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marf-cvs Digest, Vol 14, Issue 1

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      The MARF CVS Commit Log Digest
      Dispatched daily or when the size reaches 150k
      ----------------------------------------------

      Today's Topics:

      1. marf/src/marf/Storage ByteArrayFileReader.java, 1.1, 1.2
      Cluster.java, 1.15, 1.16 Database.java, 1.10, 1.11
      FeatureSet.java, 1.16, 1.17 ISampleLoader.java, 1.13, 1.14
      IStorageManager.java, 1.11, 1.12 ITrainingSample.java, 1.1, 1.2
      MARFAudioFileFormat.java, 1.13, 1.14 ModuleParams.java, 1.18,
      1.19 ResultSet.java, 1.21, 1.22 Sample.java, 1.47, 1.48
      SampleLoader.java, 1.27, 1.28 SampleLoaderFactory.java, 1.2, 1.3
      StorageManager.java, 1.31, 1.32 TrainingSample.java, 1.11, 1.12
      (Serguei A. Mokhov)
      2. marf/src/marf/Classification/RandomClassification
      RandomClassification.java, 1.20, 1.21 (Serguei A. Mokhov)
      3. marf/src/marf/Classification/Similarity
      CosineSimilarityMeasure.java, 1.2, 1.3 (Serguei A. Mokhov)
      4. marf/src/marf/Classification/NeuralNetwork Layer.java, 1.9,
      1.10 NeuralNetwork.java, 1.59, 1.60 Neuron.java, 1.18, 1.19
      (Serguei A. Mokhov)
      5. marf/src/marf/Classification/Distance ChebyshevDistance.java,
      1.18, 1.19 DiffDistance.java, 1.10, 1.11 Distance.java, 1.34,
      1.35 EuclideanDistance.java, 1.20, 1.21 HammingDistance.java,
      1.1, 1.2 MinkowskiDistance.java, 1.11, 1.12 (Serguei A. Mokhov)
      6. marf/src/marf Configuration.java, 1.2, 1.3 MARF.java, 1.109,
      1.110 Version.java, 1.5, 1.6 (Serguei A. Mokhov)
      7. marf/src/marf/gui/util BorderPanel.java,1.9,1.10
      (Serguei A. Mokhov)
      8. marf/src/marf/Classification Classification.java, 1.46, 1.47
      ClassificationFactory.java, 1.4, 1.5 (Serguei A. Mokhov)
      9. marf/src/marf/gui GUIException.java, 1.1, 1.2
      Spectrogram.java, 1.31, 1.32 (Serguei A. Mokhov)
      10. marf/src/marf/Classification/Stochastic Stochastic.java,
      1.25, 1.26 ZipfLaw.java, 1.31, 1.32 (Serguei A. Mokhov)
      11. marf/doc/src Makefile,1.8,1.9 (Serguei A. Mokhov)
      12. marf/src Makefile,1.81,1.82 test.java,1.54,1.55
      (Serguei A. Mokhov)
      13. marf/doc/src/tex Makefile, 1.29, 1.30
      lang-ident-app-usage.tex, 1.2, 1.3 legal.tex, 1.12, 1.13
      probabilistic-parsing-app-usage.tex, 1.2, 1.3 (Serguei A. Mokhov)
      14. marf/src/marf/nlp/Parsing/GrammarCompiler
      GrammarAnalyzer.java, 1.23, 1.24 (Serguei A. Mokhov)
      15. www index.html,1.80,1.81 update.sh,1.36,1.37 (Serguei A. Mokhov)
      16. marf/src/tools revision-check.sh, 1.10, 1.11 serialverupdate,
      1.4, 1.5 (Serguei A. Mokhov)
      17. marf/src/marf/nlp/Parsing Compiler.java, 1.16, 1.17
      CompilerError.java, 1.18, 1.19 GenericLexicalAnalyzer.java, 1.17,
      1.18 LexicalAnalyzer.java, 1.20, 1.21 LexicalError.java, 1.19,
      1.20 Parser.java, 1.24, 1.25 SymDataType.java, 1.10, 1.11
      SymTabEntry.java, 1.12, 1.13 SymbolTable.java, 1.17, 1.18
      SyntaxError.java, 1.20, 1.21 Token.java, 1.21, 1.22
      TokenSubType.java, 1.15, 1.16 TokenType.java, 1.15, 1.16
      (Serguei A. Mokhov)
      18. apps/TestFilters Makefile, 1.17, 1.18 TestFilters.jpx, 1.4,
      1.5 (Serguei A. Mokhov)
      19. apps/TestLoaders Makefile,1.11,1.12 (Serguei A. Mokhov)
      20. apps/TestLPC Makefile,1.15,1.16 (Serguei A. Mokhov)
      21. apps/ProbabilisticParsingApp Makefile, 1.34, 1.35
      ProbabilisticParsingApp.java, 1.36, 1.37 testing.sh, 1.38, 1.39
      (Serguei A. Mokhov)
      22. apps/ZipfLawApp Makefile, 1.25, 1.26 ZipfLaw.java, 1.28, 1.29
      testing.sh, 1.11, 1.12 (Serguei A. Mokhov)
      23. marf COPYRIGHT, 1.6, 1.7 Makefile, 1.25, 1.26 marf.jpx, 1.9,
      1.10 (Serguei A. Mokhov)


      ----------------------------------------------------------------------

      Message: 1
      Date: Sun, 23 Dec 2007 06:29:48 +0000
      From: "Serguei A. Mokhov" <mokhov@...>
      Subject: [marf-cvs] marf/src/marf/Storage ByteArrayFileReader.java,
      1.1, 1.2 Cluster.java, 1.15, 1.16 Database.java, 1.10, 1.11
      FeatureSet.java, 1.16, 1.17 ISampleLoader.java, 1.13, 1.14
      IStorageManager.java, 1.11, 1.12 ITrainingSample.java, 1.1, 1.2
      MARFAudioFileFormat.java, 1.13, 1.14 ModuleParams.java, 1.18, 1.19
      ResultSet.java, 1.21, 1.22 Sample.java, 1.47, 1.48 SampleLoader.java,
      1.27, 1.28 SampleLoaderFactory.java, 1.2, 1.3 StorageManager.java,
      1.31, 1.32 TrainingSample.java, 1.11, 1.12
      To: marf-cvs@...
      Message-ID: <E1J6KLc-0001Un-Db@...>

      Update of /cvsroot/marf/marf/src/marf/Storage
      In directory sc8-pr-cvs16.sourceforge.net:/tmp/cvs-serv8220/Storage

      Modified Files:
      ByteArrayFileReader.java Cluster.java Database.java
      FeatureSet.java ISampleLoader.java IStorageManager.java
      ITrainingSample.java MARFAudioFileFormat.java
      ModuleParams.java ResultSet.java Sample.java SampleLoader.java
      SampleLoaderFactory.java StorageManager.java
      TrainingSample.java
      Log Message:
      Primarily correct spelling mistakes comments. Massage/clean up some other
      comment-related material. Apply some other formatting fixes.

      Index: ModuleParams.java
      ===================================================================
      RCS file: /cvsroot/marf/marf/src/marf/Storage/ModuleParams.java,v
      retrieving revision 1.18
      retrieving revision 1.19
      diff -C2 -d -r1.18 -r1.19
      *** ModuleParams.java 5 Aug 2006 03:54:56 -0000 1.18
      --- ModuleParams.java 23 Dec 2007 06:29:46 -0000 1.19
      ***************
      *** 101,105 ****
      /**
      * Overwrites any possible previous value for a given module with a new one.
      ! * @param poParams Vector of paramaters
      * @param piModuleType the module these parameters are for
      * @throws IllegalArgumentException if the parameters vector is null or module type is invalid
      --- 101,105 ----
      /**
      * Overwrites any possible previous value for a given module with a new one.
      ! * @param poParams Vector of parameters
      * @param piModuleType the module these parameters are for
      * @throws IllegalArgumentException if the parameters vector is null or module type is invalid
      ***************
      *** 133,137 ****
      /**
      * Appends params vector to whatever there possibly was.
      ! * @param poParams Vector of paramaters
      * @param piModuleType the module these parameters are for
      * @throws IllegalArgumentException if module type is invalid
      --- 133,137 ----
      /**
      * Appends params vector to whatever there possibly was.
      ! * @param poParams Vector of parameters
      * @param piModuleType the module these parameters are for
      * @throws IllegalArgumentException if module type is invalid
      ***************
      *** 188,192 ****
      * Returns for a given module it's parameters vector.
      * @param piModuleType module type to get parameters for
      ! * @return Vector of paramaters
      * @throws IllegalArgumentException if module type is invalid
      */
      --- 188,192 ----
      * Returns for a given module it's parameters vector.
      * @param piModuleType module type to get parameters for
      ! * @return Vector of parameters
      * @throws IllegalArgumentException if module type is invalid
      */

      Index: Database.java
      ===================================================================
      RCS file: /cvsroot/marf/marf/src/marf/Storage/Database.java,v
      retrieving revision 1.10
      retrieving revision 1.11
      diff -C2 -d -r1.10 -r1.11
      *** Database.java 2 Jan 2006 22:24:00 -0000 1.10
      --- Database.java 23 Dec 2007 06:29:46 -0000 1.11
      ***************
      *** 103,107 ****

      /**
      ! * Implementaion of back-synchronization of Database loaded object.
      * @since 0.3.0.5
      */
      --- 103,107 ----

      /**
      ! * Implementation of back-synchronization of Database loaded object.
      * @since 0.3.0.5
      */
      ***************
      *** 117,121 ****

      /**
      ! * Default implementation of the toString() for all stoage
      * manager derivatives.
      * @see java.lang.Object#toString()
      --- 117,121 ----

      /**
      ! * Default implementation of the toString() for all storage
      * manager derivatives.
      * @see java.lang.Object#toString()
      ***************
      *** 131,135 ****

      /**
      ! * Implementes Cloneable interface for the Database object.
      * @see java.lang.Object#clone()
      * @since 0.3.0.5
      --- 131,135 ----

      /**
      ! * Implements Cloneable interface for the Database object.
      * @see java.lang.Object#clone()
      * @since 0.3.0.5

      Index: ResultSet.java
      ===================================================================
      RCS file: /cvsroot/marf/marf/src/marf/Storage/ResultSet.java,v
      retrieving revision 1.21
      retrieving revision 1.22
      diff -C2 -d -r1.21 -r1.22
      *** ResultSet.java 10 Jul 2006 16:28:38 -0000 1.21
      --- ResultSet.java 23 Dec 2007 06:29:46 -0000 1.22
      ***************
      *** 32,36 ****
      /**
      * Distances from other samples and other stats or
      ! * probabilities and likelyhood (growable and shrinkable).
      */
      protected Vector oResultSet = null;
      --- 32,36 ----
      /**
      * Distances from other samples and other stats or
      ! * probabilities and likelihood (growable and shrinkable).
      */
      protected Vector oResultSet = null;
      ***************
      *** 229,233 ****
      * Add result to the result set.
      * @param piID subject ID recognized
      ! * @param pdOutcome outcome of the recongnition distance or likelyhood
      * @param pstrDescription textual description of the result
      */
      --- 229,233 ----
      * Add result to the result set.
      * @param piID subject ID recognized
      ! * @param pdOutcome outcome of the recognition distance or likelihood
      * @param pstrDescription textual description of the result
      */
      ***************
      *** 244,248 ****
      * on the two parameters.
      * @param piID subject ID recognized
      ! * @param pdOutcome outcome of the recongnition distance or likelyhood
      */
      public final void addResult(int piID, double pdOutcome)
      --- 244,248 ----
      * on the two parameters.
      * @param piID subject ID recognized
      ! * @param pdOutcome outcome of the recognition distance or likelihood
      */
      public final void addResult(int piID, double pdOutcome)
      ***************
      *** 259,263 ****
      * Add result to the result set based on already pre-constructed
      * object.
      ! * @param poResult Result object prepared ouside
      * @throws IllegalArgumentException of the parameter is null
      */
      --- 259,263 ----
      * Add result to the result set based on already pre-constructed
      * object.
      ! * @param poResult Result object prepared outside
      * @throws IllegalArgumentException of the parameter is null
      */
      ***************
      *** 333,337 ****
      /*
      * Be pessimistic about what can be done with the
      ! * retured result set vector reference outside of this.
      * Thus, don't trust the client code anymore to keep
      * the stuff unmodified (i.e. adding/deleting new records)
      --- 333,337 ----
      /*
      * Be pessimistic about what can be done with the
      ! * returned result set vector reference outside of this.
      * Thus, don't trust the client code anymore to keep
      * the stuff unmodified (i.e. adding/deleting new records)
      ***************
      *** 396,400 ****
      * Allows querying the sort mode the result set
      * may be currently sorted in accordance with.
      ! * @return the curren sort mode
      * @since 0.3.0.5
      * @see #UNSORTED
      --- 396,400 ----
      * Allows querying the sort mode the result set
      * may be currently sorted in accordance with.
      ! * @return the current sort mode
      * @since 0.3.0.5
      * @see #UNSORTED

      Index: Cluster.java
      ===================================================================
      RCS file: /cvsroot/marf/marf/src/marf/Storage/Cluster.java,v
      retrieving revision 1.15
      retrieving revision 1.16
      diff -C2 -d -r1.15 -r1.16
      *** Cluster.java 5 Aug 2007 22:01:32 -0000 1.15
      --- Cluster.java 23 Dec 2007 06:29:46 -0000 1.16
      ***************
      *** 69,73 ****

      /**
      ! * Checks existance of the file in the training set.
      * Serves as an indication that we already trained on the given file.
      * @param pstrFilename filename to check
      --- 69,73 ----

      /**
      ! * Checks existence of the file in the training set.
      * Serves as an indication that we already trained on the given file.
      * @param pstrFilename filename to check

      Index: SampleLoader.java
      ===================================================================
      RCS file: /cvsroot/marf/marf/src/marf/Storage/SampleLoader.java,v
      retrieving revision 1.27
      retrieving revision 1.28
      diff -C2 -d -r1.27 -r1.28
      *** SampleLoader.java 20 Feb 2007 19:34:26 -0000 1.27
      --- SampleLoader.java 23 Dec 2007 06:29:46 -0000 1.28
      ***************
      *** 165,168 ****
      --- 165,169 ----
      * @see marf.Storage.ISampleLoader#saveSample(byte[])
      * @since 0.3.0.6
      + * @throws NotImplementedException incomplete
      */
      public void saveSample(byte[] patFileData)

      Index: SampleLoaderFactory.java
      ===================================================================
      RCS file: /cvsroot/marf/marf/src/marf/Storage/SampleLoaderFactory.java,v
      retrieving revision 1.2
      retrieving revision 1.3
      diff -C2 -d -r1.2 -r1.3
      *** SampleLoaderFactory.java 4 Feb 2007 07:51:29 -0000 1.2
      --- SampleLoaderFactory.java 23 Dec 2007 06:29:46 -0000 1.3
      ***************
      *** 42,46 ****
      * @return a reference to the instance of the created sample loader
      * @throws InvalidSampleFormatException if the indicated module is
      ! * uknown or could not be loaded due sample format mismatch
      *
      * @see MARF#WAV
      --- 42,46 ----
      * @return a reference to the instance of the created sample loader
      * @throws InvalidSampleFormatException if the indicated module is
      ! * unknown or could not be loaded due sample format mismatch
      *
      * @see MARF#WAV
      ***************
      *** 78,82 ****
      * @return a reference to the instance of the created sample loader
      * @throws InvalidSampleFormatException if the indicated module is
      ! * uknown or could not be loaded due sample format mismatch
      *
      * @see MARF#WAV
      --- 78,82 ----
      * @return a reference to the instance of the created sample loader
      * @throws InvalidSampleFormatException if the indicated module is
      ! * unknown or could not be loaded due sample format mismatch
      *
      * @see MARF#WAV

      Index: StorageManager.java
      ===================================================================
      RCS file: /cvsroot/marf/marf/src/marf/Storage/StorageManager.java,v
      retrieving revision 1.31
      retrieving revision 1.32
      diff -C2 -d -r1.31 -r1.32
      *** StorageManager.java 3 Aug 2006 17:55:54 -0000 1.31
      --- StorageManager.java 23 Dec 2007 06:29:46 -0000 1.32
      ***************
      *** 319,323 ****
      /**
      * Implements object dump in GZIP-compressed form. Attempts
      ! * to save internal object reference to the generater/specified filename
      * @throws StorageException in case of I/O or otherwise error during object dump
      * @since 0.3.0
      --- 319,323 ----
      /**
      * Implements object dump in GZIP-compressed form. Attempts
      ! * to save internal object reference to the generated/specified filename
      * @throws StorageException in case of I/O or otherwise error during object dump
      * @since 0.3.0
      ***************
      *** 347,351 ****
      /**
      * Implements object dump in plain binary form without compression. Attempts
      ! * to save internal object reference to the generater/specified filename
      * @throws StorageException in case of I/O or otherwise error during object dump
      * @since 0.3.0
      --- 347,351 ----
      /**
      * Implements object dump in plain binary form without compression. Attempts
      ! * to save internal object reference to the generated/specified filename
      * @throws StorageException in case of I/O or otherwise error during object dump
      * @since 0.3.0
      ***************
      *** 485,494 ****
      /**
      * Implements object loading from plain binary form without compression. Attempts
      ! * to load internal object reference with the generater/specified filename. After,
      * calls <code>backSynchronizeObject()</code> so the actual mode can reset back
      * references in its own data structures. If the file that we attempt to load
      * did not exist, it will be created.
      *
      ! * @throws StorageException in case of I/O or otherwise error during object retoration
      * @since 0.3.0
      * @see #backSynchronizeObject()
      --- 485,494 ----
      /**
      * Implements object loading from plain binary form without compression. Attempts
      ! * to load internal object reference with the generated/specified filename. After,
      * calls <code>backSynchronizeObject()</code> so the actual mode can reset back
      * references in its own data structures. If the file that we attempt to load
      * did not exist, it will be created.
      *
      ! * @throws StorageException in case of I/O or otherwise error during object restoration
      * @since 0.3.0
      * @see #backSynchronizeObject()
      ***************
      *** 548,557 ****
      /**
      * Implements object loading from GZIP-compressed binary form. Attempts
      ! * to load internal object reference with the generater/specified filename. After,
      * calls <code>backSynchronizeObject()</code> so the actual mode can reset back
      * references in its own data structures. If the file that we attempt to load
      * did not exist, it will be created.
      *
      ! * @throws StorageException in case of I/O or otherwise error during object retoration
      * @since 0.3.0
      * @see #backSynchronizeObject()
      --- 548,557 ----
      /**
      * Implements object loading from GZIP-compressed binary form. Attempts
      ! * to load internal object reference with the generated/specified filename. After,
      * calls <code>backSynchronizeObject()</code> so the actual mode can reset back
      * references in its own data structures. If the file that we attempt to load
      * did not exist, it will be created.
      *
      ! * @throws StorageException in case of I/O or otherwise error during object restoration
      * @since 0.3.0
      * @see #backSynchronizeObject()
      ***************
      *** 795,799 ****
      }

      ! // Should never happend.
      catch(CloneNotSupportedException e)
      {
      --- 795,799 ----
      }

      ! // Should never happen.
      catch(CloneNotSupportedException e)
      {
      ***************
      *** 832,836 ****

      /**
      ! * Default implementation of the toString() for all stoage
      * manager derivatives.
      * @see java.lang.Object#toString()
      --- 832,836 ----

      /**
      ! * Default implementation of the toString() for all storage
      * manager derivatives.
      * @see java.lang.Object#toString()

      Index: Sample.java
      ===================================================================
      RCS file: /cvsroot/marf/marf/src/marf/Storage/Sample.java,v
      retrieving revision 1.47
      retrieving revision 1.48
      diff -C2 -d -r1.47 -r1.48
      *** Sample.java 30 Dec 2006 04:40:57 -0000 1.47
      --- Sample.java 23 Dec 2007 06:29:46 -0000 1.48
      ***************
      *** 32,36 ****

      /**
      ! * Groupping of file format data.
      * @since 0.3.0.2
      */
      --- 32,36 ----

      /**
      ! * Grouping of file format data.
      * @since 0.3.0.2
      */
      ***************
      *** 148,152 ****
      * it's cloned. Only the data and format are copied.
      *
      ! * @param poSample sample objec to copy data off from
      * @throws InvalidSampleFormatException if the parameter format is invalid
      * @since 0.3.0.5
      --- 148,152 ----
      * it's cloned. Only the data and format are copied.
      *
      ! * @param poSample sample object to copy data off from
      * @throws InvalidSampleFormatException if the parameter format is invalid
      * @since 0.3.0.5
      ***************
      *** 351,355 ****
      /**
      * Returns textual representation of the sample object.
      ! * The contents is the format and lengthon the first line, and then
      * a column of data.
      *
      --- 351,355 ----
      /**
      * Returns textual representation of the sample object.
      ! * The contents is the format and length on the first line, and then
      * a column of data.
      *

      Index: ByteArrayFileReader.java
      ===================================================================
      RCS file: /cvsroot/marf/marf/src/marf/Storage/ByteArrayFileReader.java,v
      retrieving revision 1.1
      retrieving revision 1.2
      diff -C2 -d -r1.1 -r1.2
      *** ByteArrayFileReader.java 10 Sep 2006 01:04:13 -0000 1.1
      --- ByteArrayFileReader.java 23 Dec 2007 06:29:45 -0000 1.2
      ***************
      *** 1,5 ****
      - /**
      - *
      - */
      package marf.Storage;

      --- 1,2 ----
      ***************
      *** 14,27 ****

      import marf.util.Arrays;


      /**
      ! * Reads in a file contents into a byte array buffers.
      ! * @author serguei
      ! *
      */
      public class ByteArrayFileReader
      {
      !
      public static final int DEFAULT_NUMBER_OF_BUFFERS = 100;

      --- 11,32 ----

      import marf.util.Arrays;
      + import marf.util.MARFRuntimeException;
      + import marf.util.NotImplementedException;


      /**
      ! * <p>Reads in a file contents into a byte array buffers.</p>
      ! *
      ! * $Id$
      ! *
      ! * @author Serguei Mokhov
      ! * @version $Revision$
      ! * @since 0.3.0.6
      */
      public class ByteArrayFileReader
      {
      ! /**
      ! *
      ! */
      public static final int DEFAULT_NUMBER_OF_BUFFERS = 100;

      ***************
      *** 32,39 ****
      --- 37,58 ----


      + /**
      + *
      + */
      protected byte[][] attBuffers = new byte[DEFAULT_NUMBER_OF_BUFFERS][];

      + /**
      + *
      + */
      protected int iFileSize = 0;
      +
      + /**
      + *
      + */
      protected int iBufferCount = 0;
      +
      + /**
      + *
      + */
      protected int iBufferSize = DEFAULT_BUFFER_SIZE;

      ***************
      *** 44,50 ****
      {
      super();
      - // TODO Auto-generated constructor stub
      }

      public ByteArrayFileReader(String pstrFilename)
      throws FileNotFoundException, IOException
      --- 63,73 ----
      {
      super();
      }

      + /**
      + * @param pstrFilename
      + * @throws FileNotFoundException
      + * @throws IOException
      + */
      public ByteArrayFileReader(String pstrFilename)
      throws FileNotFoundException, IOException
      ***************
      *** 53,56 ****
      --- 76,84 ----
      }

      + /**
      + * @param poFile
      + * @throws FileNotFoundException
      + * @throws IOException
      + */
      public ByteArrayFileReader(File poFile)
      throws FileNotFoundException, IOException
      ***************
      *** 59,67 ****
      }

      public ByteArrayFileReader(URI poURI)
      {
      read(poURI);
      }
      !
      public ByteArrayFileReader(InputStream poInputStream)
      throws IOException
      --- 87,102 ----
      }

      + /**
      + * @param poURI
      + */
      public ByteArrayFileReader(URI poURI)
      {
      read(poURI);
      }
      !
      ! /**
      ! * @param poInputStream
      ! * @throws IOException
      ! */
      public ByteArrayFileReader(InputStream poInputStream)
      throws IOException
      ***************
      *** 70,78 ****
      }

      public ByteArrayFileReader(Reader poReader)
      {
      read(poReader);
      }
      !
      public byte[] read(File poFile)
      throws FileNotFoundException, IOException
      --- 105,122 ----
      }

      + /**
      + * @param poReader
      + */
      public ByteArrayFileReader(Reader poReader)
      {
      read(poReader);
      }
      !
      ! /**
      ! * @param poFile
      ! * @return
      ! * @throws FileNotFoundException
      ! * @throws IOException
      ! */
      public byte[] read(File poFile)
      throws FileNotFoundException, IOException
      ***************
      *** 80,99 ****
      return read(new BufferedInputStream(new FileInputStream(poFile)));
      }
      !
      public byte[] read(URI poURI)
      {
      ! return null;
      }

      public byte[] read(InputStream poInputStream)
      throws IOException
      {
      boolean bEOF = false;
      !
      do
      {
      this.attBuffers[this.iBufferCount] = new byte[this.iBufferSize];
      int iBytesRead = poInputStream.read(this.attBuffers[this.iBufferCount++]);
      !
      if(iBytesRead < 0)
      {
      --- 124,153 ----
      return read(new BufferedInputStream(new FileInputStream(poFile)));
      }
      !
      ! /**
      ! * @param poURI unused
      ! * @return
      ! * @throws NotImplementedException
      ! */
      public byte[] read(URI poURI)
      {
      ! throw new NotImplementedException();
      }

      + /**
      + * @param poInputStream
      + * @return
      + * @throws IOException
      + */
      public byte[] read(InputStream poInputStream)
      throws IOException
      {
      boolean bEOF = false;
      !
      do
      {
      this.attBuffers[this.iBufferCount] = new byte[this.iBufferSize];
      int iBytesRead = poInputStream.read(this.attBuffers[this.iBufferCount++]);
      !
      if(iBytesRead < 0)
      {
      ***************
      *** 101,105 ****
      break;
      }
      !
      if(iBytesRead < this.iBufferSize)
      {
      --- 155,159 ----
      break;
      }
      !
      if(iBytesRead < this.iBufferSize)
      {
      ***************
      *** 108,112 ****
      break;
      }
      !
      this.iFileSize += this.iBufferSize;
      }
      --- 162,166 ----
      break;
      }
      !
      this.iFileSize += this.iBufferSize;
      }
      ***************
      *** 114,121 ****

      poInputStream.close();
      !
      return toByteArray();
      }

      public byte[] read(Reader poReader)
      {
      --- 168,179 ----

      poInputStream.close();
      !
      return toByteArray();
      }

      + /**
      + * @param poReader
      + * @return
      + */
      public byte[] read(Reader poReader)
      {
      ***************
      *** 123,131 ****
      }

      public byte[] toByteArray()
      {
      if(this.iFileSize == 0)
      {
      ! throw new RuntimeException("No file has been read yet.");
      }

      --- 181,192 ----
      }

      + /**
      + * @return
      + */
      public byte[] toByteArray()
      {
      if(this.iFileSize == 0)
      {
      ! throw new MARFRuntimeException("No file has been read yet.");
      }


      Index: ISampleLoader.java
      ===================================================================
      RCS file: /cvsroot/marf/marf/src/marf/Storage/ISampleLoader.java,v
      retrieving revision 1.13
      retrieving revision 1.14
      diff -C2 -d -r1.13 -r1.14
      *** ISampleLoader.java 20 Feb 2007 19:34:26 -0000 1.13
      --- ISampleLoader.java 23 Dec 2007 06:29:46 -0000 1.14
      ***************
      *** 7,11 ****

      /**
      ! * <p>Common samle loading interface.
      *
      * Must be overridden by a concrete sample loader. Derivatives
      --- 7,11 ----

      /**
      ! * <p>Common sample loading interface.
      *
      * Must be overridden by a concrete sample loader. Derivatives
      ***************
      *** 55,59 ****
      *
      * In 0.3.0.6 was renamed from <code>readAudioData()</code> to <code>readSampleData()</code>
      ! * to accomodate non-audio loaders. <code>readAudioData()</code> was moved down
      * to <code>AudioSampleLoader</code> as a wrapper for this method for some
      * semblance of backwards compatibility.
      --- 55,59 ----
      *
      * In 0.3.0.6 was renamed from <code>readAudioData()</code> to <code>readSampleData()</code>
      ! * to accommodate non-audio loaders. <code>readAudioData()</code> was moved down
      * to <code>AudioSampleLoader</code> as a wrapper for this method for some
      * semblance of backwards compatibility.
      ***************
      *** 71,75 ****
      *
      * In 0.3.0.6 this method was renamed from <code>writeAudioData()</code>
      ! * to <code>writeSampleData()</code> to accomodate non-audio loaders.
      * <code>writeAudioData()</code> was moved down to <code>AudioSampleLoader</code>
      * as a wrapper for this method for some semblance of backwards compatibility.
      --- 71,75 ----
      *
      * In 0.3.0.6 this method was renamed from <code>writeAudioData()</code>
      ! * to <code>writeSampleData()</code> to accommodate non-audio loaders.
      * <code>writeAudioData()</code> was moved down to <code>AudioSampleLoader</code>
      * as a wrapper for this method for some semblance of backwards compatibility.
      ***************
      *** 86,90 ****
      /**
      * Prime SampleLoader interface.
      ! * Must be overriden by a concrete loader that knows how to load a specific sample format.
      * @param poInFile file object a sample to be read from
      * @return Sample object reference
      --- 86,90 ----
      /**
      * Prime SampleLoader interface.
      ! * Must be overridden by a concrete loader that knows how to load a specific sample format.
      * @param poInFile file object a sample to be read from
      * @return Sample object reference
      ***************
      *** 125,129 ****
      /**
      * Prime SampleLoader interface.
      ! * Must be overriden by a concrete loader that knows how to save a specific sample.
      * @param poOutFile File object of a sample to be saved to
      * @throws StorageException if there was an error saving the sample
      --- 125,129 ----
      /**
      * Prime SampleLoader interface.
      ! * Must be overridden by a concrete loader that knows how to save a specific sample.
      * @param poOutFile File object of a sample to be saved to
      * @throws StorageException if there was an error saving the sample

      Index: FeatureSet.java
      ===================================================================
      RCS file: /cvsroot/marf/marf/src/marf/Storage/FeatureSet.java,v
      retrieving revision 1.16
      retrieving revision 1.17
      diff -C2 -d -r1.16 -r1.17
      *** FeatureSet.java 5 Aug 2007 22:01:33 -0000 1.16
      --- FeatureSet.java 23 Dec 2007 06:29:46 -0000 1.17
      ***************
      *** 263,267 ****

      /**
      ! * Implementes Cloneable interface for the FeatureSet object.
      * Performs a "deep" copy of this object including all the feature vectors.
      * @see java.lang.Object#clone()
      --- 263,267 ----

      /**
      ! * Implements Cloneable interface for the FeatureSet object.
      * Performs a "deep" copy of this object including all the feature vectors.
      * @see java.lang.Object#clone()

      Index: IStorageManager.java
      ===================================================================
      RCS file: /cvsroot/marf/marf/src/marf/Storage/IStorageManager.java,v
      retrieving revision 1.11
      retrieving revision 1.12
      diff -C2 -d -r1.11 -r1.12
      *** IStorageManager.java 27 Dec 2005 23:55:30 -0000 1.11
      --- IStorageManager.java 23 Dec 2007 06:29:46 -0000 1.12
      ***************
      *** 91,95 ****

      /**
      ! * An object must know how retore its non-transient data structures from a file.
      * Options are: object serialization (possibly compressed), XML, CSV, HTML, and SQL.
      * @throws StorageException if there was a problem (re)loading the object
      --- 91,95 ----

      /**
      ! * An object must know how restore its non-transient data structures from a file.
      * Options are: object serialization (possibly compressed), XML, CSV, HTML, and SQL.
      * @throws StorageException if there was a problem (re)loading the object

      Index: ITrainingSample.java
      ===================================================================
      RCS file: /cvsroot/marf/marf/src/marf/Storage/ITrainingSample.java,v
      retrieving revision 1.1
      retrieving revision 1.2
      diff -C2 -d -r1.1 -r1.2
      *** ITrainingSample.java 5 Aug 2007 22:01:33 -0000 1.1
      --- ITrainingSample.java 23 Dec 2007 06:29:46 -0000 1.2
      ***************
      *** 3,9 ****
      import java.io.Serializable;

      /**
      ! * @author Serguei
      * @since 0.3.0.6
      */
      public interface ITrainingSample
      --- 3,16 ----
      import java.io.Serializable;

      +
      /**
      ! * <p>All training set beans should implement this interface.
      ! * </p>
      ! *
      ! * $Id$
      ! *
      ! * @author Serguei Mokhov
      * @since 0.3.0.6
      + * @version $Revision$
      */
      public interface ITrainingSample
      ***************
      *** 15,22 ****
      * @param piSubjectID
      * @return
      - * @since 0.3.0.6
      */
      ! boolean setFeatureVector(double[] padFeatureVector,
      ! String pstrFilename, int piSubjectID);

      /**
      --- 22,27 ----
      * @param piSubjectID
      * @return
      */
      ! boolean setFeatureVector(double[] padFeatureVector, String pstrFilename, int piSubjectID);

      /**
      ***************
      *** 28,33 ****
      *
      * @see #setFeatureVector(double[], String, int)
      - *
      - * @since 0.3.0.6
      */
      boolean addFeatureVector(double[] padFeatureVector, String pstrFilename, int piSubjectID);
      --- 33,36 ----
      ***************
      *** 35,51 ****
      /**
      * Sets a filename of the training sample.
      ! * Allways set the first element of the list of filenames.
      * @param pstrFilename filename to set
      */
      void setFilename(String pstrFilename);

      boolean addFilename(String pstrFilename);

      /**
      ! * Checks existance of the file in the training sample.
      * Serves as an indication that we already trained on the given file.
      * @param pstrFilename filename to check
      * @return <code>true</code> if the filename is there; <code>false</code> if not
      - * @since 0.3.0.6
      */
      boolean existsFilename(String pstrFilename);
      --- 38,57 ----
      /**
      * Sets a filename of the training sample.
      ! * Always set the first element of the list of filenames.
      * @param pstrFilename filename to set
      */
      void setFilename(String pstrFilename);

      + /**
      + * @param pstrFilename
      + * @return
      + */
      boolean addFilename(String pstrFilename);

      /**
      ! * Checks existence of the file in the training sample.
      * Serves as an indication that we already trained on the given file.
      * @param pstrFilename filename to check
      * @return <code>true</code> if the filename is there; <code>false</code> if not
      */
      boolean existsFilename(String pstrFilename);
      ***************
      *** 93,98 ****
      --- 99,110 ----
      // void setMeanVector(double[] padMeanVector);

      + /**
      + * @return
      + */
      double[] getMedianVector();

      + /**
      + * @return
      + */
      int size();
      }

      Index: TrainingSample.java
      ===================================================================
      RCS file: /cvsroot/marf/marf/src/marf/Storage/TrainingSample.java,v
      retrieving revision 1.11
      retrieving revision 1.12
      diff -C2 -d -r1.11 -r1.12
      *** TrainingSample.java 5 Aug 2007 22:01:34 -0000 1.11
      --- TrainingSample.java 23 Dec 2007 06:29:46 -0000 1.12
      ***************
      *** 38,42 ****

      /**
      ! * Array represinting either a feature vector, mean
      * vector describing the cluster, or a median vector.
      */
      --- 38,42 ----

      /**
      ! * Array representing either a feature vector, mean
      * vector describing the cluster, or a median vector.
      */
      ***************
      *** 285,289 ****
      /**
      * Simply retrieves the data vector.
      ! * Internall calls <code>getDataVector()</code>.
      * @return array of doubles representing the mean for that cluster
      * @since 0.3.0.6
      --- 285,289 ----
      /**
      * Simply retrieves the data vector.
      ! * Internally calls <code>getDataVector()</code>.
      * @return array of doubles representing the mean for that cluster
      * @since 0.3.0.6
      ***************
      *** 297,301 ****
      /**
      * Simply retrieves the data vector.
      ! * Internall calls <code>getDataVector()</code>.
      * @return array of doubles representing the mean for that cluster
      * @since 0.3.0.6
      --- 297,301 ----
      /**
      * Simply retrieves the data vector.
      ! * Internally calls <code>getDataVector()</code>.
      * @return array of doubles representing the mean for that cluster
      * @since 0.3.0.6

      Index: MARFAudioFileFormat.java
      ===================================================================
      RCS file: /cvsroot/marf/marf/src/marf/Storage/MARFAudioFileFormat.java,v
      retrieving revision 1.13
      retrieving revision 1.14
      diff -C2 -d -r1.13 -r1.14
      *** MARFAudioFileFormat.java 4 Feb 2007 07:51:29 -0000 1.13
      --- MARFAudioFileFormat.java 23 Dec 2007 06:29:46 -0000 1.14
      ***************
      *** 84,88 ****

      /**
      ! * Custom (plugin) sample format.
      * @since 0.3.0.5
      */
      --- 84,88 ----

      /**
      ! * Custom (plug-in) sample format.
      * @since 0.3.0.5
      */
      ***************
      *** 245,249 ****

      /**
      ! * In addtion to the types defined in <code>AudioFileFormat.Type</code>
      * defines MP3, MIDI, and ULAW formats and their extensions.
      *
      --- 245,249 ----

      /**
      ! * In addition to the types defined in <code>AudioFileFormat.Type</code>
      * defines MP3, MIDI, and ULAW formats and their extensions.
      *
      ***************
      *** 299,303 ****

      /**
      ! * Specifies custom plugin file.
      * @since 0.3.0.5
      */
      --- 299,303 ----

      /**
      ! * Specifies custom plug-in file.
      * @since 0.3.0.5
      */
      ***************
      *** 321,325 ****

      /**
      ! * Given valid format code returs the corresponding Type instance.
      *
      * @param piFormat the desired format code
      --- 321,325 ----

      /**
      ! * Given valid format code returns the corresponding Type instance.
      *
      * @param piFormat the desired format code




      ------------------------------

      Message: 2
      Date: Mon, 31 Dec 2007 00:17:07 +0000
      From: "Serguei A. Mokhov" <mokhov@...>
      Subject: [marf-cvs] marf/src/marf/Classification/RandomClassification
      RandomClassification.java, 1.20, 1.21
      To: marf-cvs@...
      Message-ID: <E1J98L5-0003Fw-Ng@...>

      Update of /cvsroot/marf/marf/src/marf/Classification/RandomClassification
      In directory sc8-pr-cvs16.sourceforge.net:/tmp/cvs-serv26660/Classification/RandomClassification

      Modified Files:
      RandomClassification.java
      Log Message:
      Cosmetically clean up a bit more of the code. Apply more consistently the coding conventions.
      Correct more spelling mistakes.

      Index: RandomClassification.java
      ===================================================================
      RCS file: /cvsroot/marf/marf/src/marf/Classification/RandomClassification/RandomClassification.java,v
      retrieving revision 1.20
      retrieving revision 1.21
      diff -C2 -d -r1.20 -r1.21
      *** RandomClassification.java 7 Oct 2006 19:23:28 -0000 1.20
      --- RandomClassification.java 31 Dec 2007 00:17:04 -0000 1.21
      ***************
      *** 16,20 ****
      * <p>Random Classification Module is for testing purposes.</p>
      *
      ! * <p>This represents the bottomline of the classification results.
      * All the other modules should be better than this 99% of the time.
      * If they are not, debug them.</p>
      --- 16,20 ----
      * <p>Random Classification Module is for testing purposes.</p>
      *
      ! * <p>This represents the bottom-line of the classification results.
      * All the other modules should be better than this 99% of the time.
      * If they are not, debug them.</p>
      ***************
      *** 63,67 ****
      /**
      * Picks an ID at random.
      ! * In 0.3.0.6 the generic pipelined verision of this API
      * <code>classify()</code> was refactored into the
      * <code>Classification</code>.
      --- 63,67 ----
      /**
      * Picks an ID at random.
      ! * In 0.3.0.6 the generic pipelined version of this API
      * <code>classify()</code> was refactored into the
      * <code>Classification</code>.




      ------------------------------

      Message: 3
      Date: Mon, 31 Dec 2007 00:17:07 +0000
      From: "Serguei A. Mokhov" <mokhov@...>
      Subject: [marf-cvs] marf/src/marf/Classification/Similarity
      CosineSimilarityMeasure.java, 1.2, 1.3
      To: marf-cvs@...
      Message-ID: <E1J98L6-0003GD-7P@...>

      Update of /cvsroot/marf/marf/src/marf/Classification/Similarity
      In directory sc8-pr-cvs16.sourceforge.net:/tmp/cvs-serv26660/Classification/Similarity

      Modified Files:
      CosineSimilarityMeasure.java
      Log Message:
      Cosmetically clean up a bit more of the code. Apply more consistently the coding conventions.
      Correct more spelling mistakes.

      Index: CosineSimilarityMeasure.java
      ===================================================================
      RCS file: /cvsroot/marf/marf/src/marf/Classification/Similarity/CosineSimilarityMeasure.java,v
      retrieving revision 1.2
      retrieving revision 1.3
      diff -C2 -d -r1.2 -r1.3
      *** CosineSimilarityMeasure.java 5 Aug 2007 22:01:32 -0000 1.2
      --- CosineSimilarityMeasure.java 31 Dec 2007 00:17:05 -0000 1.3
      ***************
      *** 44,49 ****
      /**
      * Classify the feature vector based on whatever
      ! * <code>distance()</code> derivatives implement.
      ! * In 0.3.0.6 the generic pipelined verision of this API
      * <code>classify()</code> was refactored into the
      * <code>Classification</code>.
      --- 44,49 ----
      /**
      * Classify the feature vector based on whatever
      ! * <code>similarity()</code> derivatives implement.
      ! * In 0.3.0.6 the generic pipelined version of this API
      * <code>classify()</code> was refactored into the
      * <code>Classification</code>.
      ***************
      *** 77,81 ****

      /*
      ! * Run through the stored training samples set (mean vetors)
      * and determine the two closest subjects to the incoming features sample
      */
      --- 77,81 ----

      /*
      ! * Run through the stored training samples set (mean vectors)
      * and determine the two closest subjects to the incoming features sample
      */




      ------------------------------

      Message: 4
      Date: Mon, 31 Dec 2007 00:17:06 +0000
      From: "Serguei A. Mokhov" <mokhov@...>
      Subject: [marf-cvs] marf/src/marf/Classification/NeuralNetwork
      Layer.java, 1.9, 1.10 NeuralNetwork.java, 1.59, 1.60 Neuron.java,
      1.18, 1.19
      To: marf-cvs@...
      Message-ID: <E1J98L6-0003GF-7j@...>

      Update of /cvsroot/marf/marf/src/marf/Classification/NeuralNetwork
      In directory sc8-pr-cvs16.sourceforge.net:/tmp/cvs-serv26660/Classification/NeuralNetwork

      Modified Files:
      Layer.java NeuralNetwork.java Neuron.java
      Log Message:
      Cosmetically clean up a bit more of the code. Apply more consistently the coding conventions.
      Correct more spelling mistakes.

      Index: Layer.java
      ===================================================================
      RCS file: /cvsroot/marf/marf/src/marf/Classification/NeuralNetwork/Layer.java,v
      retrieving revision 1.9
      retrieving revision 1.10
      diff -C2 -d -r1.9 -r1.10
      *** Layer.java 29 Jan 2007 00:42:41 -0000 1.9
      --- Layer.java 31 Dec 2007 00:17:04 -0000 1.10
      ***************
      *** 11,15 ****
      *
      * Being itself a thread, encapsulates a group of
      ! * Neuron thread comprising a neron layer of the network.
      * The actual threading is almost unimplemented yet, but the
      * class itself is properly synchronized.
      --- 11,15 ----
      *
      * Being itself a thread, encapsulates a group of
      ! * Neuron thread comprising a neuron layer of the network.
      * The actual threading is almost unimplemented yet, but the
      * class itself is properly synchronized.

      Index: Neuron.java
      ===================================================================
      RCS file: /cvsroot/marf/marf/src/marf/Classification/NeuralNetwork/Neuron.java,v
      retrieving revision 1.18
      retrieving revision 1.19
      diff -C2 -d -r1.18 -r1.19
      *** Neuron.java 5 Aug 2006 03:54:55 -0000 1.18
      --- Neuron.java 31 Dec 2007 00:17:04 -0000 1.19
      ***************
      *** 80,84 ****

      /**
      ! * Buffered weights to be comitted.
      */
      private ArrayList oWeightsBuffer = new ArrayList();
      --- 80,84 ----

      /**
      ! * Buffered weights to be committed.
      */
      private ArrayList oWeightsBuffer = new ArrayList();
      ***************
      *** 95,99 ****

      /**
      ! * Activation threshhold.
      */
      protected double dThreshold = 0.0;
      --- 95,99 ----

      /**
      ! * Activation threshold.
      */
      protected double dThreshold = 0.0;

      Index: NeuralNetwork.java
      ===================================================================
      RCS file: /cvsroot/marf/marf/src/marf/Classification/NeuralNetwork/NeuralNetwork.java,v
      retrieving revision 1.59
      retrieving revision 1.60
      diff -C2 -d -r1.59 -r1.60
      *** NeuralNetwork.java 5 Aug 2007 22:01:32 -0000 1.59
      --- NeuralNetwork.java 31 Dec 2007 00:17:04 -0000 1.60
      ***************
      *** 347,351 ****
      /**
      * Neural Network implementation of classification routine.
      ! * In 0.3.0.6 the generic pipelined verision of this API
      * <code>classify()</code> was refactored into the
      * <code>Classification</code>.
      --- 347,351 ----
      /**
      * Neural Network implementation of classification routine.
      ! * In 0.3.0.6 the generic pipelined version of this API
      * <code>classify()</code> was refactored into the
      * <code>Classification</code>.
      ***************
      *** 1307,1311 ****

      /**
      ! * Constructs our error handlier with the given writer.
      * @param poOut writer to write errors to
      */
      --- 1307,1311 ----

      /**
      ! * Constructs our error handler with the given writer.
      * @param poOut writer to write errors to
      */




      ------------------------------

      Message: 5
      Date: Mon, 31 Dec 2007 00:17:06 +0000
      From: "Serguei A. Mokhov" <mokhov@...>
      Subject: [marf-cvs] marf/src/marf/Classification/Distance
      ChebyshevDistance.java, 1.18, 1.19 DiffDistance.java, 1.10, 1.11
      Distance.java, 1.34, 1.35 EuclideanDistance.java, 1.20, 1.21
      HammingDistance.java, 1.1, 1.2 MinkowskiDistance.java, 1.11, 1.12
      To: marf-cvs@...
      Message-ID: <E1J98L6-0003Gc-Jc@...>

      Update of /cvsroot/marf/marf/src/marf/Classification/Distance
      In directory sc8-pr-cvs16.sourceforge.net:/tmp/cvs-serv26660/Classification/Distance

      Modified Files:
      ChebyshevDistance.java DiffDistance.java Distance.java
      EuclideanDistance.java HammingDistance.java
      MinkowskiDistance.java
      Log Message:
      Cosmetically clean up a bit more of the code. Apply more consistently the coding conventions.
      Correct more spelling mistakes.

      Index: ChebyshevDistance.java
      ===================================================================
      RCS file: /cvsroot/marf/marf/src/marf/Classification/Distance/ChebyshevDistance.java,v
      retrieving revision 1.18
      retrieving revision 1.19
      diff -C2 -d -r1.18 -r1.19
      *** ChebyshevDistance.java 3 Sep 2006 18:02:11 -0000 1.18
      --- ChebyshevDistance.java 31 Dec 2007 00:17:04 -0000 1.19
      ***************
      *** 46,50 ****
      --- 46,52 ----

      for(int f = 0; f < padVector1.length; f++)
      + {
      dDistance += Math.abs(padVector1[f] - padVector2[f]);
      + }

      return dDistance;

      Index: Distance.java
      ===================================================================
      RCS file: /cvsroot/marf/marf/src/marf/Classification/Distance/Distance.java,v
      retrieving revision 1.34
      retrieving revision 1.35
      diff -C2 -d -r1.34 -r1.35
      *** Distance.java 5 Aug 2007 22:01:29 -0000 1.34
      --- Distance.java 31 Dec 2007 00:17:04 -0000 1.35
      ***************
      *** 44,48 ****
      * Classify the feature vector based on whatever
      * <code>distance()</code> derivatives implement.
      ! * In 0.3.0.6 the generic pipelined verision of this API
      * <code>classify()</code> was refactored into the
      * <code>Classification</code>.
      --- 44,48 ----
      * Classify the feature vector based on whatever
      * <code>distance()</code> derivatives implement.
      ! * In 0.3.0.6 the generic pipelined version of this API
      * <code>classify()</code> was refactored into the
      * <code>Classification</code>.

      Index: MinkowskiDistance.java
      ===================================================================
      RCS file: /cvsroot/marf/marf/src/marf/Classification/Distance/MinkowskiDistance.java,v
      retrieving revision 1.11
      retrieving revision 1.12
      diff -C2 -d -r1.11 -r1.12
      *** MinkowskiDistance.java 14 Aug 2005 01:15:54 -0000 1.11
      --- MinkowskiDistance.java 31 Dec 2007 00:17:04 -0000 1.12
      ***************
      *** 10,14 ****
      * <p>Class MinkowskiDistance.</p>
      *
      ! * <p>$Id$</p>
      *
      * @author Serguei Mokhov
      --- 10,14 ----
      * <p>Class MinkowskiDistance.</p>
      *
      ! * $Id$
      *
      * @author Serguei Mokhov
      ***************
      *** 48,52 ****
      --- 48,54 ----

      if(oParams.size() > 1)
      + {
      this.r = ((Double)oParams.elementAt(1)).doubleValue();
      + }
      }
      }
      ***************
      *** 63,67 ****
      --- 65,71 ----

      for(int f = 0; f < paVector1.length; f++)
      + {
      dDistance += Math.pow(Math.abs(paVector1[f] - paVector2[f]), this.r);
      + }

      return Math.pow(dDistance, 1 / this.r);
      ***************
      *** 71,75 ****
      * Retrieves class' revision.
      * @return revision string
      ! * @since 0.3.0
      */
      public static String getMARFSourceCodeRevision()
      --- 75,79 ----
      * Retrieves class' revision.
      * @return revision string
      ! * @since 0.3.0.2
      */
      public static String getMARFSourceCodeRevision()

      Index: EuclideanDistance.java
      ===================================================================
      RCS file: /cvsroot/marf/marf/src/marf/Classification/Distance/EuclideanDistance.java,v
      retrieving revision 1.20
      retrieving revision 1.21
      diff -C2 -d -r1.20 -r1.21
      *** EuclideanDistance.java 11 Aug 2005 00:44:50 -0000 1.20
      --- EuclideanDistance.java 31 Dec 2007 00:17:04 -0000 1.21
      ***************
      *** 7,11 ****
      * <p>Class EuclideanDistance.</p>
      *
      ! * <p>$Id$</p>
      *
      * @author Stephen Sinclair
      --- 7,11 ----
      * <p>Class EuclideanDistance.</p>
      *
      ! * $Id$
      *
      * @author Stephen Sinclair
      ***************
      *** 46,50 ****
      --- 46,52 ----

      for(int f = 0; f < paVector1.length; f++)
      + {
      dDistance += (paVector1[f] - paVector2[f]) * (paVector1[f] - paVector2[f]);
      + }

      return dDistance;

      Index: HammingDistance.java
      ===================================================================
      RCS file: /cvsroot/marf/marf/src/marf/Classification/Distance/HammingDistance.java,v
      retrieving revision 1.1
      retrieving revision 1.2
      diff -C2 -d -r1.1 -r1.2
      *** HammingDistance.java 1 Apr 2007 01:04:27 -0000 1.1
      --- HammingDistance.java 31 Dec 2007 00:17:04 -0000 1.2
      ***************
      *** 30,34 ****

      /**
      ! * Indicates to compare double array elements linently
      * allowing some margin for error.
      */
      --- 30,34 ----

      /**
      ! * Indicates to compare double array elements leniently
      * allowing some margin for error.
      */
      ***************
      *** 99,103 ****
      case STRICT_BITWISE:
      {
      ! // XOR betwise each element and count how many 1's left;
      // accumulate that count in dDistance
      throw new NotImplementedException();
      --- 99,103 ----
      case STRICT_BITWISE:
      {
      ! // XOR bitwise each element and count how many 1's left;
      // accumulate that count in dDistance
      throw new NotImplementedException();

      Index: DiffDistance.java
      ===================================================================
      RCS file: /cvsroot/marf/marf/src/marf/Classification/Distance/DiffDistance.java,v
      retrieving revision 1.10
      retrieving revision 1.11
      diff -C2 -d -r1.10 -r1.11
      *** DiffDistance.java 11 Aug 2005 00:44:50 -0000 1.10
      --- DiffDistance.java 31 Dec 2007 00:17:04 -0000 1.11
      ***************
      *** 7,15 ****
      * <p>Diff-Distance Classifier.</p>
      *
      ! * <p>$Id$</p>
      *
      * @author Serguei Mokhov
      * @version $Revision$
      ! * @since 0.3.0
      */
      public class DiffDistance
      --- 7,15 ----
      * <p>Diff-Distance Classifier.</p>
      *
      ! * $Id$
      *
      * @author Serguei Mokhov
      * @version $Revision$
      ! * @since 0.3.0.2
      */
      public class DiffDistance




      ------------------------------

      Message: 6
      Date: Mon, 31 Dec 2007 00:17:07 +0000
      From: "Serguei A. Mokhov" <mokhov@...>
      Subject: [marf-cvs] marf/src/marf Configuration.java, 1.2, 1.3
      MARF.java, 1.109, 1.110 Version.java, 1.5, 1.6
      To: marf-cvs@...
      Message-ID: <E1J98L6-0003Gl-Ru@...>

      Update of /cvsroot/marf/marf/src/marf
      In directory sc8-pr-cvs16.sourceforge.net:/tmp/cvs-serv26660

      Modified Files:
      Configuration.java MARF.java Version.java
      Log Message:
      Cosmetically clean up a bit more of the code. Apply more consistently the coding conventions.
      Correct more spelling mistakes.

      Index: Configuration.java
      ===================================================================
      RCS file: /cvsroot/marf/marf/src/marf/Configuration.java,v
      retrieving revision 1.2
      retrieving revision 1.3
      diff -C2 -d -r1.2 -r1.3
      *** Configuration.java 15 Oct 2006 16:40:13 -0000 1.2
      --- Configuration.java 31 Dec 2007 00:17:05 -0000 1.3
      ***************
      *** 1,5 ****
      - /**
      - *
      - */
      package marf;

      --- 1,2 ----
      ***************
      *** 79,98 ****

      /**
      ! * Class of a sample loader plugin.
      */
      protected String strSampleLoaderPluginClass = null;

      /**
      ! * Class of a preprocessing plugin.
      */
      protected String strPreprocessingPluginClass = null;

      /**
      ! * Class of a feature extraction plugin.
      */
      protected String strFeatureExtractionPluginClass = null;

      /**
      ! * Class of a classification plugin.
      */
      protected String strClassificationPluginClass = null;
      --- 76,95 ----

      /**
      ! * Class of a sample loader plug-in.
      */
      protected String strSampleLoaderPluginClass = null;

      /**
      ! * Class of a preprocessing plug-in.
      */
      protected String strPreprocessingPluginClass = null;

      /**
      ! * Class of a feature extraction plug-in.
      */
      protected String strFeatureExtractionPluginClass = null;

      /**
      ! * Class of a classification plug-in.
      */
      protected String strClassificationPluginClass = null;
      ***************
      *** 112,155 ****
      }

      -
      -
      /**
      * All-fields constructor.
      ! * @param preprocessingMethod
      ! * @param featureExtractionMethod
      ! * @param classificationMethod
      ! * @param sampleFormat
      ! * @param currentSubject
      ! * @param strFileName
      ! * @param strSamplesDir
      ! * @param moduleParams
      ! * @param dumpSpectrogram
      ! * @param dumpWaveGraph
      ! * @param strSampleLoaderPluginClass
      ! * @param strPreprocessingPluginClass
      ! * @param strFeatureExtractionPluginClass
      ! * @param strClassificationPluginClass
      ! * @param debug
      */
      ! public Configuration(int preprocessingMethod, int featureExtractionMethod, int classificationMethod, int sampleFormat, int currentSubject, String strFileName, String strSamplesDir, ModuleParams moduleParams, boolean dumpSpectrogram, boolean dumpWaveGraph, String strSampleLoaderPluginClass, String strPreprocessingPluginClass, String strFeatureExtractionPluginClass, String strClassificationPluginClass, boolean debug) {
      ! iPreprocessingMethod = preprocessingMethod;
      ! iFeatureExtractionMethod = featureExtractionMethod;
      ! iClassificationMethod = classificationMethod;
      ! iSampleFormat = sampleFormat;
      ! iCurrentSubject = currentSubject;
      ! this.strFileName = strFileName;
      ! this.strSamplesDir = strSamplesDir;
      ! oModuleParams = moduleParams;
      ! bDumpSpectrogram = dumpSpectrogram;
      ! bDumpWaveGraph = dumpWaveGraph;
      ! this.strSampleLoaderPluginClass = strSampleLoaderPluginClass;
      ! this.strPreprocessingPluginClass = strPreprocessingPluginClass;
      ! this.strFeatureExtractionPluginClass = strFeatureExtractionPluginClass;
      ! this.strClassificationPluginClass = strClassificationPluginClass;
      ! bDebug = debug;
      }

      -
      -
      /**
      * Copy-constructor.
      --- 109,166 ----
      }

      /**
      * All-fields constructor.
      ! * @param piPreprocessingMethod
      ! * @param piFeatureExtractionMethod
      ! * @param piClassificationMethod
      ! * @param piSampleFormat
      ! * @param piCurrentSubject
      ! * @param pstrFileName
      ! * @param pstrSamplesDir
      ! * @param poModuleParams
      ! * @param pbDumpSpectrogram
      ! * @param pbDumpWaveGraph
      ! * @param pstrSampleLoaderPluginClass
      ! * @param pstrPreprocessingPluginClass
      ! * @param pstrFeatureExtractionPluginClass
      ! * @param pstrClassificationPluginClass
      ! * @param pbDebug
      */
      ! public Configuration
      ! (
      ! int piPreprocessingMethod,
      ! int piFeatureExtractionMethod,
      ! int piClassificationMethod,
      ! int piSampleFormat,
      ! int piCurrentSubject,
      ! String pstrFileName,
      ! String pstrSamplesDir,
      ! ModuleParams poModuleParams,
      ! boolean pbDumpSpectrogram,
      ! boolean pbDumpWaveGraph,
      ! String pstrSampleLoaderPluginClass,
      ! String pstrPreprocessingPluginClass,
      ! String pstrFeatureExtractionPluginClass,
      ! String pstrClassificationPluginClass,
      ! boolean pbDebug
      ! )
      ! {
      ! this.iPreprocessingMethod = piPreprocessingMethod;
      ! this.iFeatureExtractionMethod = piFeatureExtractionMethod;
      ! this.iClassificationMethod = piClassificationMethod;
      ! this.iSampleFormat = piSampleFormat;
      ! this.iCurrentSubject = piCurrentSubject;
      ! this.strFileName = pstrFileName;
      ! this.strSamplesDir = pstrSamplesDir;
      ! this.oModuleParams = poModuleParams;
      ! this.bDumpSpectrogram = pbDumpSpectrogram;
      ! this.bDumpWaveGraph = pbDumpWaveGraph;
      ! this.strSampleLoaderPluginClass = pstrSampleLoaderPluginClass;
      ! this.strPreprocessingPluginClass = pstrPreprocessingPluginClass;
      ! this.strFeatureExtractionPluginClass = pstrFeatureExtractionPluginClass;
      ! this.strClassificationPluginClass = pstrClassificationPluginClass;
      ! this.bDebug = pbDebug;
      }

      /**
      * Copy-constructor.
      ***************
      *** 182,186 ****
      * at this point.
      *
      ! * TODO: document/standartize property keys.
      *
      * @return instance of java.util.Properties with MARF configuration.
      --- 193,197 ----
      * at this point.
      *
      ! * TODO: document/standardize/constify property keys.
      *
      * @return instance of java.util.Properties with MARF configuration.
      ***************
      *** 217,220 ****
      --- 228,235 ----


      + /**
      + * @return
      + * @throws NotImplementedException
      + */
      public ModuleParams toModuleParams()
      {
      ***************
      *** 269,273 ****
      return argv;
      }
      !
      public Vector toVector()
      {
      --- 284,291 ----
      return argv;
      }
      !
      ! /**
      ! * @return
      ! */
      public Vector toVector()
      {
      ***************
      *** 278,290 ****
      * @return Returns the bDebug.
      */
      ! public boolean isDebugOn() {
      ! return bDebug;
      }

      /**
      ! * @param debug The bDebug to set.
      */
      ! public void setDebug(boolean debug) {
      ! bDebug = debug;
      }

      --- 296,310 ----
      * @return Returns the bDebug.
      */
      ! public boolean isDebugOn()
      ! {
      ! return this.bDebug;
      }

      /**
      ! * @param pbDebug The bDebug to set.
      */
      ! public void setDebug(boolean pbDebug)
      ! {
      ! this.bDebug = pbDebug;
      }

      ***************
      *** 292,304 ****
      * @return Returns the bDumpSpectrogram.
      */
      ! public boolean isDumpSpectrogramOn() {
      ! return bDumpSpectrogram;
      }

      /**
      ! * @param dumpSpectrogram The bDumpSpectrogram to set.
      */
      ! public void setDumpSpectrogram(boolean dumpSpectrogram) {
      ! bDumpSpectrogram = dumpSpectrogram;
      }

      --- 312,326 ----
      * @return Returns the bDumpSpectrogram.
      */
      ! public boolean isDumpSpectrogramOn()
      ! {
      ! return this.bDumpSpectrogram;
      }

      /**
      ! * @param pbDumpSpectrogram The bDumpSpectrogram to set.
      */
      ! public void setDumpSpectrogram(boolean pbDumpSpectrogram)
      ! {
      ! this.bDumpSpectrogram = pbDumpSpectrogram;
      }

      ***************
      *** 306,318 ****
      * @return Returns the bDumpWaveGraph.
      */
      ! public boolean isDumpWaveGraphOn() {
      ! return bDumpWaveGraph;
      }

      /**
      ! * @param dumpWaveGraph The bDumpWaveGraph to set.
      */
      ! public void setDumpWaveGraph(boolean dumpWaveGraph) {
      ! bDumpWaveGraph = dumpWaveGraph;
      }

      --- 328,342 ----
      * @return Returns the bDumpWaveGraph.
      */
      ! public boolean isDumpWaveGraphOn()
      ! {
      ! return this.bDumpWaveGraph;
      }

      /**
      ! * @param pbDumpWaveGraph The bDumpWaveGraph to set.
      */
      ! public void setDumpWaveGraph(boolean pbDumpWaveGraph)
      ! {
      ! this.bDumpWaveGraph = pbDumpWaveGraph;
      }

      ***************
      *** 320,332 ****
      * @return Returns the iClassificationMethod.
      */
      ! public int getClassificationMethod() {
      ! return iClassificationMethod;
      }

      /**
      ! * @param classificationMethod The iClassificationMethod to set.
      */
      ! public void setClassificationMethod(int classificationMethod) {
      ! iClassificationMethod = classificationMethod;
      }

      --- 344,358 ----
      * @return Returns the iClassificationMethod.
      */
      ! public int getClassificationMethod()
      ! {
      ! return this.iClassificationMethod;
      }

      /**
      ! * @param piClassificationMethod The iClassificationMethod to set.
      */
      ! public void setClassificationMethod(int piClassificationMethod)
      ! {
      ! this.iClassificationMethod = piClassificationMethod;
      }

      ***************
      *** 334,346 ****
      * @return Returns the iCurrentSubject.
      */
      ! public int getCurrentSubject() {
      ! return iCurrentSubject;
      }

      /**
      ! * @param currentSubject The iCurrentSubject to set.
      */
      ! public void setCurrentSubject(int currentSubject) {
      ! iCurrentSubject = currentSubject;
      }

      --- 360,374 ----
      * @return Returns the iCurrentSubject.
      */
      ! public int getCurrentSubject()
      ! {
      ! return this.iCurrentSubject;
      }

      /**
      ! * @param piCurrentSubject The iCurrentSubject to set.
      */
      ! public void setCurrentSubject(int piCurrentSubject)
      ! {
      ! this.iCurrentSubject = piCurrentSubject;
      }

      ***************
      *** 348,360 ****
      * @return Returns the iFeatureExtractionMethod.
      */
      ! public int getFeatureExtractionMethod() {
      ! return iFeatureExtractionMethod;
      }

      /**
      ! * @param featureExtractionMethod The iFeatureExtractionMethod to set.
      */
      ! public void setFeatureExtractionMethod(int featureExtractionMethod) {
      ! iFeatureExtractionMethod = featureExtractionMethod;
      }

      --- 376,390 ----
      * @return Returns the iFeatureExtractionMethod.
      */
      ! public int getFeatureExtractionMethod()
      ! {
      ! return this.iFeatureExtractionMethod;
      }

      /**
      ! * @param piFeatureExtractionMethod The iFeatureExtractionMethod to set.
      */
      ! public void setFeatureExtractionMethod(int piFeatureExtractionMethod)
      ! {
      ! this.iFeatureExtractionMethod = piFeatureExtractionMethod;
      }

      ***************
      *** 362,374 ****
      * @return Returns the iPreprocessingMethod.
      */
      ! public int getPreprocessingMethod() {
      ! return iPreprocessingMethod;
      }

      /**
      ! * @param preprocessingMethod The iPreprocessingMethod to set.
      */
      ! public void setPreprocessingMethod(int preprocessingMethod) {
      ! iPreprocessingMethod = preprocessingMethod;
      }

      --- 392,406 ----
      * @return Returns the iPreprocessingMethod.
      */
      ! public int getPreprocessingMethod()
      ! {
      ! return this.iPreprocessingMethod;
      }

      /**
      ! * @param piPreprocessingMethod The iPreprocessingMethod to set.
      */
      ! public void setPreprocessingMethod(int piPreprocessingMethod)
      ! {
      ! this.iPreprocessingMethod = piPreprocessingMethod;
      }

      ***************
      *** 376,388 ****
      * @return Returns the iSampleFormat.
      */
      ! public int getSampleFormat() {
      ! return iSampleFormat;
      }

      /**
      ! * @param sampleFormat The iSampleFormat to set.
      */
      ! public void setSampleFormat(int sampleFormat) {
      ! iSampleFormat = sampleFormat;
      }

      --- 408,422 ----
      * @return Returns the iSampleFormat.
      */
      ! public int getSampleFormat()
      ! {
      ! return this.iSampleFormat;
      }

      /**
      ! * @param piSampleFormat The iSampleFormat to set.
      */
      ! public void setSampleFormat(int piSampleFormat)
      ! {
      ! this.iSampleFormat = piSampleFormat;
      }

      ***************
      *** 390,402 ****
      * @return Returns the oClassificationPluginClass.
      */
      ! public String getClassificationPluginClass() {
      ! return strClassificationPluginClass;
      }

      /**
      ! * @param classificationPluginClass The oClassificationPluginClass to set.
      */
      ! public void setClassificationPluginClass(String classificationPluginClass) {
      ! strClassificationPluginClass = classificationPluginClass;
      }

      --- 424,438 ----
      * @return Returns the oClassificationPluginClass.
      */
      ! public String getClassificationPluginClass()
      ! {
      ! return this.strClassificationPluginClass;
      }

      /**
      ! * @param pstrClassificationPluginClass The oClassificationPluginClass to set.
      */
      ! public void setClassificationPluginClass(String pstrClassificationPluginClass)
      ! {
      ! this.strClassificationPluginClass = pstrClassificationPluginClass;
      }

      ***************
      *** 404,416 ****
      * @return Returns the oFeatureExtractionPluginClass.
      */
      ! public String getFeatureExtractionPluginClass() {
      ! return strFeatureExtractionPluginClass;
      }

      /**
      ! * @param featureExtractionPluginClass The oFeatureExtractionPluginClass to set.
      */
      ! public void setFeatureExtractionPluginClass(String featureExtractionPluginClass) {
      ! strFeatureExtractionPluginClass = featureExtractionPluginClass;
      }

      --- 440,454 ----
      * @return Returns the oFeatureExtractionPluginClass.
      */
      ! public String getFeatureExtractionPluginClass()
      ! {
      ! return this.strFeatureExtractionPluginClass;
      }

      /**
      ! * @param pstrFeatureExtractionPluginClass The oFeatureExtractionPluginClass to set.
      */
      ! public void setFeatureExtractionPluginClass(String pstrFeatureExtractionPluginClass)
      ! {
      ! this.strFeatureExtractionPluginClass = pstrFeatureExtractionPluginClass;
      }

      ***************
      *** 418,430 ****
      * @return Returns the oModuleParams.
      */
      ! public ModuleParams getModuleParams() {
      ! return oModuleParams;
      }

      /**
      ! * @param moduleParams The oModuleParams to set.
      */
      ! public void setModuleParams(ModuleParams moduleParams) {
      ! oModuleParams = moduleParams;
      }

      --- 456,470 ----
      * @return Returns the oModuleParams.
      */
      ! public ModuleParams getModuleParams()
      ! {
      ! return this.oModuleParams;
      }

      /**
      ! * @param poModuleParams The oModuleParams to set.
      */
      ! public void setModuleParams(ModuleParams poModuleParams)
      ! {
      ! this.oModuleParams = poModuleParams;
      }

      ***************
      *** 432,444 ****
      * @return Returns the oPreprocessingPluginClass.
      */
      ! public String getPreprocessingPluginClass() {
      ! return strPreprocessingPluginClass;
      }

      /**
      ! * @param preprocessingPluginClass The oPreprocessingPluginClass to set.
      */
      ! public void setPreprocessingPluginClass(String preprocessingPluginClass) {
      ! strPreprocessingPluginClass = preprocessingPluginClass;
      }

      --- 472,486 ----
      * @return Returns the oPreprocessingPluginClass.
      */
      ! public String getPreprocessingPluginClass()
      ! {
      ! return this.strPreprocessingPluginClass;
      }

      /**
      ! * @param pstrPreprocessingPluginClass The oPreprocessingPluginClass to set.
      */
      ! public void setPreprocessingPluginClass(String pstrPreprocessingPluginClass)
      ! {
      ! this.strPreprocessingPluginClass = pstrPreprocessingPluginClass;
      }

      ***************
      *** 446,458 ****
      * @return Returns the oSampleLoaderPluginClass.
      */
      ! public String getSampleLoaderPluginClass() {
      ! return strSampleLoaderPluginClass;
      }

      /**
      ! * @param sampleLoaderPluginClass The oSampleLoade<br/><br/>(Message over 64 KB, truncated)
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