Added class javadoc
Merge branch 'master' into jurgens-updates
Merge branch 'master' of https://github.com/fozziethebeat/S-Space into jurgens-updates
Fixed typo in email address
Checking in a version Brandes' betweeness-centrality code.  This version could
be cleaned up to use the latest util.primitive (or Trove) classes.
Fixing typo on the main page in the URL to the javadoc
Moving graph code to opt module so that the rest of the code base compiles.
Moving Grefenstette to opt.
Updated root pom to include tests that end with Tests.java.
Updated opt pom to function correctly, it is now an independent pom file.
Adds a new Faster implmentation of Agglomerative Clustering.

	new file:   src/main/java/edu/ucla/sspace/clustering/NeighborChainAgglomerativeClustering.java
    - Adding a new N^2 implementation of Agglomerative clustering that depends
      on nearest neighbor chains and recurrence relations for computing cluster
      similarities.
Added ability include stack trace in unit test output
Lots and lots of bug fixes with a few minor functionality enhancements.

	modified:   src/main/java/edu/ucla/sspace/common/Similarity.java

- Added warnings for invalid KL-divergence computations

- Added Kruskal-Goodman Gamma

- Discovered Spearman's rho and Kendall's tau are both wrong (not fixed)  :(

	modified:   src/main/java/edu/ucla/sspace/common/statistics/LogLikelihoodTest.java

- Fixed implementation

	new file:   src/main/java/edu/ucla/sspace/graph/ChineseWhispersClustering.java

- Added CW clustering, but it doesn't appear to produce the same results as the
  existing code (needs investigation)

	modified:   src/main/java/edu/ucla/sspace/graph/GraphIO.java

- Tweaked logging

	modified:   src/main/java/edu/ucla/sspace/graph/LinkClustering.java

- Made thread count based on processors instead of fixed

	new file:   src/main/java/edu/ucla/sspace/graph/SimpleWeightedDirectedTypedEdge.java
	new file:   src/main/java/edu/ucla/sspace/graph/SimpleWeightedTypedEdge.java
	new file:   src/main/java/edu/ucla/sspace/graph/SparseWeightedDirectedEdgeSet.java
	new file:   src/main/java/edu/ucla/sspace/graph/SparseWeightedDirectedTypedEdgeSet.java
	new file:   src/main/java/edu/ucla/sspace/graph/WeightedDirectedMultigraph.java
	modified:   src/main/java/edu/ucla/sspace/graph/WeightedDirectedTypedEdge.java

- Added partial support for weighted multigraphs.  More features are probably needed eventually

	modified:   src/main/java/edu/ucla/sspace/graph/io/EdgeListReader.java

- Added better logging instead of printf

	new file:   src/main/java/edu/ucla/sspace/graph/io/GraphMLReader.java

- Added initial GraphML implementation for reading large GraphML files.  Only partial support is in place

	modified:   src/main/java/edu/ucla/sspace/index/DefaultPermutationFunction.java

- Fixed outstanding bug.  Not sure how the bug was there in the first place, as
  the code was currently very broken in an odd way.

	new file:   src/main/java/edu/ucla/sspace/text/AnnotatedDocument.java

- Added support for a new document that has a creation date and a label

	new file:   src/main/java/edu/ucla/sspace/text/BufferedFileListDocumentIterator.java

- Added a new iterator that pre-caches the contents of files in a file list
  using a separate thread to cut down on disk I/O

	modified:   src/main/java/edu/ucla/sspace/text/FileDocument.java

- Added support for a document back by a file whose contents are loaded into memory on demand

	new file:   src/main/java/edu/ucla/sspace/tools/IterativeBigramExtractor.java

- Added a tool for finding statistical associations between terms in an
  iterative pair-wise manner

	new file:   src/main/java/edu/ucla/sspace/tools/LinkClusteringTool.java

- Copied over code from the SVN branch for running link clustering from a jar

	modified:   src/main/java/edu/ucla/sspace/util/CombinedIterator.java

- Corrected the Exception to be thrown in remove()

	modified:   src/main/java/edu/ucla/sspace/util/HashMultiMap.java

- Correct a few errors in removing keys during iterator

- Fixed a bug where null was returned instead of the empty set

	new file:   src/main/java/edu/ucla/sspace/util/KrippendorffsAlpha.java

- Added a partial implementation of Krippendorff's alpha for ordinal-valued data

	modified:   src/main/java/edu/ucla/sspace/util/MultiMap.java

- Clarified the javadoc

	modified:   src/main/java/edu/ucla/sspace/util/ObjectCounter.java

- Implemented max() and min()

	modified:   src/main/java/edu/ucla/sspace/util/Pair.java

- Made Serializable

	modified:   src/main/java/edu/ucla/sspace/util/SetDecorator.java

- Clarified javadoc

	new file:   src/test/java/edu/ucla/sspace/graph/ChineseWhispersTest.java
	new file:   src/test/java/edu/ucla/sspace/graph/SparseWeightedDirectedTypedEdgeSetTest.java
	new file:   src/test/java/edu/ucla/sspace/graph/WeightedDirectedMultigraphTest.java

- More unit tests

	modified:   src/test/java/edu/ucla/sspace/index/DefaultPermutationFunctionTest.java

- Added some debugging output
	modified:   pom.xml

- Added support for picking up the *Tests.java unit tests

	modified:   src/main/java/edu/ucla/sspace/common/statistics/LogLikelihoodTest.java

- Removed dead code
Compile fixes for unit tests
Merge branch 'master' of https://github.com/fozziethebeat/S-Space into jurgens-updates
Fixed type erasure issue with DynamicGraph (hopefully); moved graph package back into main code line
Fixed generics-compilation issue for non OS X systems
moved graph tests back into main code line
modified unit test regex to pick up missing tests
added unit test that shows Spearman's rho is broken; fix is still in progress.
bumping version number to 2.0.1
Serializablility additions and minor bug and javadoc fixes

	modified:   pom.xml

- bumping version to 2.0.2

	modified:   src/main/java/edu/ucla/sspace/graph/UndirectedMultigraph.java
	modified:   src/main/java/edu/ucla/sspace/index/RandomOrthogonalVectorGenerator.java
	modified:   src/main/java/edu/ucla/sspace/mains/GenericMain.java

- javadoc improvements

	modified:   src/main/java/edu/ucla/sspace/matrix/ArrayMatrix.java
	modified:   src/main/java/edu/ucla/sspace/matrix/AtomicGrowingMatrix.java
	modified:   src/main/java/edu/ucla/sspace/matrix/AtomicGrowingSparseHashMatrix.java
	modified:   src/main/java/edu/ucla/sspace/matrix/AtomicGrowingSparseMatrix.java
	modified:   src/main/java/edu/ucla/sspace/matrix/CellMaskedMatrix.java
	modified:   src/main/java/edu/ucla/sspace/matrix/CellMaskedSparseMatrix.java
	modified:   src/main/java/edu/ucla/sspace/matrix/DiagonalMatrix.java
	modified:   src/main/java/edu/ucla/sspace/matrix/GrowingSparseMatrix.java
	modified:   src/main/java/edu/ucla/sspace/matrix/ListMatrix.java
	modified:   src/main/java/edu/ucla/sspace/matrix/MatrixFile.java
	modified:   src/main/java/edu/ucla/sspace/matrix/RowMaskedMatrix.java
	modified:   src/main/java/edu/ucla/sspace/matrix/RowScaledMatrix.java
	modified:   src/main/java/edu/ucla/sspace/matrix/RowScaledSparseMatrix.java
	modified:   src/main/java/edu/ucla/sspace/matrix/SimpleEntry.java
	modified:   src/main/java/edu/ucla/sspace/matrix/SparseHashMatrix.java
	modified:   src/main/java/edu/ucla/sspace/matrix/SparseListMatrix.java
	modified:   src/main/java/edu/ucla/sspace/matrix/SparseRowMaskedMatrix.java
	modified:   src/main/java/edu/ucla/sspace/matrix/SynchronizedMatrix.java
	modified:   src/main/java/edu/ucla/sspace/matrix/SynchronizedSparseMatrix.java
	modified:   src/main/java/edu/ucla/sspace/matrix/TransposedMatrix.java
	modified:   src/main/java/edu/ucla/sspace/matrix/YaleSparseMatrix.java

- Made classes serializable where appropriate

	modified:   src/main/java/edu/ucla/sspace/text/StringUtils.java

- Double checked the & replacement

	modified:   src/main/java/edu/ucla/sspace/tools/SemanticSpaceExplorer.java

- SSE now supports multi-token queries for nearest neighbors

	modified:   src/main/java/edu/ucla/sspace/util/PartitioningNearestNeighborFinder.java

Fixed race condition