang/weiwei/tools/ToolICTCLAS.html" title="class in yang.weiwei.tools" target="classFrame">ToolICTCLAS</a></li>
-<li><a href="yang/weiwei/tools/ToolInterface.html" title="class in yang.weiwei.tools" target="classFrame">ToolInterface</a></li>
-<li><a href="yang/weiwei/tools/lda/ToolLDA.html" title="class in yang.weiwei.tools.lda" target="classFrame">ToolLDA</a></li>
-<li><a href="yang/weiwei/tools/ToolLDAInterface.html" title="class in yang.weiwei.tools" target="classFrame">ToolLDAInterface</a></li>
-<li><a href="yang/weiwei/tools/ToolLDAInterface2.html" title="class in yang.weiwei.tools" target="classFrame">ToolLDAInterface2</a></li>
-<li><a href="yang/weiwei/tools/ToolLemmatizer.html" title="class in yang.weiwei.tools" target="classFrame">ToolLemmatizer</a></li>
-<li><a href="yang/weiwei/tools/lda/ToolLexWSBBSLDA.html" title="class in yang.weiwei.tools.lda" target="classFrame">ToolLexWSBBSLDA</a></li>
-<li><a href="yang/weiwei/tools/lda/ToolLexWSBMedLDA.html" title="class in yang.weiwei.tools.lda" target="classFrame">ToolLexWSBMedLDA</a></li>
-<li><a href="yang/weiwei/tools/lda/ToolLexWSBMedRTM.html" title="class in yang.weiwei.tools.lda" target="classFrame">ToolLexWSBMedRTM</a></li>
-<li><a href="yang/weiwei/tools/lda/ToolLexWSBRTM.html" title="class in yang.weiwei.tools.lda" target="classFrame">ToolLexWSBRTM</a></li>
-<li><a href="yang/weiwei/tools/ToolPOSTagger.html" title="class in yang.weiwei.tools" target="classFrame">ToolPOSTagger</a></li>
-<li><a href="yang/weiwei/tools/lda/ToolRTM.html" title="class in yang.weiwei.tools.lda" target="classFrame">ToolRTM</a></li>
-<li><a href="yang/weiwei/Tools.html" title="class in yang.weiwei" target="classFrame">Tools</a></li>
-<li><a href="yang/weiwei/tools/ToolSCC.html" title="class in yang.weiwei.tools" target="classFrame">ToolSCC</a></li>
-<li><a href="yang/weiwei/tools/lda/ToolSLDA.html" title="class in yang.weiwei.tools.lda" target="classFrame">ToolSLDA</a></li>
-<li><a href="yang/weiwei/tools/ToolStemmer.html" title="class in yang.weiwei.tools" target="classFrame">ToolStemmer</a></li>
-<li><a href="yang/weiwei/tools/lda/ToolSTLDA.html" title="class in yang.weiwei.tools.lda" target="classFrame">ToolSTLDA</a></li>
-<li><a href="yang/weiwei/tools/ToolStoplist.html" title="class in yang.weiwei.tools" target="classFrame">ToolStoplist</a></li>
-<li><a href="yang/weiwei/tools/ToolTest.html" title="class in yang.weiwei.tools" target="classFrame">ToolTest</a></li>
-<li><a href="yang/weiwei/tools/ToolTokenizer.html" title="class in yang.weiwei.tools" target="classFrame">ToolTokenizer</a></li>
-<li><a href="yang/weiwei/tools/ToolWSBM.html" title="class in yang.weiwei.tools" target="classFrame">ToolWSBM</a></li>
-<li><a href="yang/weiwei/tools/lda/ToolWSBTM.html" title="class in yang.weiwei.tools.lda" target="classFrame">ToolWSBTM</a></li>
 <li><a href="yang/weiwei/wsbm/WSBM.html" title="class in yang.weiwei.wsbm" target="classFrame">WSBM</a></li>
 <li><a href="yang/weiwei/wsbm/WSBMCfg.html" title="class in yang.weiwei.wsbm" target="classFrame">WSBMCfg</a></li>
 <li><a href="yang/weiwei/wsbm/WSBMParam.html" title="class in yang.weiwei.wsbm" target="classFrame">WSBMParam</a></li>

doc/allclasses-noframe.html

@@ -15,9 +15,7 @@ <h1 class="bar">All&nbsp;Classes</h1>
 <li><a href="yang/weiwei/lda/slda/bs_lda/BSLDA.html" title="class in yang.weiwei.lda.slda.bs_lda">BSLDA</a></li>
 <li><a href="yang/weiwei/lda/slda/bs_lda/BSLDAFunction.html" title="class in yang.weiwei.lda.slda.bs_lda">BSLDAFunction</a></li>
 <li><a href="yang/weiwei/lda/slda/bs_lda/BSLDASyn.html" title="class in yang.weiwei.lda.slda.bs_lda">BSLDASyn</a></li>
-<li><a href="yang/weiwei/cfg/Cfg.html" title="class in yang.weiwei.cfg">Cfg</a></li>
 <li><a href="yang/weiwei/util/format/CorpusConverter.html" title="class in yang.weiwei.util.format">CorpusConverter</a></li>
-<li><a href="yang/weiwei/tools/EmptyTool.html" title="class in yang.weiwei.tools">EmptyTool</a></li>
 <li><a href="yang/weiwei/preprocess/FileMerger.html" title="class in yang.weiwei.preprocess">FileMerger</a></li>
 <li><a href="yang/weiwei/util/format/Fourmat.html" title="class in yang.weiwei.util.format">Fourmat</a></li>
 <li><a href="yang/weiwei/ICTCLAS/ICTCLAS.html" title="class in yang.weiwei.ICTCLAS">ICTCLAS</a></li>
@@ -65,31 +63,6 @@ <h1 class="bar">All&nbsp;Classes</h1>
 <li><a href="yang/weiwei/lda/st_lda/STLDASyn.html" title="class in yang.weiwei.lda.st_lda">STLDASyn</a></li>
 <li><a href="yang/weiwei/preprocess/StopList.html" title="class in yang.weiwei.preprocess">StopList</a></li>
 <li><a href="yang/weiwei/preprocess/Tokenizer.html" title="class in yang.weiwei.preprocess">Tokenizer</a></li>
-<li><a href="yang/weiwei/tools/lda/ToolBPLDA.html" title="class in yang.weiwei.tools.lda">ToolBPLDA</a></li>
-<li><a href="yang/weiwei/tools/lda/ToolBSLDA.html" title="class in yang.weiwei.tools.lda">ToolBSLDA</a></li>
-<li><a href="yang/weiwei/tools/ToolCorpusConverter.html" title="class in yang.weiwei.tools">ToolCorpusConverter</a></li>
-<li><a href="yang/weiwei/tools/ToolICTCLAS.html" title="class in yang.weiwei.tools">ToolICTCLAS</a></li>
-<li><a href="yang/weiwei/tools/ToolInterface.html" title="class in yang.weiwei.tools">ToolInterface</a></li>
-<li><a href="yang/weiwei/tools/lda/ToolLDA.html" title="class in yang.weiwei.tools.lda">ToolLDA</a></li>
-<li><a href="yang/weiwei/tools/ToolLDAInterface.html" title="class in yang.weiwei.tools">ToolLDAInterface</a></li>
-<li><a href="yang/weiwei/tools/ToolLDAInterface2.html" title="class in yang.weiwei.tools">ToolLDAInterface2</a></li>
-<li><a href="yang/weiwei/tools/ToolLemmatizer.html" title="class in yang.weiwei.tools">ToolLemmatizer</a></li>
-<li><a href="yang/weiwei/tools/lda/ToolLexWSBBSLDA.html" title="class in yang.weiwei.tools.lda">ToolLexWSBBSLDA</a></li>
-<li><a href="yang/weiwei/tools/lda/ToolLexWSBMedLDA.html" title="class in yang.weiwei.tools.lda">ToolLexWSBMedLDA</a></li>
-<li><a href="yang/weiwei/tools/lda/ToolLexWSBMedRTM.html" title="class in yang.weiwei.tools.lda">ToolLexWSBMedRTM</a></li>
-<li><a href="yang/weiwei/tools/lda/ToolLexWSBRTM.html" title="class in yang.weiwei.tools.lda">ToolLexWSBRTM</a></li>
-<li><a href="yang/weiwei/tools/ToolPOSTagger.html" title="class in yang.weiwei.tools">ToolPOSTagger</a></li>
-<li><a href="yang/weiwei/tools/lda/ToolRTM.html" title="class in yang.weiwei.tools.lda">ToolRTM</a></li>
-<li><a href="yang/weiwei/Tools.html" title="class in yang.weiwei">Tools</a></li>
-<li><a href="yang/weiwei/tools/ToolSCC.html" title="class in yang.weiwei.tools">ToolSCC</a></li>
-<li><a href="yang/weiwei/tools/lda/ToolSLDA.html" title="class in yang.weiwei.tools.lda">ToolSLDA</a></li>
-<li><a href="yang/weiwei/tools/ToolStemmer.html" title="class in yang.weiwei.tools">ToolStemmer</a></li>
-<li><a href="yang/weiwei/tools/lda/ToolSTLDA.html" title="class in yang.weiwei.tools.lda">ToolSTLDA</a></li>
-<li><a href="yang/weiwei/tools/ToolStoplist.html" title="class in yang.weiwei.tools">ToolStoplist</a></li>
-<li><a href="yang/weiwei/tools/ToolTest.html" title="class in yang.weiwei.tools">ToolTest</a></li>
-<li><a href="yang/weiwei/tools/ToolTokenizer.html" title="class in yang.weiwei.tools">ToolTokenizer</a></li>
-<li><a href="yang/weiwei/tools/ToolWSBM.html" title="class in yang.weiwei.tools">ToolWSBM</a></li>
-<li><a href="yang/weiwei/tools/lda/ToolWSBTM.html" title="class in yang.weiwei.tools.lda">ToolWSBTM</a></li>
 <li><a href="yang/weiwei/wsbm/WSBM.html" title="class in yang.weiwei.wsbm">WSBM</a></li>
 <li><a href="yang/weiwei/wsbm/WSBMCfg.html" title="class in yang.weiwei.wsbm">WSBMCfg</a></li>
 <li><a href="yang/weiwei/wsbm/WSBMParam.html" title="class in yang.weiwei.wsbm">WSBMParam</a></li>

doc/index-files/index-1.html

@@ -74,7 +74,9 @@
 <h2 class="title">A</h2>
 <dl>
 <dt><span class="memberNameLink"><a href="../yang/weiwei/lda/LDAParam.html#a">a</a></span> - Variable in class yang.weiwei.lda.<a href="../yang/weiwei/lda/LDAParam.html" title="class in yang.weiwei.lda">LDAParam</a></dt>
-<dd>&nbsp;</dd>
+<dd>
+<div class="block">Parameter of Gamma prior in WSBM (default 1.0)</div>
+</dd>
 <dt><span class="memberNameLink"><a href="../yang/weiwei/lda/LDASynParam.html#a">a</a></span> - Variable in class yang.weiwei.lda.<a href="../yang/weiwei/lda/LDASynParam.html" title="class in yang.weiwei.lda">LDASynParam</a></dt>
 <dd>&nbsp;</dd>
 <dt><span class="memberNameLink"><a href="../yang/weiwei/wsbm/WSBMParam.html#a">a</a></span> - Variable in class yang.weiwei.wsbm.<a href="../yang/weiwei/wsbm/WSBMParam.html" title="class in yang.weiwei.wsbm">WSBMParam</a></dt>
@@ -84,13 +86,17 @@ <h2 class="title">A</h2>
 <dt><span class="memberNameLink"><a href="../yang/weiwei/wsbm/WSBMSynParam.html#a">a</a></span> - Variable in class yang.weiwei.wsbm.<a href="../yang/weiwei/wsbm/WSBMSynParam.html" title="class in yang.weiwei.wsbm">WSBMSynParam</a></dt>
 <dd>&nbsp;</dd>
 <dt><span class="memberNameLink"><a href="../yang/weiwei/lda/util/LDAResult.html#add-int-double-">add(int, double)</a></span> - Method in class yang.weiwei.lda.util.<a href="../yang/weiwei/lda/util/LDAResult.html" title="class in yang.weiwei.lda.util">LDAResult</a></dt>
-<dd>&nbsp;</dd>
+<dd>
+<div class="block">Add a result</div>
+</dd>
 <dt><span class="memberNameLink"><a href="../yang/weiwei/util/PorterStemmer.html#add-char-">add(char)</a></span> - Method in class yang.weiwei.util.<a href="../yang/weiwei/util/PorterStemmer.html" title="class in yang.weiwei.util">PorterStemmer</a></dt>
 <dd>
 <div class="block">Add a character to the word being stemmed.</div>
 </dd>
 <dt><span class="memberNameLink"><a href="../yang/weiwei/lda/LDA.html#addResults-yang.weiwei.lda.util.LDAResult-">addResults(LDAResult)</a></span> - Method in class yang.weiwei.lda.<a href="../yang/weiwei/lda/LDA.html" title="class in yang.weiwei.lda">LDA</a></dt>
-<dd>&nbsp;</dd>
+<dd>
+<div class="block">Add log likelihood and perplexity results to result collector</div>
+</dd>
 <dt><span class="memberNameLink"><a href="../yang/weiwei/lda/rtm/lex_wsb_rtm/LexWSBRTM.html#addResults-yang.weiwei.lda.util.LDAResult-">addResults(LDAResult)</a></span> - Method in class yang.weiwei.lda.rtm.lex_wsb_rtm.<a href="../yang/weiwei/lda/rtm/lex_wsb_rtm/LexWSBRTM.html" title="class in yang.weiwei.lda.rtm.lex_wsb_rtm">LexWSBRTM</a></dt>
 <dd>&nbsp;</dd>
 <dt><span class="memberNameLink"><a href="../yang/weiwei/lda/rtm/RTM.html#addResults-yang.weiwei.lda.util.LDAResult-">addResults(LDAResult)</a></span> - Method in class yang.weiwei.lda.rtm.<a href="../yang/weiwei/lda/rtm/RTM.html" title="class in yang.weiwei.lda.rtm">RTM</a></dt>
@@ -106,15 +112,21 @@ <h2 class="title">A</h2>
 <div class="block">Add stemmed stop words to stoplist</div>
 </dd>
 <dt><span class="memberNameLink"><a href="../yang/weiwei/lda/util/LDATopic.html#addVocab-int-">addVocab(int)</a></span> - Method in class yang.weiwei.lda.util.<a href="../yang/weiwei/lda/util/LDATopic.html" title="class in yang.weiwei.lda.util">LDATopic</a></dt>
-<dd>&nbsp;</dd>
+<dd>
+<div class="block">Assign a word to this topic</div>
+</dd>
 <dt><span class="memberNameLink"><a href="../yang/weiwei/lda/util/LDAVocab.html#addVocab-java.lang.String-">addVocab(String)</a></span> - Static method in class yang.weiwei.lda.util.<a href="../yang/weiwei/lda/util/LDAVocab.html" title="class in yang.weiwei.lda.util">LDAVocab</a></dt>
 <dd>&nbsp;</dd>
 <dt><span class="memberNameLink"><a href="../yang/weiwei/lda/LDASynParam.html#alpha">alpha</a></span> - Variable in class yang.weiwei.lda.<a href="../yang/weiwei/lda/LDASynParam.html" title="class in yang.weiwei.lda">LDASynParam</a></dt>
 <dd>&nbsp;</dd>
 <dt><span class="memberNameLink"><a href="../yang/weiwei/lda/LDAParam.html#alphaSum">alphaSum</a></span> - Variable in class yang.weiwei.lda.<a href="../yang/weiwei/lda/LDAParam.html" title="class in yang.weiwei.lda">LDAParam</a></dt>
-<dd>&nbsp;</dd>
+<dd>
+<div class="block">Sum of alpha (parameter of document-topic distribution's Dirichlet prior), i.e.</div>
+</dd>
 <dt><span class="memberNameLink"><a href="../yang/weiwei/lda/util/LDADoc.html#assignTopic-int-int-">assignTopic(int, int)</a></span> - Method in class yang.weiwei.lda.util.<a href="../yang/weiwei/lda/util/LDADoc.html" title="class in yang.weiwei.lda.util">LDADoc</a></dt>
-<dd>&nbsp;</dd>
+<dd>
+<div class="block">Assign a topic to a token</div>
+</dd>
 <dt><span class="memberNameLink"><a href="../yang/weiwei/util/MathUtil.html#average-double:A-">average(double[])</a></span> - Static method in class yang.weiwei.util.<a href="../yang/weiwei/util/MathUtil.html" title="class in yang.weiwei.util">MathUtil</a></dt>
 <dd>&nbsp;</dd>
 <dt><span class="memberNameLink"><a href="../yang/weiwei/util/MathUtil.html#average-java.util.ArrayList-">average(ArrayList&lt;Double&gt;)</a></span> - Static method in class yang.weiwei.util.<a href="../yang/weiwei/util/MathUtil.html" title="class in yang.weiwei.util">MathUtil</a></dt>

doc/index-files/index-10.html

@@ -117,10 +117,6 @@ <h2 class="title">M</h2>
 <dd>&nbsp;</dd>
 <dt><span class="memberNameLink"><a href="../yang/weiwei/scc/SCC.html#main-java.lang.String:A-">main(String[])</a></span> - Static method in class yang.weiwei.scc.<a href="../yang/weiwei/scc/SCC.html" title="class in yang.weiwei.scc">SCC</a></dt>
 <dd>&nbsp;</dd>
-<dt><span class="memberNameLink"><a href="../yang/weiwei/Tools.html#main-java.lang.String:A-">main(String[])</a></span> - Static method in class yang.weiwei.<a href="../yang/weiwei/Tools.html" title="class in yang.weiwei">Tools</a></dt>
-<dd>&nbsp;</dd>
-<dt><span class="memberNameLink"><a href="../yang/weiwei/tools/ToolTest.html#main-java.lang.String:A-">main(String[])</a></span> - Static method in class yang.weiwei.tools.<a href="../yang/weiwei/tools/ToolTest.html" title="class in yang.weiwei.tools">ToolTest</a></dt>
-<dd>&nbsp;</dd>
 <dt><span class="memberNameLink"><a href="../yang/weiwei/wsbm/WSBM.html#main-java.lang.String:A-">main(String[])</a></span> - Static method in class yang.weiwei.wsbm.<a href="../yang/weiwei/wsbm/WSBM.html" title="class in yang.weiwei.wsbm">WSBM</a></dt>
 <dd>&nbsp;</dd>
 <dt><span class="memberNameLink"><a href="../yang/weiwei/wsbm/WSBMSyn.html#main-java.lang.String:A-">main(String[])</a></span> - Static method in class yang.weiwei.wsbm.<a href="../yang/weiwei/wsbm/WSBMSyn.html" title="class in yang.weiwei.wsbm">WSBMSyn</a></dt>