Generating Javadoc
Javadoc execution
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Constructing Javadoc information...
Standard Doclet version 1.4.2_02
Generating target/docs/apidocs/constant-values.html...
Copying file /users/pavlidis/.maven/plugins/maven-javadoc-plugin-1.5.1-SNAPSHOT/plugin-resources/stylesheet.css to file target/docs/apidocs/stylesheet.css...
Building tree for all the packages and classes...
src/baseCode/bio/geneset/GONames.java:69: warning - @return tag has no arguments.
src/baseCode/dataStructure/matrix/AbstractNamedDoubleMatrix.java:22: warning - The first sentence is interpreted to be:
Generating target/docs/apidocs/baseCode/dataStructure/matrix/class-use/AbstractNamedMatrix.html...
"<hr>
"
This sentence is different from what will be interpreted as the first sentence in the
src/baseCode/dataStructure/matrix/SparseDoubleMatrix2DNamed.java:26: warning - The first sentence is interpreted to be:
next major release (when that interpretation will be internationalized), which is:
"<hr>
<p>Copyright (c) 2004 Columbia University"
To avoid this note, change the doc comment to make this a proper first sentence, then
use -breakiterator from that point forward, which will output this new sentence.
"<p>
Title: SparseDoubleMatrix2DNamed
"
This sentence is different from what would be generated using -breakiterator:
"<p>
Title: SparseDoubleMatrix2DNamed
</p>
<p>
Description: A sparse matrix that knows about row and column names.
"
src/baseCode/dataFilter/RowNameFilter.java:53: warning - @return tag has no arguments.
src/baseCode/dataFilter/RowLevelFilter.java:116: warning - @return tag has no arguments.
Generating target/docs/apidocs/baseCode/dataStructure/matrix/class-use/NamedMatrix.html...
"<hr>
"
src/baseCode/dataStructure/matrix/AbstractNamedDoubleMatrix.java:22: warning - The first sentence is interpreted to be:
This sentence is different from what would be generated using -breakiterator:
"<hr>
<p>Copyright (c) 2004 Columbia University"
"<p>
src/baseCode/dataStructure/matrix/SparseDoubleMatrix2DNamed.java:26: warning - The first sentence is interpreted to be:
Title: SparseDoubleMatrix2DNamed
"
This sentence is different from what would be generated using -breakiterator:
"<p>
Title: SparseDoubleMatrix2DNamed
</p>
<p>
Description: A sparse matrix that knows about row and column names.
"
src/baseCode/io/reader/SparseDoubleMatrixReader.java:175: warning - The first sentence is interpreted to be:
"Read a sparse matrix that is expressed as an adjacency list in a tab-delimited file:
"
This sentence is different from what would be generated using -breakiterator:
src/baseCode/io/reader/SparseRaggedDouble2DNamedMatrixReader.java:120: warning - @return tag has no arguments.
"Read a sparse matrix that is expressed as an adjacency list in a tab-delimited file:
<pre>
item1 item2 weight
src/baseCode/io/reader/SparseRaggedDouble2DNamedMatrixReader.java:120: warning - The first sentence is interpreted to be:
item1 item5 weight
</pre>
<p>
By definition the resulting matrix is square and symmetric.
"
src/baseCode/io/reader/SparseRaggedDouble2DNamedMatrixReader.java:168: warning - @return tag has no arguments.
"Read a sparse symmetric square matrix that is expressed as an adjacency list in a tab-delimited file:
"
This sentence is different from what would be generated using -breakiterator:
src/baseCode/algorithm/learning/unsupervised/RankProp.java:31: warning - @return tag has no arguments.
"Read a sparse symmetric square matrix that is expressed as an adjacency list in a tab-delimited file:
<pre>
src/baseCode/algorithm/learning/unsupervised/RankProp.java:48: warning - @return tag has no arguments.
item1 item2 weight
item1 item5 weight
src/baseCode/dataStructure/matrix/SparseDoubleMatrix2DNamed.java:26: warning - The first sentence is interpreted to be:
</pre>
<p>
src/baseCode/bio/GOEntry.java:13: warning - The first sentence is interpreted to be:
IMPORTANT: By definition the resulting matrix is square and symmetric, even if the symmetric edges are not
explicitly listed."
src/baseCode/dataStructure/Link.java:23: warning - The first sentence is interpreted to be:
Generating target/docs/apidocs/baseCode/dataStructure/matrix/class-use/AbstractNamedDoubleMatrix.html...
"<p>
Title: SparseDoubleMatrix2DNamed
"
This sentence is different from what would be generated using -breakiterator:
"<p>
Title: SparseDoubleMatrix2DNamed
</p>
<p>
Description: A sparse matrix that knows about row and column names.
"
src/baseCode/dataStructure/tree/BinaryTreeNode.java:63: warning - @return tag has no arguments.
src/baseCode/dataStructure/tree/BinaryTreeNode.java:79: warning - @return tag has no arguments.
Generating target/docs/apidocs/baseCode/dataStructure/class-use/OntologyEntry.html...
"<hr>
"
This sentence is different from what would be generated using -breakiterator:
"<hr>
<p>Copyright (c) 2004 Columbia University"
Generating target/docs/apidocs/baseCode/dataStructure/class-use/Point.html...
"<p>
Title:
"
This sentence is different from what would be generated using -breakiterator:
"<p>
Title:
</p>
<p>
Description:
</p>
<p>
Copyright (c) 2004
</p>
<p>
Institution:: Columbia University
</p>"
src/baseCode/math/distribution/UniformDensityComputer.java:11: warning - The first sentence is interpreted to be:
src/baseCode/math/distribution/NormalProbabilityComputer.java:13: warning - The first sentence is interpreted to be:
Generating target/docs/apidocs/baseCode/math/distribution/class-use/DensityGenerator.html...
"<hr>
"
This sentence is different from what would be generated using -breakiterator:
"<hr>
<p>
Copyright (c) 2004 Columbia University"
src/baseCode/math/metaanalysis/MeanDifferenceMetaAnalysis.java:26: warning - The first sentence is interpreted to be:
Generating target/docs/apidocs/baseCode/math/distribution/class-use/ProbabilityComputer.html...
"<hr>
"
This sentence is different from what would be generated using -breakiterator:
"<hr>
<p>
Copyright (c) 2004 Columbia University"
src/baseCode/gui/StatusJlabel.java:27: warning - The first sentence is interpreted to be:
src/baseCode/util/StatusStderr.java:12: warning - The first sentence is interpreted to be:
src/baseCode/io/reader/SparseDoubleMatrixReader.java:37: warning - The first sentence is interpreted to be:
src/baseCode/io/reader/SparseRaggedDouble2DNamedMatrixReader.java:78: warning - The first sentence is interpreted to be:
src/baseCode/io/reader/StringMatrixReader.java:27: warning - The first sentence is interpreted to be:
Generating target/docs/apidocs/baseCode/math/metaanalysis/class-use/MetaAnalysis.html...
"Meta-analysis methods from chapter 18 of Cooper and Hedges, sections 2.1 and 3.1
"
This sentence is different from what would be generated using -breakiterator:
"Meta-analysis methods from chapter 18 of Cooper and Hedges, sections 2.1 and 3.1
<p>
These methods use the standardized mean difference statistic d:
<pre>
d_i = ( X_i ˆ t - X_i ˆ c ) / s_i
</pre>
where X <sub>i </sub> <sup>t </sup> is the mean of the treatment group in the ith study, X <sub>i </sub> <sup>ct
</sup> is the mean of the control group in the treatment group in the ith study, and s <sub>i </sub> is the pooled
standard deviation of the two groups. "
src/baseCode/algorithm/learning/unsupervised/cluster/AverageLinkageDistancer.java:16: warning - The first sentence is interpreted to be:
Generating target/docs/apidocs/baseCode/util/class-use/StatusViewer.html...
"<p>
Title:
"
This sentence is different from what would be generated using -breakiterator:
"<p>
Title:
</p>
<p>
Description:
</p>
<p>
Copyright: Copyright (c) 2003
</p>
<p>
Company:
</p>"
"Prints status info to stderr
"
This sentence is different from what would be generated using -breakiterator:
"Prints status info to stderr
src/baseCode/algorithm/learning/unsupervised/cluster/ClusteringAlgorithm.java:13: warning - The first sentence is interpreted to be:
<hr>
<p>
Copyright (c) 2004 Columbia University"
Generating target/docs/apidocs/baseCode/io/reader/class-use/AbstractNamedMatrixReader.html...
"<hr>
"
This sentence is different from what would be generated using -breakiterator:
"<hr>
<p>
Copyright (c) 2004 Columbia University"
"Best data structure for reading really big, really sparse matrices when a matrix represetation is needed."
This sentence is different from what would be generated using -breakiterator:
"Best data structure for reading really big, really sparse matrices when a matrix represetation is needed. *
<p>
The standard format looks like this:
<pre>
2 <--- number of items - the first line of the file only. "
src/baseCode/algorithm/learning/unsupervised/cluster/Cluster.java:16: warning - The first sentence is interpreted to be:
"Reader for {@link baseCode.dataStructure.matrix.StringMatrix2DNamed}
"
This sentence is different from what would be generated using -breakiterator:
src/baseCode/algorithm/learning/unsupervised/cluster/Distancer.java:20: warning - @return tag has no arguments.
"Reader for {@link baseCode.dataStructure.matrix.StringMatrix2DNamed}
src/baseCode/common/Distanceable.java:21: warning - @return tag has no arguments.
<p>
Copyright (c) 2004
</p>
<p>
Institution:: Columbia University
</p>"
src/baseCode/algorithm/learning/unsupervised/cluster/Cluster.java:16: warning - The first sentence is interpreted to be:
src/baseCode/dataStructure/tree/BinaryTreeNode.java:13: warning - The first sentence is interpreted to be:
src/baseCode/dataStructure/tree/TreeNode.java:13: warning - The first sentence is interpreted to be:
src/baseCode/algorithm/Algorithm.java:14: warning - The first sentence is interpreted to be:
src/baseCode/algorithm/Algorithm.java:14: warning - The first sentence is interpreted to be:
src/baseCode/algorithm/learning/unsupervised/cluster/Cluster.java:16: warning - The first sentence is interpreted to be:
src/baseCode/algorithm/learning/unsupervised/cluster/ClusteringAlgorithm.java:13: warning - The first sentence is interpreted to be:
src/baseCode/algorithm/learning/unsupervised/cluster/Distancer.java:13: warning - The first sentence is interpreted to be:
src/baseCode/common/Visitable.java:11: warning - The first sentence is interpreted to be:
src/baseCode/common/Visitable.java:11: warning - The first sentence is interpreted to be:
Generating target/docs/apidocs/baseCode/algorithm/learning/unsupervised/cluster/class-use/Distancer.html...
"<hr>
"
src/baseCode/common/Visitable.java:11: warning - The first sentence is interpreted to be:
This sentence is different from what would be generated using -breakiterator:
"<hr>
<p>
Copyright (c) 2004 Columbia University"
src/baseCode/common/Visitable.java:11: warning - The first sentence is interpreted to be:
src/baseCode/dataStructure/Point.java:21: warning - The first sentence is interpreted to be:
src/baseCode/dataStructure/matrix/AbstractNamedDoubleMatrix.java:22: warning - The first sentence is interpreted to be:
src/baseCode/dataStructure/matrix/NamedMatrix.java:18: warning - The first sentence is interpreted to be:
Generating target/docs/apidocs/baseCode/algorithm/class-use/Algorithm.html...
"<hr>
"
This sentence is different from what would be generated using -breakiterator:
src/baseCode/dataStructure/matrix/AbstractNamedDoubleMatrix.java:22: warning - The first sentence is interpreted to be:
"<hr>
<p>Copyright (c) 2004 Columbia University"
src/baseCode/dataStructure/matrix/NamedMatrix.java:18: warning - The first sentence is interpreted to be:
src/baseCode/dataStructure/matrix/SparseDoubleMatrix2DNamed.java:26: warning - The first sentence is interpreted to be:
Generating target/docs/apidocs/baseCode/common/class-use/Distanceable.html...
"<hr>
"
This sentence is different from what would be generated using -breakiterator:
src/baseCode/dataStructure/matrix/AbstractNamedDoubleMatrix.java:22: warning - The first sentence is interpreted to be:
"<hr>
<p>
Copyright (c) 2004 Columbia University"
Generating target/docs/apidocs/baseCode/common/class-use/Visitable.html...
"<hr>
"
This sentence is different from what would be generated using -breakiterator:
src/baseCode/dataStructure/matrix/NamedMatrix.java:18: warning - The first sentence is interpreted to be:
"<hr>
<p>
Copyright (c) 2004 Columbia University"
"<hr>
"
This sentence is different from what would be generated using -breakiterator:
src/baseCode/dataStructure/matrix/AbstractNamedDoubleMatrix.java:22: warning - The first sentence is interpreted to be:
"<hr>
<p>
Copyright (c) 2004 Columbia University"
"<hr>
"
This sentence is different from what would be generated using -breakiterator:
src/baseCode/dataStructure/matrix/SparseDoubleMatrix2DNamed.java:26: warning - The first sentence is interpreted to be:
"<hr>
<p>Copyright (c) 2004 Columbia University"
Generating target/docs/apidocs/baseCode/algorithm/package-use.html...
"<hr>
"
This sentence is different from what would be generated using -breakiterator:
src/baseCode/dataStructure/matrix/AbstractNamedDoubleMatrix.java:22: warning - The first sentence is interpreted to be:
"<hr>
<p>Copyright (c) 2004 Columbia University"
"<hr>
"
This sentence is different from what would be generated using -breakiterator:
src/baseCode/dataStructure/tree/BinaryTreeNode.java:13: warning - The first sentence is interpreted to be:
"<hr>
<p>Copyright (c) 2004 Columbia University"
src/baseCode/dataStructure/tree/TreeNode.java:13: warning - The first sentence is interpreted to be:
Generating target/docs/apidocs/baseCode/algorithm/learning/unsupervised/cluster/package-use.html...
"<hr>
"
This sentence is different from what would be generated using -breakiterator:
"<hr>
<p>
Copyright (c) 2004 Columbia University"
"<hr>
"
This sentence is different from what would be generated using -breakiterator:
"<hr>
<p>Copyright (c) 2004 Columbia University"
"<hr>
"
This sentence is different from what would be generated using -breakiterator:
"<hr>
<p>
Copyright (c) 2004 Columbia University"
src/baseCode/gui/ColorMatrix.java:30: warning - The first sentence is interpreted to be:
src/baseCode/gui/Wizard.java:30: warning - The first sentence is interpreted to be:
src/baseCode/gui/WizardStep.java:27: warning - The first sentence is interpreted to be:
Generating target/docs/apidocs/baseCode/common/package-use.html...
"<hr>
"
This sentence is different from what would be generated using -breakiterator:
"<hr>
<p>Copyright (c) 2004 Columbia University"
"<hr>
src/baseCode/gui/JMatrixDisplay.java:36: warning - The first sentence is interpreted to be:
"
This sentence is different from what would be generated using -breakiterator:
"<hr>
<p>Copyright (c) 2004 Columbia University"
"<hr>
"
This sentence is different from what would be generated using -breakiterator:
"<hr>
<p>Copyright (c) 2004 Columbia University"
"<hr>
"
This sentence is different from what would be generated using -breakiterator:
"<hr>
<p>Copyright (c) 2004 Columbia University"
Generating target/docs/apidocs/baseCode/dataStructure/package-use.html...
"<p>
Title:
"
This sentence is different from what would be generated using -breakiterator:
"<p>
Title:
</p>
<p>
Description:
</p>
<p>
Copyright (c) 2004
</p>
<p>
Institution:: Columbia University
</p>"
Generating target/docs/apidocs/baseCode/dataStructure/matrix/package-use.html...
"<hr>
"
This sentence is different from what would be generated using -breakiterator:
"<hr>
<p>Copyright (c) 2004 Columbia University"
"<p>
Copyright (c) 2004
"
This sentence is different from what would be generated using -breakiterator:
"<p>
Copyright (c) 2004
</p>
<p>
Institution:: Columbia University
</p>"
"<hr>
"
This sentence is different from what would be generated using -breakiterator:
"<hr>
<p>Copyright (c) 2004 Columbia University"
"<p>
Copyright (c) 2004
"
This sentence is different from what would be generated using -breakiterator:
"<p>
Copyright (c) 2004
</p>
<p>
Institution:: Columbia University
</p>"
"<p>
Title: SparseDoubleMatrix2DNamed
"
This sentence is different from what would be generated using -breakiterator:
"<p>
Title: SparseDoubleMatrix2DNamed
</p>
<p>
Description: A sparse matrix that knows about row and column names.
"
"<hr>
"
This sentence is different from what would be generated using -breakiterator:
"<hr>
<p>Copyright (c) 2004 Columbia University"
"<p>
Copyright (c) 2004
"
This sentence is different from what would be generated using -breakiterator:
"<p>
Copyright (c) 2004
</p>
<p>
Institution:: Columbia University
</p>"
"<hr>
"
This sentence is different from what would be generated using -breakiterator:
"<hr>
<p>Copyright (c) 2004 Columbia University"
"<p>
Title: SparseDoubleMatrix2DNamed
"
This sentence is different from what would be generated using -breakiterator:
"<p>
Title: SparseDoubleMatrix2DNamed
</p>
<p>
Description: A sparse matrix that knows about row and column names.
"
"<hr>
"
src/baseCode/dataStructure/matrix/AbstractNamedDoubleMatrix.java:22: warning - The first sentence is interpreted to be:
This sentence is different from what would be generated using -breakiterator:
"<hr>
<p>Copyright (c) 2004 Columbia University"
src/baseCode/algorithm/Algorithm.java:14: warning - The first sentence is interpreted to be:
Generating target/docs/apidocs/baseCode/dataStructure/tree/package-use.html...
"<hr>
"
src/baseCode/gui/AppDialog.java:42: warning - The first sentence is interpreted to be:
This sentence is different from what would be generated using -breakiterator:
src/baseCode/algorithm/learning/unsupervised/cluster/AverageLinkageDistancer.java:16: warning - The first sentence is interpreted to be:
"<hr>
<p>
Copyright (c) 2004 Columbia University"
"<hr>
"
This sentence is different from what would be generated using -breakiterator:
"<hr>
<p>Copyright (c) 2004 Columbia University"
src/baseCode/dataStructure/tree/BinaryTree.java:11: warning - The first sentence is interpreted to be:
src/baseCode/dataStructure/tree/BinaryTreeNode.java:13: warning - The first sentence is interpreted to be:
src/baseCode/io/ByteArrayConverter.java:35: warning - @return tag has no arguments.
Generating target/docs/apidocs/baseCode/gui/package-use.html...
"<p>
Title: ColorMatrix
"
This sentence is different from what would be generated using -breakiterator:
"<p>
src/baseCode/algorithm/learning/unsupervised/cluster/Cluster.java:16: warning - The first sentence is interpreted to be:
Title: ColorMatrix
</p>
<p>
Description: Creates a color matrix from a matrix of doubles
</p>
<p>
Copyright (c) 2004
</p>
<p>
Institution:: Columbia University
</p>"
"<hr>
"
src/baseCode/algorithm/learning/unsupervised/cluster/ClusteringAlgorithm.java:13: warning - The first sentence is interpreted to be:
This sentence is different from what would be generated using -breakiterator:
"<hr>
<p>Copyright (c) 2004-2005 Columbia University"
"<p>
Title:
"
This sentence is different from what would be generated using -breakiterator:
src/baseCode/gui/ColorMap.java:23: warning - The first sentence is interpreted to be:
"<p>
Title:
</p>
<p>
Description:
</p>
<p>
Copyright: Copyright (c) 2003
src/baseCode/gui/ColorMatrix.java:30: warning - The first sentence is interpreted to be:
</p>
<p>
Company:
</p>"
"<p>
Title: JMatrixDisplay
"
This sentence is different from what would be generated using -breakiterator:
src/baseCode/dataStructure/matrix/SparseDoubleMatrix2DNamed.java:210: warning - @return tag has no arguments.
"<p>
Title: JMatrixDisplay
</p>
<p>
Description: a visual component for displaying a color matrix
</p>
src/baseCode/util/RegressionTesting.java:103: warning - @return tag has no arguments.
<p>
Copyright: Copyright (c) 2004
</p>
<p>
Institution:: Columbia University
</p>"
src/baseCode/util/RegressionTesting.java:149: warning - @return tag has no arguments.
src/baseCode/dataStructure/matrix/SparseDoubleMatrix2DNamed.java:144: warning - @return tag has no arguments.
src/baseCode/dataStructure/matrix/StringMatrix2DNamed.java:82: warning - @return tag has no arguments.
src/baseCode/dataStructure/matrix/NamedMatrix.java:174: warning - @return tag has no arguments.
src/baseCode/dataStructure/matrix/NamedMatrix.java:168: warning - @return tag has no arguments.
src/baseCode/util/RegressionTesting.java:169: warning - @return tag has no arguments.
src/baseCode/util/RegressionTesting.java:185: warning - @return tag has no arguments.
src/baseCode/util/RegressionTesting.java:207: warning - @return tag has no arguments.
src/baseCode/gui/file/DataFileFilter.java:17: warning - The first sentence is interpreted to be:
src/baseCode/math/distribution/Dirichlet.java:19: warning - The first sentence is interpreted to be:
Building index for all the packages and classes...
Generating target/docs/apidocs/index-all.html...
"<hr>
"
src/baseCode/algorithm/learning/unsupervised/cluster/DistanceFactory.java:11: warning - The first sentence is interpreted to be:
This sentence is different from what would be generated using -breakiterator:
"<hr>
<p>Copyright (c) 2004 Columbia University"
"<hr>
"
src/baseCode/algorithm/learning/unsupervised/cluster/Distancer.java:13: warning - The first sentence is interpreted to be:
This sentence is different from what would be generated using -breakiterator:
"<hr>
<p>Copyright (c) 2004 Columbia University"
"<p>
Title:
src/baseCode/io/StringConverter.java:39: warning - @return tag has no arguments.
"
This sentence is different from what would be generated using -breakiterator:
"<p>
Title:
</p>
<p>
Description:
</p>
src/baseCode/math/SpecFunc.java:132: warning - @return tag has no arguments.
<p>
Copyright: Copyright (c) 2003
</p>
<p>
Company:
</p>"
"<hr>
"
This sentence is different from what would be generated using -breakiterator:
"<hr>
<p>
src/baseCode/math/SpecFunc.java:21: warning - Tag @see: missing final >: "<a
Copyright (c) 2004 Columbia University"
"<hr>
"
href="http://hoschek.home.cern.ch/hoschek/colt/V1.0.3/doc/cern/jet/math/Arithmetic.html">cern.jet.math.arithmetic
</a>
This sentence is different from what would be generated using -breakiterator:
<p>
"<hr>
Copyright (c) 2004 Columbia University"
<p>
Copyright (c) 2004 Columbia University"
"<hr>
"
This sentence is different from what would be generated using -breakiterator:
"<hr>
<p>
Copyright (c) 2004 Columbia University"
"<hr>
"
This sentence is different from what would be generated using -breakiterator:
"<hr>
src/baseCode/math/SpecFunc.java:102: warning - The first sentence is interpreted to be:
<p>
Copyright (c) 2004 Columbia University"
"<hr>
"
This sentence is different from what would be generated using -breakiterator:
"<hr>
<p>Copyright (c) 2004 Columbia University"
src/baseCode/math/metaanalysis/MetaAnalysis.java:49: warning - The first sentence is interpreted to be:
"<p>
Title: ColorMap
src/baseCode/math/CorrelationStats.java:120: warning - @return tag has no arguments.
"
This sentence is different from what would be generated using -breakiterator:
"<p>
Title: ColorMap
</p>
<p>
Description: contains predefined color maps for visualization and color palette methods
src/baseCode/math/metaanalysis/CorrelationEffectMetaAnalysis.java:184: warning - @return tag has no arguments.
</p>
<p>
Copyright (c) 2004
</p>
<p>
src/baseCode/math/metaanalysis/CorrelationEffectMetaAnalysis.java:197: warning - @return tag has no arguments.
Institution:: Columbia University
</p>"
"<p>
Title: ColorMatrix
"
This sentence is different from what would be generated using -breakiterator:
"<p>
src/baseCode/dataStructure/matrix/RCDoubleMatrix1D.java:127: warning - @return tag has no arguments.
Title: ColorMatrix
</p>
<p>
Description: Creates a color matrix from a matrix of doubles
</p>
<p>
Copyright (c) 2004
</p>
<p>
Institution:: Columbia University
</p>"
"<hr>
"
This sentence is different from what would be generated using -breakiterator:
src/baseCode/bio/GOEntry.java:13: warning - The first sentence is interpreted to be:
"<hr>
<p>
Copyright (c) 2004 Columbia University"
"<hr>
"
src/baseCode/bio/GOTermList.java:11: warning - The first sentence is interpreted to be:
This sentence is different from what would be generated using -breakiterator:
"<hr>
<p>
Copyright (c) 2004 Columbia University"
"<hr>
"
src/baseCode/bio/GOTermProbability.java:11: warning - The first sentence is interpreted to be:
This sentence is different from what would be generated using -breakiterator:
"<hr>
<p>Copyright (c) 2004 Columbia University"
"<hr>
"
This sentence is different from what would be generated using -breakiterator:
src/baseCode/dataStructure/matrix/SparseDoubleMatrix2DNamed.java:153: warning - @return tag has no arguments.
"<hr>
<p>
Copyright (c) 2004 Columbia University"
src/baseCode/dataStructure/matrix/SparseRaggedDoubleMatrix2DNamed.java:166: warning - @return tag has no arguments.
"Ported from R (Catherine Loader)
"
This sentence is different from what would be generated using -breakiterator:
src/baseCode/dataStructure/matrix/StringMatrix2DNamed.java:91: warning - @return tag has no arguments.
"Ported from R (Catherine Loader)
<p>
DESCRIPTION
<p>
Given a sequence of r successes and b failures, we sample n (\le b+r) items without replacement. "
"Fisher's method for combining p values (Cooper and Hedges 15-8)
"
src/baseCode/dataStructure/graph/DirectedGraphNode.java:172: warning - @return tag has no arguments.
This sentence is different from what would be generated using -breakiterator:
"Fisher's method for combining p values (Cooper and Hedges 15-8)
<p>
Use for p values that have already been log transformed."
"<hr>
src/baseCode/bio/geneset/GONames.java:135: warning - @return tag has no arguments.
"
This sentence is different from what would be generated using -breakiterator:
src/baseCode/dataStructure/tree/BinaryTreeNode.java:47: warning - @return tag has no arguments.
"<hr>
<p>Copyright (c) 2004 Columbia University"
"<hr>
"
src/baseCode/dataStructure/OntologyEntry.java:50: warning - @return tag has no arguments.
This sentence is different from what would be generated using -breakiterator:
"<hr>
<p>Copyright (c) 2004 Columbia University"
"<hr>
"
src/baseCode/bio/geneset/GeneAnnotations.java:316: warning - @return tag has no arguments.
This sentence is different from what would be generated using -breakiterator:
"<hr>
<p>Copyright (c) 2004 Columbia University"
"<hr>
"
This sentence is different from what would be generated using -breakiterator:
"<hr>
src/baseCode/dataStructure/OntologyEntry.java:43: warning - @return tag has no arguments.
<p>
Copyright (c) 2004 Columbia University"
"<p>
Title: JMatrixDisplay
"
src/baseCode/dataStructure/graph/AbstractGraphNode.java:27: warning - @return tag has no arguments.
This sentence is different from what would be generated using -breakiterator:
"<p>
Title: JMatrixDisplay
</p>
<p>
Description: a visual component for displaying a color matrix
src/baseCode/dataStructure/OntologyEntry.java:36: warning - @return tag has no arguments.
</p>
<p>
Copyright: Copyright (c) 2004
</p>
<p>
Institution:: Columbia University
</p>"
src/baseCode/bio/geneset/GONames.java:178: warning - @return tag has no arguments.
"<p>
Title:
"
This sentence is different from what would be generated using -breakiterator:
"<p>
Title:
</p>
<p>
Description:
</p>
<p>
Copyright (c) 2004
</p>
<p>
Institution:: Columbia University
</p>"
"<hr>
"
src/baseCode/dataStructure/matrix/AbstractNamedDoubleMatrix.java:66: warning - @return tag has no arguments.
This sentence is different from what would be generated using -breakiterator:
"<hr>
<p>
Copyright (c) 2004 Columbia University"
"Meta-analysis methods from chapter 18 of Cooper and Hedges, sections 2.1 and 3.1
src/baseCode/dataStructure/matrix/SparseDoubleMatrix2DNamed.java:162: warning - @return tag has no arguments.
"
This sentence is different from what would be generated using -breakiterator:
src/baseCode/dataStructure/matrix/StringMatrix2DNamed.java:100: warning - @return tag has no arguments.
"Meta-analysis methods from chapter 18 of Cooper and Hedges, sections 2.1 and 3.1
<p>
src/baseCode/bio/geneset/GeneSetMapTools.java:485: warning - @return tag has no arguments.
These methods use the standardized mean difference statistic d:
<pre>
d_i = ( X_i ˆ t - X_i ˆ c ) / s_i
</pre>
src/baseCode/bio/geneset/GeneSetMapTools.java:514: warning - @return tag has no arguments.
where X <sub>i </sub> <sup>t </sup> is the mean of the treatment group in the ith study, X <sub>i </sub> <sup>ct
</sup> is the mean of the control group in the treatment group in the ith study, and s <sub>i </sub> is the pooled
standard deviation of the two groups. "
src/baseCode/algorithm/learning/unsupervised/cluster/HierarchicalClusterer.java:109: warning - @return tag has no arguments.
"Under a random effects model, CH eqn."
This sentence is different from what would be generated using -breakiterator:
"Under a random effects model, CH eqn. 18-24, we replace the conditional variance with the sum of the
src/baseCode/dataStructure/matrix/SparseRaggedDoubleMatrix2DNamed.java:177: warning - @return tag has no arguments.
between-sample variance and the conditional variance.
"
"CH 18-3 version 2 for quality weighted."
src/baseCode/bio/geneset/GeneSetMapTools.java:500: warning - @return tag has no arguments.
src/baseCode/gui/JLinkLabel.java:56: warning - @return tag has no arguments.
This sentence is different from what would be generated using -breakiterator:
"CH 18-3 version 2 for quality weighted. ( page 266 ) in Fixed effects model.
"
"<p>
Copyright (c) 2004
"
src/baseCode/util/FileTools.java:65: warning - @return tag has no arguments.
This sentence is different from what would be generated using -breakiterator:
"<p>
Copyright (c) 2004
</p>
<p>
Institution:: Columbia University
</p>"
"<hr>
"
src/baseCode/io/writer/HistogramWriter.java:26: warning - Tag @link: reference not found: hep.aidia.IHistogram1D
This sentence is different from what would be generated using -breakiterator:
"<hr>
<p>
src/baseCode/util/FileTools.java:123: warning - @return tag has no arguments.
Copyright (c) 2004 Columbia University"
"Based on R code from Francesca Dominici, <a
src/baseCode/util/FileTools.java:90: warning - @return tag has no arguments.
href="http://www.biostat.jhsph.edu/~fdominic/teaching/BM/bm.html">http://www.biostat.jhsph.edu/~fdominic/teaching/BM/bm.html
</a>
"
src/baseCode/util/FileTools.java:107: warning - @return tag has no arguments.
This sentence is different from what would be generated using -breakiterator:
"Based on R code from Francesca Dominici, <a
src/baseCode/gui/file/ImageFileFilter.java:17: warning - The first sentence is interpreted to be:
href="http://www.biostat.jhsph.edu/~fdominic/teaching/BM/bm.html">http://www.biostat.jhsph.edu/~fdominic/teaching/BM/bm.html
</a>
<p>
Returns
<pre>
src/baseCode/dataStructure/graph/DirectedGraphNode.java:128: warning - @return tag has no arguments.
w=(RU)'RU
</pre>
where
<pre>
Cov=U'U (U is upper triang)
</pre>
and where upper-tri R is
<pre>
src/baseCode/dataStructure/tree/BinaryTreeNode.java:95: warning - @return tag has no arguments.
R_ij˜N(0,1), i<j ; (R_ii)ˆ2˜Chisq(nu-s+i)
</pre>"
"<p>
Title:
"
src/baseCode/math/CorrelationStats.java:249: warning - @return tag has no arguments.
This sentence is different from what would be generated using -breakiterator:
"<p>
Title:
</p>
<p>
Description:
</p>
<p>
Copyright (c) 2004
</p>
<p>
src/baseCode/gui/JMatrixDisplay.java:36: warning - The first sentence is interpreted to be:
Institution:: Columbia University
</p>"
"Ported from R phyper.c
"
src/baseCode/dataStructure/Link.java:23: warning - The first sentence is interpreted to be:
This sentence is different from what would be generated using -breakiterator:
"Ported from R phyper.c
<p>
src/baseCode/math/MatrixStats.java:19: warning - The first sentence is interpreted to be:
Sample of n balls from NR red and NB black ones; x are red
<p>"
"<hr>
"
This sentence is different from what would be generated using -breakiterator:
"<hr>
src/baseCode/math/metaanalysis/MeanDifferenceMetaAnalysis.java:26: warning - The first sentence is interpreted to be:
<p>Copyright (c) 2004 Columbia University"
"Read a sparse matrix that is expressed as an adjacency list in a tab-delimited file:
"
src/baseCode/math/metaanalysis/MetaAnalysis.java:306: warning - @return tag has no arguments.
This sentence is different from what would be generated using -breakiterator:
src/baseCode/math/metaanalysis/MetaAnalysis.java:211: warning - @param tag has no arguments.
"Read a sparse matrix that is expressed as an adjacency list in a tab-delimited file:
<pre>
item1 item2 weight
item1 item5 weight
</pre>
<p>
By definition the resulting matrix is square and symmetric.
"
src/baseCode/math/metaanalysis/MetaAnalysis.java:211: warning - @return tag has no arguments.
"Read a sparse symmetric square matrix that is expressed as an adjacency list in a tab-delimited file:
"
This sentence is different from what would be generated using -breakiterator:
"Read a sparse symmetric square matrix that is expressed as an adjacency list in a tab-delimited file:
src/baseCode/math/metaanalysis/MetaAnalysis.java:258: warning - @return tag has no arguments.
<pre>
src/baseCode/math/metaanalysis/MetaAnalysis.java:288: warning - @return tag has no arguments.
item1 item2 weight
item1 item5 weight
src/baseCode/math/metaanalysis/MetaAnalysis.java:288: warning - The first sentence is interpreted to be:
</pre>
src/baseCode/math/metaanalysis/MetaAnalysis.java:145: warning - @return tag has no arguments.
<p>
IMPORTANT: By definition the resulting matrix is square and symmetric, even if the symmetric edges are not
explicitly listed."
src/baseCode/math/metaanalysis/MetaAnalysis.java:181: warning - @return tag has no arguments.
"<hr>
"
This sentence is different from what would be generated using -breakiterator:
"<hr>
<p>
Copyright (c) 2004 Columbia University"
src/baseCode/math/metaanalysis/MetaAnalysis.java:181: warning - The first sentence is interpreted to be:
"<p>
Title: SparseDoubleMatrix2DNamed
"
This sentence is different from what would be generated using -breakiterator:
"<p>
Title: SparseDoubleMatrix2DNamed
</p>
<p>
Description: A sparse matrix that knows about row and column names.
src/baseCode/math/metaanalysis/MetaAnalysis.java:201: warning - @return tag has no arguments.
"
"<hr>
"
This sentence is different from what would be generated using -breakiterator:
"<hr>
<p>
Copyright (c) 2004 Columbia University"
src/baseCode/dataStructure/matrix/NamedMatrix.java:18: warning - The first sentence is interpreted to be:
src/baseCode/math/distribution/NormalProbabilityComputer.java:13: warning - The first sentence is interpreted to be:
"Best data structure for reading really big, really sparse matrices when a matrix represetation is needed."
This sentence is different from what would be generated using -breakiterator:
src/baseCode/bio/geneset/GONames.java:169: warning - @return tag has no arguments.
"Best data structure for reading really big, really sparse matrices when a matrix represetation is needed. *
<p>
The standard format looks like this:
<pre>
src/baseCode/math/distribution/Wishart.java:117: warning - @return tag has no arguments.
src/baseCode/math/distribution/Wishart.java:117: warning - The first sentence is interpreted to be:
2 <--- number of items - the first line of the file only. "
"<p>
Title:
src/baseCode/bio/geneset/GeneAnnotations.java:629: warning - @return tag has no arguments.
"
This sentence is different from what would be generated using -breakiterator:
"<p>
Title:
</p>
<p>
Description:
</p>
<p>
Copyright: Copyright (c) 2003
</p>
<p>
Company:
</p>"
"Prints status info to stderr
"
src/baseCode/bio/geneset/GeneAnnotations.java:346: warning - @return tag has no arguments.
This sentence is different from what would be generated using -breakiterator:
"Prints status info to stderr
<hr>
<p>
src/baseCode/dataStructure/matrix/NamedMatrix.java:162: warning - @return tag has no arguments.
Copyright (c) 2004 Columbia University"
"Reader for {@link baseCode.dataStructure.matrix.StringMatrix2DNamed}
"
This sentence is different from what would be generated using -breakiterator:
"Reader for {@link baseCode.dataStructure.matrix.StringMatrix2DNamed}
<p>
Copyright (c) 2004
src/baseCode/bio/geneset/GeneAnnotations.java:336: warning - @return tag has no arguments.
src/baseCode/math/Rank.java:34: warning - @return tag has no arguments.
</p>
<p>
Institution:: Columbia University
</p>"
src/baseCode/dataStructure/Point.java:21: warning - The first sentence is interpreted to be:
"Returns <tt>Sum( (data[i]-c)<sup>k</sup> )</tt>; optimized for common parameters like <tt>c == 0.0</tt>
src/baseCode/math/SpecFunc.java:36: warning - The first sentence is interpreted to be:
and/or <tt>k == -2 .."
This sentence is different from what would be generated using -breakiterator:
"Returns <tt>Sum( (data[i]-c)<sup>k</sup> )</tt>; optimized for common parameters like <tt>c == 0.0</tt>
and/or <tt>k == -2 .. 4</tt>."
"<hr>
"
src/baseCode/math/distribution/ProbabilityComputer.java:20: warning - @return tag has no arguments.
This sentence is different from what would be generated using -breakiterator:
"<hr>
<p>Copyright (c) 2004 Columbia University"
"<hr>
"
src/baseCode/math/distribution/ProbabilityComputer.java:28: warning - @return tag has no arguments.
This sentence is different from what would be generated using -breakiterator:
src/baseCode/algorithm/Ranker.java:13: warning - The first sentence is interpreted to be:
"<hr>
<p>Copyright (c) 2004 Columbia University"
src/baseCode/io/reader/SparseDoubleMatrixReader.java:175: warning - The first sentence is interpreted to be:
src/baseCode/io/reader/SparseRaggedDouble2DNamedMatrixReader.java:120: warning - The first sentence is interpreted to be:
src/baseCode/util/RegressionTesting.java:54: warning - @return tag has no arguments.
"<hr>
"
This sentence is different from what would be generated using -breakiterator:
"<hr>
<p>
src/baseCode/util/RegressionTesting.java:90: warning - @return tag has no arguments.
Copyright (c) 2004 Columbia University"
src/baseCode/dataStructure/matrix/SparseDoubleMatrix2DNamed.java:169: warning - @return tag has no arguments.
src/baseCode/dataStructure/matrix/StringMatrix2DNamed.java:107: warning - @return tag has no arguments.
"<hr>
"
This sentence is different from what would be generated using -breakiterator:
"<hr>
<p>Copyright (c) 2004 Columbia University"
src/baseCode/math/metaanalysis/MeanDifferenceMetaAnalysis.java:81: warning - @return tag has no arguments.
src/baseCode/algorithm/learning/unsupervised/cluster/Similarity.java:11: warning - The first sentence is interpreted to be:
src/baseCode/dataStructure/matrix/SparseDoubleMatrix2DNamed.java:26: warning - The first sentence is interpreted to be:
src/baseCode/io/reader/SparseDoubleMatrixReader.java:37: warning - The first sentence is interpreted to be:
src/baseCode/io/reader/SparseRaggedDouble2DNamedMatrixReader.java:78: warning - The first sentence is interpreted to be:
"<hr>
"
This sentence is different from what would be generated using -breakiterator:
"<hr>
<p>Copyright (c) 2004-2005 Columbia University"
src/baseCode/gui/StatusJlabel.java:27: warning - The first sentence is interpreted to be:
src/baseCode/util/StatusStderr.java:12: warning - The first sentence is interpreted to be:
"<p>
Title:
"
This sentence is different from what would be generated using -breakiterator:
"<p>
Title:
</p>
<p>
src/baseCode/io/reader/StringMatrixReader.java:27: warning - The first sentence is interpreted to be:
Description:
</p>
<p>
Copyright: Copyright (c) 2003
</p>
<p>
Company:
</p>"
"<hr>
"
This sentence is different from what would be generated using -breakiterator:
src/baseCode/math/metaanalysis/CorrelationEffectMetaAnalysis.java:127: warning - @return tag has no arguments.
"<hr>
<p>
Copyright (c) 2004 Columbia University"
src/baseCode/math/metaanalysis/MeanDifferenceMetaAnalysis.java:120: warning - @return tag has no arguments.
src/baseCode/math/metaanalysis/CorrelationEffectMetaAnalysis.java:156: warning - @return tag has no arguments.
src/baseCode/math/metaanalysis/MeanDifferenceMetaAnalysis.java:132: warning - @return tag has no arguments.
src/baseCode/dataStructure/matrix/SparseDoubleMatrix2DNamed.java:222: warning - @return tag has no arguments.
src/baseCode/dataStructure/matrix/StringMatrix2DNamed.java:114: warning - @return tag has no arguments.
src/baseCode/bio/geneset/GeneAnnotations.java:247: warning - @return tag has no arguments.
src/baseCode/math/DescriptiveWithMissing.java:738: warning - The first sentence is interpreted to be:
src/baseCode/dataStructure/tree/Tree.java:14: warning - The first sentence is interpreted to be:
Building index for all classes...
src/baseCode/dataStructure/tree/TreeNode.java:13: warning - The first sentence is interpreted to be:
src/baseCode/gui/GuiUtil.java:55: warning - @return tag has no arguments.
src/baseCode/util/FileTools.java:156: warning - @return tag has no arguments.
src/baseCode/gui/GuiUtil.java:43: warning - @return tag has no arguments.
src/baseCode/util/FileTools.java:170: warning - @return tag has no arguments.
src/baseCode/util/FileTools.java:185: warning - @return tag has no arguments.
src/baseCode/bio/geneset/GeneAnnotations.java:449: warning - @return tag has no arguments.
src/baseCode/math/distribution/UniformDensityComputer.java:11: warning - The first sentence is interpreted to be:
src/baseCode/math/CorrelationStats.java:96: warning - @return tag has no arguments.
src/baseCode/common/Visitable.java:11: warning - The first sentence is interpreted to be:
src/baseCode/dataStructure/matrix/SparseDoubleMatrix2DNamed.java:195: warning - @return tag has no arguments.
Generating target/docs/apidocs/baseCode/algorithm/package-summary.html...
"<hr>
"
This sentence is different from what would be generated using -breakiterator:
"<hr>
src/baseCode/dataStructure/matrix/StringMatrix2DNamed.java:122: warning - @return tag has no arguments.
<p>Copyright (c) 2004 Columbia University"
"<hr>
"
This sentence is different from what would be generated using -breakiterator:
"<hr>
src/baseCode/dataStructure/matrix/AbstractNamedDoubleMatrix.java:75: warning - @return tag has no arguments.
<p>Copyright (c) 2004 Columbia University"
src/baseCode/dataStructure/matrix/SparseDoubleMatrix2DNamed.java:203: warning - @return tag has no arguments.
src/baseCode/dataStructure/matrix/StringMatrix2DNamed.java:130: warning - @return tag has no arguments.
src/baseCode/gui/Wizard.java:30: warning - The first sentence is interpreted to be:
src/baseCode/gui/WizardStep.java:27: warning - The first sentence is interpreted to be:
src/baseCode/math/metaanalysis/MetaAnalysis.java:99: warning - @return tag has no arguments.
src/baseCode/math/metaanalysis/MetaAnalysis.java:123: warning - @return tag has no arguments.
src/baseCode/gui/file/XMLFileFilter.java:17: warning - The first sentence is interpreted to be:
Generating target/docs/apidocs/baseCode/algorithm/learning/unsupervised/cluster/package-summary.html...
"<hr>
"
This sentence is different from what would be generated using -breakiterator:
"<hr>
<p>
src/baseCode/algorithm/Algorithm.java:14: warning - The first sentence is interpreted to be:
Copyright (c) 2004 Columbia University"
"<hr>
"
This sentence is different from what would be generated using -breakiterator:
src/baseCode/algorithm/Ranker.java:13: warning - The first sentence is interpreted to be:
"<hr>
<p>
Copyright (c) 2004 Columbia University"
"<hr>
"
This sentence is different from what would be generated using -breakiterator:
"<hr>
<p>
Copyright (c) 2004 Columbia University"
"<hr>
"
src/baseCode/algorithm/learning/unsupervised/cluster/Distancer.java:13: warning - The first sentence is interpreted to be:
This sentence is different from what would be generated using -breakiterator:
"<hr>
<p>
Copyright (c) 2004 Columbia University"
"<hr>
"
src/baseCode/algorithm/learning/unsupervised/cluster/Similarity.java:11: warning - The first sentence is interpreted to be:
This sentence is different from what would be generated using -breakiterator:
"<hr>
<p>Copyright (c) 2004 Columbia University"
"<hr>
"
src/baseCode/algorithm/learning/unsupervised/cluster/AverageLinkageDistancer.java:16: warning - The first sentence is interpreted to be:
This sentence is different from what would be generated using -breakiterator:
"<hr>
<p>Copyright (c) 2004 Columbia University"
src/baseCode/algorithm/learning/unsupervised/cluster/Cluster.java:16: warning - The first sentence is interpreted to be:
src/baseCode/algorithm/learning/unsupervised/cluster/ClusteringAlgorithm.java:13: warning - The first sentence is interpreted to be:
Generating target/docs/apidocs/baseCode/bio/package-summary.html...
"<hr>
"
This sentence is different from what would be generated using -breakiterator:
"<hr>
<p>Copyright (c) 2004 Columbia University"
"<hr>
"
src/baseCode/algorithm/learning/unsupervised/cluster/DistanceFactory.java:11: warning - The first sentence is interpreted to be:
This sentence is different from what would be generated using -breakiterator:
"<hr>
<p>Copyright (c) 2004 Columbia University"
"<hr>
"
src/baseCode/bio/GOEntry.java:13: warning - The first sentence is interpreted to be:
This sentence is different from what would be generated using -breakiterator:
"<hr>
<p>Copyright (c) 2004 Columbia University"
src/baseCode/bio/GOTermList.java:11: warning - The first sentence is interpreted to be:
src/baseCode/bio/GOTermProbability.java:11: warning - The first sentence is interpreted to be:
src/baseCode/common/Visitable.java:11: warning - The first sentence is interpreted to be:
src/baseCode/dataStructure/Link.java:23: warning - The first sentence is interpreted to be:
src/baseCode/dataStructure/Point.java:21: warning - The first sentence is interpreted to be:
src/baseCode/dataStructure/matrix/NamedMatrix.java:18: warning - The first sentence is interpreted to be:
Generating target/docs/apidocs/baseCode/common/package-summary.html...
"<hr>
"
This sentence is different from what would be generated using -breakiterator:
"<hr>
<p>Copyright (c) 2004 Columbia University"
src/baseCode/dataStructure/matrix/AbstractNamedDoubleMatrix.java:22: warning - The first sentence is interpreted to be:
src/baseCode/dataStructure/matrix/SparseDoubleMatrix2DNamed.java:26: warning - The first sentence is interpreted to be:
src/baseCode/dataStructure/tree/BinaryTree.java:11: warning - The first sentence is interpreted to be:
src/baseCode/dataStructure/tree/BinaryTreeNode.java:13: warning - The first sentence is interpreted to be:
src/baseCode/dataStructure/tree/Tree.java:14: warning - The first sentence is interpreted to be:
Generating target/docs/apidocs/baseCode/dataStructure/package-summary.html...
"<p>
Title:
"
src/baseCode/dataStructure/tree/TreeNode.java:13: warning - The first sentence is interpreted to be:
This sentence is different from what would be generated using -breakiterator:
"<p>
Title:
</p>
<p>
Description:
</p>
<p>
Copyright (c) 2004
</p>
<p>
src/baseCode/gui/AppDialog.java:42: warning - The first sentence is interpreted to be:
Institution:: Columbia University
</p>"
"<p>
Title:
"
This sentence is different from what would be generated using -breakiterator:
"<p>
Title:
</p>
src/baseCode/gui/ColorMap.java:23: warning - The first sentence is interpreted to be:
<p>
Description:
</p>
<p>
Copyright (c) 2004
</p>
<p>
Institution:: Columbia University
</p>"
src/baseCode/gui/ColorMatrix.java:30: warning - The first sentence is interpreted to be:
src/baseCode/gui/JMatrixDisplay.java:36: warning - The first sentence is interpreted to be:
src/baseCode/gui/StatusJlabel.java:27: warning - The first sentence is interpreted to be:
src/baseCode/gui/Wizard.java:30: warning - The first sentence is interpreted to be:
src/baseCode/gui/WizardStep.java:27: warning - The first sentence is interpreted to be:
Generating target/docs/apidocs/baseCode/dataStructure/matrix/package-summary.html...
"<p>
Copyright (c) 2004
"
This sentence is different from what would be generated using -breakiterator:
"<p>
Copyright (c) 2004
</p>
<p>
Institution:: Columbia University
</p>"
"<hr>
"
This sentence is different from what would be generated using -breakiterator:
"<hr>
<p>Copyright (c) 2004 Columbia University"
"<p>
Title: SparseDoubleMatrix2DNamed
"
This sentence is different from what would be generated using -breakiterator:
"<p>
Title: SparseDoubleMatrix2DNamed
</p>
<p>
src/baseCode/gui/file/DataFileFilter.java:17: warning - The first sentence is interpreted to be:
Description: A sparse matrix that knows about row and column names.
"
src/baseCode/gui/file/ImageFileFilter.java:17: warning - The first sentence is interpreted to be:
src/baseCode/gui/file/XMLFileFilter.java:17: warning - The first sentence is interpreted to be:
Generating target/docs/apidocs/baseCode/dataStructure/tree/package-summary.html...
"<hr>
"
This sentence is different from what would be generated using -breakiterator:
"<hr>
<p>
Copyright (c) 2004 Columbia University"
"<hr>
"
This sentence is different from what would be generated using -breakiterator:
src/baseCode/io/reader/SparseDoubleMatrixReader.java:37: warning - The first sentence is interpreted to be:
"<hr>
<p>
Copyright (c) 2004 Columbia University"
"<hr>
"
This sentence is different from what would be generated using -breakiterator:
"<hr>
<p>Copyright (c) 2004 Columbia University"
"<hr>
"
This sentence is different from what would be generated using -breakiterator:
"<hr>
<p>Copyright (c) 2004 Columbia University"
src/baseCode/io/reader/SparseRaggedDouble2DNamedMatrixReader.java:78: warning - The first sentence is interpreted to be:
src/baseCode/io/reader/StringMatrixReader.java:27: warning - The first sentence is interpreted to be:
src/baseCode/io/writer/HistogramWriter.java:26: warning - Tag @link: reference not found: hep.aidia.IHistogram1D
Generating target/docs/apidocs/baseCode/gui/package-summary.html...
"<p>
Title:
"
This sentence is different from what would be generated using -breakiterator:
"<p>
Title:
</p>
src/baseCode/math/MatrixStats.java:19: warning - The first sentence is interpreted to be:
<p>
Description:
</p>
<p>
Copyright: Copyright (c) 2003
</p>
<p>
Company:
</p>"
"<p>
Title: ColorMap
"
This sentence is different from what would be generated using -breakiterator:
"<p>
Title: ColorMap
</p>
<p>
Description: contains predefined color maps for visualization and color palette methods
</p>
<p>
Copyright (c) 2004
</p>
<p>
Institution:: Columbia University
</p>"
"<p>
Title: ColorMatrix
"
This sentence is different from what would be generated using -breakiterator:
"<p>
Title: ColorMatrix
</p>
<p>
Description: Creates a color matrix from a matrix of doubles
</p>
<p>
Copyright (c) 2004
</p>
<p>
Institution:: Columbia University
</p>"
"<p>
Title: JMatrixDisplay
"
This sentence is different from what would be generated using -breakiterator:
"<p>
Title: JMatrixDisplay
</p>
<p>
Description: a visual component for displaying a color matrix
</p>
<p>
Copyright: Copyright (c) 2004
</p>
<p>
Institution:: Columbia University
</p>"
"<p>
Title:
"
This sentence is different from what would be generated using -breakiterator:
"<p>
Title:
</p>
<p>
Description:
</p>
<p>
Copyright: Copyright (c) 2003
</p>
<p>
Company:
</p>"
"<hr>
"
This sentence is different from what would be generated using -breakiterator:
"<hr>
<p>Copyright (c) 2004-2005 Columbia University"
"<p>
Title:
"
This sentence is different from what would be generated using -breakiterator:
"<p>
Title:
</p>
<p>
Description:
</p>
<p>
Copyright: Copyright (c) 2003
</p>
<p>
Company:
</p>"
src/baseCode/math/distribution/Dirichlet.java:19: warning - The first sentence is interpreted to be:
src/baseCode/math/distribution/NormalProbabilityComputer.java:13: warning - The first sentence is interpreted to be:
src/baseCode/math/distribution/UniformDensityComputer.java:11: warning - The first sentence is interpreted to be:
Generating target/docs/apidocs/baseCode/gui/file/package-summary.html...
"<hr>
"
This sentence is different from what would be generated using -breakiterator:
"<hr>
<p>
src/baseCode/math/metaanalysis/MeanDifferenceMetaAnalysis.java:26: warning - The first sentence is interpreted to be:
Copyright (c) 2004 Columbia University"
"<hr>
"
This sentence is different from what would be generated using -breakiterator:
"<hr>
<p>
Copyright (c) 2004 Columbia University"
"<hr>
"
This sentence is different from what would be generated using -breakiterator:
"<hr>
<p>
Copyright (c) 2004 Columbia University"
Generating target/docs/apidocs/baseCode/io/reader/package-summary.html...
"<hr>
"
This sentence is different from what would be generated using -breakiterator:
"<hr>
<p>
Copyright (c) 2004 Columbia University"
"Best data structure for reading really big, really sparse matrices when a matrix represetation is needed."
src/baseCode/util/StatusStderr.java:12: warning - The first sentence is interpreted to be:
This sentence is different from what would be generated using -breakiterator:
"Best data structure for reading really big, really sparse matrices when a matrix represetation is needed. *
<p>
The standard format looks like this:
<pre>
2 <--- number of items - the first line of the file only. "
"Reader for {@link baseCode.dataStructure.matrix.StringMatrix2DNamed}
"
This sentence is different from what would be generated using -breakiterator:
"Reader for {@link baseCode.dataStructure.matrix.StringMatrix2DNamed}
<p>
Copyright (c) 2004
</p>
<p>
Institution:: Columbia University
</p>"
src/baseCode/io/StringConverter.java:56: warning - @param argument "stringToConvert" is not a parameter name.
Generating target/docs/apidocs/baseCode/math/package-summary.html...
"<hr>
"
This sentence is different from what would be generated using -breakiterator:
"<hr>
<p>
Copyright (c) 2004 Columbia University"
Generating target/docs/apidocs/baseCode/math/distribution/package-summary.html...
"<hr>
"
This sentence is different from what would be generated using -breakiterator:
"<hr>
<p>
Copyright (c) 2004 Columbia University"
"<hr>
"
This sentence is different from what would be generated using -breakiterator:
"<hr>
<p>
Copyright (c) 2004 Columbia University"
"<hr>
"
This sentence is different from what would be generated using -breakiterator:
"<hr>
<p>
Copyright (c) 2004 Columbia University"
Generating target/docs/apidocs/baseCode/math/metaanalysis/package-summary.html...
"Meta-analysis methods from chapter 18 of Cooper and Hedges, sections 2.1 and 3.1
"
src/baseCode/dataStructure/graph/DirectedGraph.java:27: warning - @todo is an unknown tag.
This sentence is different from what would be generated using -breakiterator:
"Meta-analysis methods from chapter 18 of Cooper and Hedges, sections 2.1 and 3.1
<p>
src/baseCode/dataStructure/graph/DirectedGraph.java:231: warning - @todo is an unknown tag.
These methods use the standardized mean difference statistic d:
<pre>
d_i = ( X_i ˆ t - X_i ˆ c ) / s_i
</pre>
where X <sub>i </sub> <sup>t </sup> is the mean of the treatment group in the ith study, X <sub>i </sub> <sup>ct
</sup> is the mean of the control group in the treatment group in the ith study, and s <sub>i </sub> is the pooled
standard deviation of the two groups. "
Generating target/docs/apidocs/baseCode/util/package-summary.html...
"Prints status info to stderr
"
This sentence is different from what would be generated using -breakiterator:
"Prints status info to stderr
<hr>
src/baseCode/io/reader/SparseDoubleMatrixReader.java:175: warning - The first sentence is interpreted to be:
<p>
Copyright (c) 2004 Columbia University"
src/baseCode/io/reader/SparseDoubleMatrixReader.java:98: warning - @param argument "wantedRowNames" is not a parameter name.
src/baseCode/io/reader/SparseRaggedDouble2DNamedMatrixReader.java:120: warning - The first sentence is interpreted to be:
src/baseCode/io/reader/SparseRaggedDouble2DNamedMatrixReader.java:120: warning - @param argument "name" is not a parameter name.
src/baseCode/io/reader/SparseRaggedDouble2DNamedMatrixReader.java:295: warning - @param argument "stream" is not a parameter name.
src/baseCode/io/writer/HistogramWriter.java:26: warning - Tag @link: reference not found: hep.aidia.IHistogram1D
src/baseCode/dataStructure/tree/BinaryTreeNode.java:24: warning - @param argument "left" is not a parameter name.
src/baseCode/dataStructure/tree/BinaryTreeNode.java:24: warning - @param argument "right" is not a parameter name.
src/baseCode/bio/geneset/GeneSetMapTools.java:67: warning - @param argument "sum" is not a parameter name.
src/baseCode/bio/geneset/GONames.java:148: warning - @todo is an unknown tag.
src/baseCode/bio/geneset/GONames.java:158: warning - @todo is an unknown tag.
src/baseCode/math/metaanalysis/CorrelationEffectMetaAnalysis.java:56: warning - @param argument "correlations" is not a parameter name.
src/baseCode/math/metaanalysis/CorrelationEffectMetaAnalysis.java:127: warning - @param argument "n" is not a parameter name.
src/baseCode/math/metaanalysis/CorrelationEffectMetaAnalysis.java:156: warning - Tag @see: reference not found: samplingVariance
src/baseCode/math/metaanalysis/CorrelationEffectMetaAnalysis.java:184: warning - @param argument "n" is not a parameter name.
src/baseCode/math/metaanalysis/MeanDifferenceMetaAnalysis.java:41: warning - @param argument "b" is not a parameter name.
src/baseCode/math/metaanalysis/MetaAnalysis.java:49: warning - The first sentence is interpreted to be:
src/baseCode/math/metaanalysis/MetaAnalysis.java:288: warning - The first sentence is interpreted to be:
Generating target/docs/apidocs/baseCode/io/reader/SparseDoubleMatrixReader.html...
"Read a sparse matrix that is expressed as an adjacency list in a tab-delimited file:
"
This sentence is different from what would be generated using -breakiterator:
src/baseCode/math/metaanalysis/MetaAnalysis.java:181: warning - The first sentence is interpreted to be:
"Read a sparse matrix that is expressed as an adjacency list in a tab-delimited file:
<pre>
src/baseCode/math/metaanalysis/MetaAnalysis.java:85: warning - Tag @see: reference not found: qStatistic
item1 item2 weight
item1 item5 weight
</pre>
<p>
By definition the resulting matrix is square and symmetric.
"
src/baseCode/math/metaanalysis/MetaAnalysis.java:99: warning - @param argument "sampleSizes" is not a parameter name.
Generating target/docs/apidocs/baseCode/io/reader/SparseRaggedDouble2DNamedMatrixReader.html...
"Read a sparse symmetric square matrix that is expressed as an adjacency list in a tab-delimited file:
"
src/baseCode/math/metaanalysis/MetaAnalysis.java:123: warning - @param argument "sampleSizes" is not a parameter name.
This sentence is different from what would be generated using -breakiterator:
src/baseCode/math/metaanalysis/MetaAnalysis.java:181: warning - @param argument "variances" is not a parameter name.
"Read a sparse symmetric square matrix that is expressed as an adjacency list in a tab-delimited file:
<pre>
src/baseCode/math/metaanalysis/MetaAnalysis.java:211: warning - @param argument "" is not a parameter name.
item1 item2 weight
item1 item5 weight
src/baseCode/math/DescriptiveWithMissing.java:738: warning - The first sentence is interpreted to be:
</pre>
<p>
IMPORTANT: By definition the resulting matrix is square and symmetric, even if the symmetric edges are not
explicitly listed."
src/baseCode/math/DescriptiveWithMissing.java:173: warning - @todo is an unknown tag.
src/baseCode/math/DescriptiveWithMissing.java:483: warning - @todo is an unknown tag.
src/baseCode/math/DescriptiveWithMissing.java:533: warning - @todo is an unknown tag.
src/baseCode/math/MatrixRowStats.java:20: warning - @todo is an unknown tag.
src/baseCode/math/MatrixRowStats.java:64: warning - @todo is an unknown tag.
src/baseCode/math/MatrixStats.java:26: warning - @todo is an unknown tag.
src/baseCode/math/SpecFunc.java:102: warning - The first sentence is interpreted to be:
src/baseCode/math/SpecFunc.java:36: warning - The first sentence is interpreted to be:
src/baseCode/math/Stats.java:48: warning - @todo is an unknown tag.
Generating target/docs/apidocs/baseCode/math/metaanalysis/MetaAnalysis.html...
"Fisher's method for combining p values (Cooper and Hedges 15-8)
"
This sentence is different from what would be generated using -breakiterator:
src/baseCode/math/distribution/DensityGenerator.java:18: warning - @param argument "value" is not a parameter name.
"Fisher's method for combining p values (Cooper and Hedges 15-8)
<p>
Use for p values that have already been log transformed."
"Under a random effects model, CH eqn."
This sentence is different from what would be generated using -breakiterator:
"Under a random effects model, CH eqn. 18-24, we replace the conditional variance with the sum of the
between-sample variance and the conditional variance.
"
"CH 18-3 version 2 for quality weighted."
This sentence is different from what would be generated using -breakiterator:
src/baseCode/math/distribution/Wishart.java:117: warning - The first sentence is interpreted to be:
"CH 18-3 version 2 for quality weighted. ( page 266 ) in Fixed effects model.
"
Generating target/docs/apidocs/baseCode/math/DescriptiveWithMissing.html...
"Returns <tt>Sum( (data[i]-c)<sup>k</sup> )</tt>; optimized for common parameters like <tt>c == 0.0</tt>
and/or <tt>k == -2 .."
This sentence is different from what would be generated using -breakiterator:
"Returns <tt>Sum( (data[i]-c)<sup>k</sup> )</tt>; optimized for common parameters like <tt>c == 0.0</tt>
src/baseCode/math/distribution/Wishart.java:43: warning - @param argument "s" is not a parameter name.
and/or <tt>k == -2 .. 4</tt>."
src/baseCode/math/distribution/Wishart.java:117: warning - @param argument "s" is not a parameter name.
src/baseCode/math/distribution/Wishart.java:117: warning - @param argument "nu" is not a parameter name.
src/baseCode/math/distribution/Wishart.java:117: warning - @param argument "covariance" is not a parameter name.
Generating target/docs/apidocs/baseCode/math/SpecFunc.html...
"Ported from R (Catherine Loader)
"
This sentence is different from what would be generated using -breakiterator:
"Ported from R (Catherine Loader)
<p>
DESCRIPTION
<p>
Given a sequence of r successes and b failures, we sample n (\le b+r) items without replacement. "
"Ported from R phyper.c
src/baseCode/dataStructure/matrix/DenseDoubleMatrix2DNamed.java:83: warning - @param argument "col" is not a parameter name.
"
This sentence is different from what would be generated using -breakiterator:
"Ported from R phyper.c
<p>
src/baseCode/dataStructure/matrix/DenseDoubleMatrix2DNamed.java:239: warning - Tag @see: reference not found: AbstractMatrix2D#rows()
Sample of n balls from NR red and NB black ones; x are red
<p>"
src/baseCode/dataStructure/matrix/DenseDoubleMatrix2DNamed.java:247: warning - Tag @see: reference not found: AbstractMatrix2D#size()
src/baseCode/dataStructure/matrix/SparseDoubleMatrix2DNamed.java:144: warning - @return tag has no arguments.
src/baseCode/dataStructure/matrix/SparseDoubleMatrix2DNamed.java:169: warning - @return tag has no arguments.
src/baseCode/dataStructure/matrix/SparseRaggedDoubleMatrix2DNamed.java:166: warning - @param argument "row" is not a parameter name.
src/baseCode/dataStructure/matrix/SparseRaggedDoubleMatrix2DNamed.java:166: warning - @param argument "column" is not a parameter name.
src/baseCode/dataStructure/matrix/StringMatrix2DNamed.java:82: warning - @return tag has no arguments.
src/baseCode/dataStructure/matrix/StringMatrix2DNamed.java:107: warning - @return tag has no arguments.
Generating target/docs/apidocs/baseCode/math/distribution/Wishart.html...
"Based on R code from Francesca Dominici, <a
href="http://www.biostat.jhsph.edu/~fdominic/teaching/BM/bm.html">http://www.biostat.jhsph.edu/~fdominic/teaching/BM/bm.html
</a>
"
This sentence is different from what would be generated using -breakiterator:
"Based on R code from Francesca Dominici, <a
href="http://www.biostat.jhsph.edu/~fdominic/teaching/BM/bm.html">http://www.biostat.jhsph.edu/~fdominic/teaching/BM/bm.html
</a>
<p>
Returns
<pre>
w=(RU)'RU
</pre>
where
<pre>
Cov=U'U (U is upper triang)
</pre>
and where upper-tri R is
<pre>
R_ij˜N(0,1), i<j ; (R_ii)ˆ2˜Chisq(nu-s+i)
</pre>"
src/baseCode/dataFilter/RowLevelFilter.java:116: warning - @return tag has no arguments.
src/baseCode/gui/GuiUtil.java:55: warning - @param argument "text" is not a parameter name.
src/baseCode/gui/JMatrixDisplay.java:297: warning - @todo is an unknown tag.
src/baseCode/gui/TreePanel.java:28: warning - @todo is an unknown tag.
src/baseCode/gui/WizardStep.java:59: warning - @todo is an unknown tag.
src/baseCode/algorithm/learning/unsupervised/RankProp.java:48: warning - @param argument "matrix1D" is not a parameter name.
src/baseCode/algorithm/learning/unsupervised/RankProp.java:48: warning - @param argument "k" is not a parameter name.
src/baseCode/algorithm/learning/unsupervised/RankProp.java:115: warning - @param argument "max_loops" is not a parameter name.
src/baseCode/algorithm/learning/unsupervised/cluster/HierarchicalClusterer.java:69: warning - Tag @see: reference not found: baseCode.algorithm.learning.unsupervised.cluster.Algorithm#Run()
src/baseCode/gui/AppDialog.java:52: warning - Tag @author cannot be used in field documentation. It can only be used in the following types of documentation: overview, package, class/interface.
src/baseCode/gui/AppDialog.java:52: warning - Tag @version cannot be used in field documentation. It can only be used in the following types of documentation: overview, package, class/interface.
Generating target/docs/apidocs/help-doc.html...
303 warnings
