"rio" work

diff --git a/forester/java/src/org/forester/application/gsdi.java b/forester/java/src/org/forester/application/gsdi.java
index eab52df..e062730 100644 (file)
--- a/forester/java/src/org/forester/application/gsdi.java
+++ b/forester/java/src/org/forester/application/gsdi.java
@@ -50,6 +50,7 @@ import org.forester.phylogeny.factories.PhylogenyFactory;
 import org.forester.sdi.GSDI;
 import org.forester.sdi.GSDIR;
 import org.forester.sdi.SDI;
 import org.forester.sdi.GSDI;
 import org.forester.sdi.GSDIR;
 import org.forester.sdi.SDI;

+import org.forester.sdi.SDI.ALGORITHM;

 import org.forester.sdi.SDI.TaxonomyComparisonBase;
 import org.forester.sdi.SDIException;
 import org.forester.sdi.SDIse;
 import org.forester.sdi.SDI.TaxonomyComparisonBase;
 import org.forester.sdi.SDIException;
 import org.forester.sdi.SDIse;

@@ -60,9 +61,6 @@ import org.forester.util.ForesterUtil;
 
 public final class gsdi {
 
 
 public final class gsdi {
 

-    private enum BASE_ALGORITHM {
-        GSDIR, GSDI, SDI
-    }

     final static public boolean REPLACE_UNDERSCORES_IN_NH_SPECIES_TREE = true;
     final static private String ALLOW_STRIPPING_OF_GENE_TREE_OPTION    = "g";
     final static private String SDISE_OPTION                           = "b";
     final static public boolean REPLACE_UNDERSCORES_IN_NH_SPECIES_TREE = true;
     final static private String ALLOW_STRIPPING_OF_GENE_TREE_OPTION    = "g";
     final static private String SDISE_OPTION                           = "b";

@@ -127,23 +125,23 @@ public final class gsdi {
     }
 
     private static void execute( final CommandLineArguments cla ) throws IOException {
     }
 
     private static void execute( final CommandLineArguments cla ) throws IOException {

-        BASE_ALGORITHM base_algorithm = BASE_ALGORITHM.GSDI;
+        ALGORITHM base_algorithm = ALGORITHM.GSDI;

         boolean most_parsimonous_duplication_model = false;
         boolean allow_stripping_of_gene_tree = false;
         if ( cla.isOptionSet( gsdi.GSDIR_OPTION ) ) {
         boolean most_parsimonous_duplication_model = false;
         boolean allow_stripping_of_gene_tree = false;
         if ( cla.isOptionSet( gsdi.GSDIR_OPTION ) ) {

-            base_algorithm = BASE_ALGORITHM.GSDIR;
+            base_algorithm = ALGORITHM.GSDIR;

         }
         else if ( cla.isOptionSet( gsdi.SDISE_OPTION ) ) {
         }
         else if ( cla.isOptionSet( gsdi.SDISE_OPTION ) ) {

-            base_algorithm = BASE_ALGORITHM.SDI;
+            base_algorithm = ALGORITHM.SDI;

         }
         if ( cla.isOptionSet( gsdi.MOST_PARSIMONIOUS_OPTION ) ) {
         }
         if ( cla.isOptionSet( gsdi.MOST_PARSIMONIOUS_OPTION ) ) {

-            if ( base_algorithm == BASE_ALGORITHM.SDI ) {
+            if ( base_algorithm == ALGORITHM.SDI ) {

                 ForesterUtil.fatalError( gsdi.PRG_NAME, "Cannot use most parsimonious duplication mode with SDI" );
             }
             most_parsimonous_duplication_model = true;
         }
         if ( cla.isOptionSet( gsdi.ALLOW_STRIPPING_OF_GENE_TREE_OPTION ) ) {
                 ForesterUtil.fatalError( gsdi.PRG_NAME, "Cannot use most parsimonious duplication mode with SDI" );
             }
             most_parsimonous_duplication_model = true;
         }
         if ( cla.isOptionSet( gsdi.ALLOW_STRIPPING_OF_GENE_TREE_OPTION ) ) {

-            if ( base_algorithm == BASE_ALGORITHM.SDI ) {
+            if ( base_algorithm == ALGORITHM.SDI ) {

                 ForesterUtil.fatalError( gsdi.PRG_NAME, "Cannot allow stripping of gene tree with SDI" );
             }
             allow_stripping_of_gene_tree = true;
                 ForesterUtil.fatalError( gsdi.PRG_NAME, "Cannot allow stripping of gene tree with SDI" );
             }
             allow_stripping_of_gene_tree = true;

@@ -254,7 +252,7 @@ public final class gsdi {
         if ( !gene_tree.isCompletelyBinary() ) {
             fatalError( "user error", "gene tree is not completely binary", log_writer );
         }
         if ( !gene_tree.isCompletelyBinary() ) {
             fatalError( "user error", "gene tree is not completely binary", log_writer );
         }

-        if ( base_algorithm == BASE_ALGORITHM.SDI ) {
+        if ( base_algorithm == ALGORITHM.SDI ) {

             if ( !species_tree.isCompletelyBinary() ) {
                 fatalError( "user error",
                             "species tree is not completely binary, use GSDI or GSDIR instead",
             if ( !species_tree.isCompletelyBinary() ) {
                 fatalError( "user error",
                             "species tree is not completely binary, use GSDI or GSDIR instead",

@@ -285,12 +283,12 @@ public final class gsdi {
         SDI sdi = null;
         final long start_time = new Date().getTime();
         try {
         SDI sdi = null;
         final long start_time = new Date().getTime();
         try {

-            if ( ( base_algorithm == BASE_ALGORITHM.GSDI ) || ( base_algorithm == BASE_ALGORITHM.GSDIR ) ) {
-                if ( base_algorithm == BASE_ALGORITHM.GSDI ) {
+            if ( ( base_algorithm == ALGORITHM.GSDI ) || ( base_algorithm == ALGORITHM.GSDIR ) ) {
+                if ( base_algorithm == ALGORITHM.GSDI ) {

                     System.out.println( "Algorithm       : GSDI" );
                     log_writer.println( "Algorithm       : GSDI" );
                 }
                     System.out.println( "Algorithm       : GSDI" );
                     log_writer.println( "Algorithm       : GSDI" );
                 }

-                else if ( base_algorithm == BASE_ALGORITHM.GSDIR ) {
+                else if ( base_algorithm == ALGORITHM.GSDIR ) {

                     System.out.println( "Algorithm       : GSDIR" );
                     log_writer.println( "Algorithm       : GSDIR" );
                 }
                     System.out.println( "Algorithm       : GSDIR" );
                     log_writer.println( "Algorithm       : GSDIR" );
                 }

@@ -299,14 +297,14 @@ public final class gsdi {
                 log_writer.println( "Use most parsimonous duplication model   : " + most_parsimonous_duplication_model );
                 log_writer.println( "Allow stripping of gene tree nodes       : " + allow_stripping_of_gene_tree );
                 log_writer.flush();
                 log_writer.println( "Use most parsimonous duplication model   : " + most_parsimonous_duplication_model );
                 log_writer.println( "Allow stripping of gene tree nodes       : " + allow_stripping_of_gene_tree );
                 log_writer.flush();

-                if ( base_algorithm == BASE_ALGORITHM.GSDI ) {
+                if ( base_algorithm == ALGORITHM.GSDI ) {

                     sdi = new GSDI( gene_tree,
                                     species_tree,
                                     most_parsimonous_duplication_model,
                                     allow_stripping_of_gene_tree,
                                     true );
                 }
                     sdi = new GSDI( gene_tree,
                                     species_tree,
                                     most_parsimonous_duplication_model,
                                     allow_stripping_of_gene_tree,
                                     true );
                 }

-                else if ( base_algorithm == BASE_ALGORITHM.GSDIR ) {
+                else if ( base_algorithm == ALGORITHM.GSDIR ) {

                     sdi = new GSDIR( gene_tree, species_tree, allow_stripping_of_gene_tree, 1 );
                 }
             }
                     sdi = new GSDIR( gene_tree, species_tree, allow_stripping_of_gene_tree, 1 );
                 }
             }

@@ -332,12 +330,12 @@ public final class gsdi {
                 + "ms" );
         log_writer.println( "Running time (excluding I/O)             : " + ( new Date().getTime() - start_time )
                 + "ms" );
                 + "ms" );
         log_writer.println( "Running time (excluding I/O)             : " + ( new Date().getTime() - start_time )
                 + "ms" );

-        if ( ( base_algorithm == BASE_ALGORITHM.GSDI ) ) {
+        if ( ( base_algorithm == ALGORITHM.GSDI ) ) {

             final GSDI gsdi = ( GSDI ) sdi;
             System.out.println( "Mapping based on                         : " + gsdi.getTaxCompBase() );
             log_writer.println( "Mapping based on                         : " + gsdi.getTaxCompBase() );
         }
             final GSDI gsdi = ( GSDI ) sdi;
             System.out.println( "Mapping based on                         : " + gsdi.getTaxCompBase() );
             log_writer.println( "Mapping based on                         : " + gsdi.getTaxCompBase() );
         }

-        if ( ( base_algorithm == BASE_ALGORITHM.GSDIR ) ) {
+        if ( ( base_algorithm == ALGORITHM.GSDIR ) ) {

             final GSDIR gsdir = ( GSDIR ) sdi;
             System.out.println( "Mapping based on                         : " + gsdir.getTaxCompBase() );
             log_writer.println( "Mapping based on                         : " + gsdir.getTaxCompBase() );
             final GSDIR gsdir = ( GSDIR ) sdi;
             System.out.println( "Mapping based on                         : " + gsdir.getTaxCompBase() );
             log_writer.println( "Mapping based on                         : " + gsdir.getTaxCompBase() );

@@ -348,7 +346,7 @@ public final class gsdi {
         }
         try {
             final PhylogenyWriter writer = new PhylogenyWriter();
         }
         try {
             final PhylogenyWriter writer = new PhylogenyWriter();

-            if ( base_algorithm == BASE_ALGORITHM.GSDIR ) {
+            if ( base_algorithm == ALGORITHM.GSDIR ) {

                 writer.toPhyloXML( out_file,
                                    ( ( GSDIR ) sdi ).getMinDuplicationsSumGeneTrees(),
                                    0,
                 writer.toPhyloXML( out_file,
                                    ( ( GSDIR ) sdi ).getMinDuplicationsSumGeneTrees(),
                                    0,

@@ -364,12 +362,12 @@ public final class gsdi {
         }
         System.out.println( "Wrote resulting gene tree to             : " + out_file.getCanonicalPath() );
         log_writer.println( "Wrote resulting gene tree to             : " + out_file.getCanonicalPath() );
         }
         System.out.println( "Wrote resulting gene tree to             : " + out_file.getCanonicalPath() );
         log_writer.println( "Wrote resulting gene tree to             : " + out_file.getCanonicalPath() );

-        if ( base_algorithm == BASE_ALGORITHM.SDI ) {
+        if ( base_algorithm == ALGORITHM.SDI ) {

             sdi.computeMappingCostL();
             System.out.println( "Mapping cost                             : " + sdi.computeMappingCostL() );
             log_writer.println( "Mapping cost                             : " + sdi.computeMappingCostL() );
         }
             sdi.computeMappingCostL();
             System.out.println( "Mapping cost                             : " + sdi.computeMappingCostL() );
             log_writer.println( "Mapping cost                             : " + sdi.computeMappingCostL() );
         }

-        else if ( ( base_algorithm == BASE_ALGORITHM.GSDI ) || ( base_algorithm == BASE_ALGORITHM.GSDIR ) ) {
+        else if ( ( base_algorithm == ALGORITHM.GSDI ) || ( base_algorithm == ALGORITHM.GSDIR ) ) {

             final GSDI gsdi = ( GSDI ) sdi;
             final File species_tree_used_file = new File( ForesterUtil.removeSuffix( out_file.toString() )
                     + SUFFIX_FOR_SPECIES_TREE_USED );
             final GSDI gsdi = ( GSDI ) sdi;
             final File species_tree_used_file = new File( ForesterUtil.removeSuffix( out_file.toString() )
                     + SUFFIX_FOR_SPECIES_TREE_USED );

@@ -400,7 +398,7 @@ public final class gsdi {
                 + sdi.getSpeciesTree().getNumberOfExternalNodes() );
         log_writer.println( "Number of external nodes in species tree : "
                 + sdi.getSpeciesTree().getNumberOfExternalNodes() );
                 + sdi.getSpeciesTree().getNumberOfExternalNodes() );
         log_writer.println( "Number of external nodes in species tree : "
                 + sdi.getSpeciesTree().getNumberOfExternalNodes() );

-        if ( ( base_algorithm == BASE_ALGORITHM.GSDI ) ) {
+        if ( ( base_algorithm == ALGORITHM.GSDI ) ) {

             final GSDI gsdi = ( GSDI ) sdi;
             final int poly = PhylogenyMethods.countNumberOfPolytomies( gsdi.getSpeciesTree() );
             System.out.println( "Number of polytomies in species tree     : " + poly );
             final GSDI gsdi = ( GSDI ) sdi;
             final int poly = PhylogenyMethods.countNumberOfPolytomies( gsdi.getSpeciesTree() );
             System.out.println( "Number of polytomies in species tree     : " + poly );

@@ -417,7 +415,7 @@ public final class gsdi {
         System.out.println();
         System.out.println( "Number of duplications                   : " + sdi.getDuplicationsSum() );
         log_writer.println( "Number of duplications                   : " + sdi.getDuplicationsSum() );
         System.out.println();
         System.out.println( "Number of duplications                   : " + sdi.getDuplicationsSum() );
         log_writer.println( "Number of duplications                   : " + sdi.getDuplicationsSum() );

-        if ( ( base_algorithm == BASE_ALGORITHM.GSDI ) ) {
+        if ( ( base_algorithm == ALGORITHM.GSDI ) ) {

             final GSDI gsdi = ( GSDI ) sdi;
             if ( !most_parsimonous_duplication_model ) {
                 final int u = gsdi.getSpeciationOrDuplicationEventsSum();
             final GSDI gsdi = ( GSDI ) sdi;
             if ( !most_parsimonous_duplication_model ) {
                 final int u = gsdi.getSpeciationOrDuplicationEventsSum();

diff --git a/forester/java/src/org/forester/application/rio.java b/forester/java/src/org/forester/application/rio.java
index 7d7632c..80a34ab 100644 (file)
--- a/forester/java/src/org/forester/application/rio.java
+++ b/forester/java/src/org/forester/application/rio.java
@@ -41,6 +41,8 @@ import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
 import org.forester.phylogeny.factories.PhylogenyFactory;
 import org.forester.rio.RIO;
 import org.forester.rio.RIOException;
 import org.forester.phylogeny.factories.PhylogenyFactory;
 import org.forester.rio.RIO;
 import org.forester.rio.RIOException;

+import org.forester.sdi.SDI;
+import org.forester.sdi.SDI.ALGORITHM;

 import org.forester.sdi.SDIException;
 import org.forester.util.CommandLineArguments;
 import org.forester.util.EasyWriter;
 import org.forester.sdi.SDIException;
 import org.forester.util.CommandLineArguments;
 import org.forester.util.EasyWriter;

@@ -48,19 +50,20 @@ import org.forester.util.ForesterUtil;
 
 public class rio {
 
 
 public class rio {
 

-    final static private String PRG_NAME              = "rio";
-    final static private String PRG_VERSION           = "3.00 beta 3";
-    final static private String PRG_DATE              = "2012.12.05";
-    final static private String E_MAIL                = "czmasek@burnham.org";
-    final static private String WWW                   = "www.phylosoft.org/forester/";
-    final static private String HELP_OPTION_1         = "help";
-    final static private String HELP_OPTION_2         = "h";
-    final static private String QUERY_OPTION          = "q";
-    final static private String SORT_OPTION           = "s";
-    final static private String OUTPUT_ULTRA_P_OPTION = "u";
-    final static private String CUTOFF_ULTRA_P_OPTION = "cu";
-    final static private String CUTOFF_ORTHO_OPTION   = "co";
-    final static private String TABLE_OUTPUT_OPTION   = "t";
+    final static private String PRG_NAME                          = "rio";
+    final static private String PRG_VERSION                       = "3.00 beta 4";
+    final static private String PRG_DATE                          = "2012.12.10";
+    final static private String E_MAIL                            = "czmasek@burnham.org";
+    final static private String WWW                               = "www.phylosoft.org/forester/";
+    final static private String HELP_OPTION_1                     = "help";
+    final static private String HELP_OPTION_2                     = "h";
+    final static private String QUERY_OPTION                      = "q";
+    final static private String SORT_OPTION                       = "s";
+    final static private String ALLOW_NON_BIN_SPECIES_TREE_OPTION = "g";
+    final static private String OUTPUT_ULTRA_P_OPTION             = "u";
+    final static private String CUTOFF_ULTRA_P_OPTION             = "cu";
+    final static private String CUTOFF_ORTHO_OPTION               = "co";
+    final static private String TABLE_OUTPUT_OPTION               = "t";

 
     public static void main( final String[] args ) {
         ForesterUtil.printProgramInformation( PRG_NAME,
 
     public static void main( final String[] args ) {
         ForesterUtil.printProgramInformation( PRG_NAME,

@@ -93,6 +96,7 @@ public class rio {
         allowed_options.add( CUTOFF_ORTHO_OPTION );
         allowed_options.add( TABLE_OUTPUT_OPTION );
         allowed_options.add( OUTPUT_ULTRA_P_OPTION );
         allowed_options.add( CUTOFF_ORTHO_OPTION );
         allowed_options.add( TABLE_OUTPUT_OPTION );
         allowed_options.add( OUTPUT_ULTRA_P_OPTION );

+        allowed_options.add( ALLOW_NON_BIN_SPECIES_TREE_OPTION );

         final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options );
         if ( dissallowed_options.length() > 0 ) {
             ForesterUtil.fatalError( PRG_NAME, "unknown option(s): " + dissallowed_options );
         final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options );
         if ( dissallowed_options.length() > 0 ) {
             ForesterUtil.fatalError( PRG_NAME, "unknown option(s): " + dissallowed_options );

@@ -123,6 +127,10 @@ public class rio {
         if ( cla.isOptionSet( OUTPUT_ULTRA_P_OPTION ) ) {
             output_ultraparalogs = true;
         }
         if ( cla.isOptionSet( OUTPUT_ULTRA_P_OPTION ) ) {
             output_ultraparalogs = true;
         }

+        boolean gsdir = false;
+        if ( cla.isOptionSet( ALLOW_NON_BIN_SPECIES_TREE_OPTION ) ) {
+            gsdir = true;
+        }

         double cutoff_for_orthologs = 50;
         double cutoff_for_ultra_paralogs = 50;
         int sort = 1;
         double cutoff_for_orthologs = 50;
         double cutoff_for_ultra_paralogs = 50;
         int sort = 1;

@@ -159,6 +167,12 @@ public class rio {
         long time = 0;
         System.out.println( "Gene trees                : " + gene_trees_file );
         System.out.println( "Species tree              : " + species_tree_file );
         long time = 0;
         System.out.println( "Gene trees                : " + gene_trees_file );
         System.out.println( "Species tree              : " + species_tree_file );

+        if ( gsdir ) {
+            System.out.println( "Non binary species tree   : allowed (GSDIR algorithm)" );
+        }
+        else {
+            System.out.println( "Non binary species tree   : disallowed (SDIR algorithm)" );
+        }

         if ( query != null ) {
             System.out.println( "Query                     : " + query );
             System.out.println( "Outfile                   : " + outfile );
         if ( query != null ) {
             System.out.println( "Query                     : " + query );
             System.out.println( "Outfile                   : " + outfile );

@@ -185,16 +199,20 @@ public class rio {
         if ( !species_tree.isRooted() ) {
             ForesterUtil.fatalError( PRG_NAME, "species tree is not rooted" );
         }
         if ( !species_tree.isRooted() ) {
             ForesterUtil.fatalError( PRG_NAME, "species tree is not rooted" );
         }

-        if ( !species_tree.isCompletelyBinary() ) {
-            ForesterUtil.fatalError( PRG_NAME, "species tree is not completely binary" );
+        final SDI.ALGORITHM algorithm;
+        if ( gsdir ) {
+            algorithm = ALGORITHM.GSDIR;
+        }
+        else {
+            algorithm = ALGORITHM.SDIR;

         }
         try {
             final RIO rio;
             if ( ForesterUtil.isEmpty( query ) ) {
         }
         try {
             final RIO rio;
             if ( ForesterUtil.isEmpty( query ) ) {

-                rio = new RIO( gene_trees_file, species_tree );
+                rio = new RIO( gene_trees_file, species_tree, algorithm );

             }
             else {
             }
             else {

-                rio = new RIO( gene_trees_file, species_tree, query );
+                rio = new RIO( gene_trees_file, species_tree, query, algorithm );

             }
             if ( outfile != null ) {
                 final StringBuilder output = new StringBuilder();
             }
             if ( outfile != null ) {
                 final StringBuilder output = new StringBuilder();

@@ -236,7 +254,7 @@ public class rio {
     }
 
     private static void tableOutput( final File table_outfile, final RIO rio ) throws IOException, RIOException {
     }
 
     private static void tableOutput( final File table_outfile, final RIO rio ) throws IOException, RIOException {

-        final IntMatrix m = RIO.calculateOrthologTable( rio.getAnalyzedGeneTrees() );
+        final IntMatrix m = RIO.calculateOrthologTable( rio.getAnalyzedGeneTrees(), true );

         writeTable( table_outfile, rio, m );
     }
 
         writeTable( table_outfile, rio, m );
     }
 

@@ -275,6 +293,7 @@ public class rio {
         System.out.println( PRG_NAME + " [options] <gene trees file> <species tree file> [outfile]" );
         System.out.println();
         System.out.println( " Options" );
         System.out.println( PRG_NAME + " [options] <gene trees file> <species tree file> [outfile]" );
         System.out.println();
         System.out.println( " Options" );

+        System.out.println( "  -" + ALLOW_NON_BIN_SPECIES_TREE_OPTION + "  : to allow non-binary species tree" );

         System.out.println( "  -" + CUTOFF_ORTHO_OPTION + " : cutoff for ortholog output (default: 50)" );
         System.out.println( "  -" + TABLE_OUTPUT_OPTION
                 + "  : file-name for output table of all vs. all ortholgy support" );
         System.out.println( "  -" + CUTOFF_ORTHO_OPTION + " : cutoff for ortholog output (default: 50)" );
         System.out.println( "  -" + TABLE_OUTPUT_OPTION
                 + "  : file-name for output table of all vs. all ortholgy support" );

diff --git a/forester/java/src/org/forester/rio/RIO.java b/forester/java/src/org/forester/rio/RIO.java
index 5a9be41..dea0492 100644 (file)
--- a/forester/java/src/org/forester/rio/RIO.java
+++ b/forester/java/src/org/forester/rio/RIO.java
@@ -32,6 +32,7 @@ import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Arrays;

+import java.util.Collections;

 import java.util.HashMap;
 import java.util.HashSet;
 import java.util.List;
 import java.util.HashMap;
 import java.util.HashSet;
 import java.util.List;

@@ -47,6 +48,8 @@ import org.forester.phylogeny.PhylogenyNode;
 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
 import org.forester.phylogeny.factories.PhylogenyFactory;
 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
 import org.forester.phylogeny.factories.PhylogenyFactory;
 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;

+import org.forester.sdi.GSDIR;
+import org.forester.sdi.SDI;

 import org.forester.sdi.SDIException;
 import org.forester.sdi.SDIR;
 import org.forester.util.ForesterUtil;
 import org.forester.sdi.SDIException;
 import org.forester.sdi.SDIR;
 import org.forester.util.ForesterUtil;

@@ -70,19 +73,21 @@ public final class RIO {
      * @throws IOException 
      * @throws RIOException 
      */
      * @throws IOException 
      * @throws RIOException 
      */

-    public RIO( final File gene_trees_file, final Phylogeny species_tree, final String query ) throws IOException,
-            SDIException, RIOException {
+    public RIO( final File gene_trees_file,
+                final Phylogeny species_tree,
+                final String query,
+                final SDI.ALGORITHM algorithm ) throws IOException, SDIException, RIOException {

         if ( ForesterUtil.isEmpty( query ) ) {
             throw new IllegalArgumentException( "query is empty" );
         }
         init();
         if ( ForesterUtil.isEmpty( query ) ) {
             throw new IllegalArgumentException( "query is empty" );
         }
         init();

-        inferOrthologs( gene_trees_file, species_tree, query );
+        inferOrthologs( gene_trees_file, species_tree, query, algorithm );

     }
 
     }
 

-    public RIO( final File gene_trees_file, final Phylogeny species_tree ) throws IOException, SDIException,
-            RIOException {
+    public RIO( final File gene_trees_file, final Phylogeny species_tree, final SDI.ALGORITHM algorithm )
+            throws IOException, SDIException, RIOException {

         init();
         init();

-        inferOrthologs( gene_trees_file, species_tree, null );
+        inferOrthologs( gene_trees_file, species_tree, null, algorithm );

     }
 
     public final Phylogeny[] getAnalyzedGeneTrees() {
     }
 
     public final Phylogeny[] getAnalyzedGeneTrees() {

@@ -381,8 +386,11 @@ public final class RIO {
      * @throws IOException 
      * @throws FileNotFoundException 
      */
      * @throws IOException 
      * @throws FileNotFoundException 
      */

-    private final void inferOrthologs( final File gene_trees_file, final Phylogeny species_tree, final String query )
-            throws SDIException, RIOException, FileNotFoundException, IOException {
+    private final void inferOrthologs( final File gene_trees_file,
+                                       final Phylogeny species_tree,
+                                       final String query,
+                                       final SDI.ALGORITHM algorithm ) throws SDIException, RIOException,
+            FileNotFoundException, IOException {

         // Read in first tree to get its sequence names
         // and strip species_tree.
         final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
         // Read in first tree to get its sequence names
         // and strip species_tree.
         final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();

@@ -433,22 +441,37 @@ public final class RIO {
                         + " has a different number of external nodes (" + gt.getNumberOfExternalNodes()
                         + ") than those gene trees preceding it (" + gene_tree_ext_nodes + ")" );
             }
                         + " has a different number of external nodes (" + gt.getNumberOfExternalNodes()
                         + ") than those gene trees preceding it (" + gene_tree_ext_nodes + ")" );
             }

-            _analyzed_gene_trees[ c++ ] = performOrthologInference( gt, species_tree, query );
+            _analyzed_gene_trees[ c++ ] = performOrthologInference( gt, species_tree, query, algorithm );

         }
         setNumberOfSamples( gene_trees.length );
     }
 
     private final Phylogeny performOrthologInference( final Phylogeny gene_tree,
                                                       final Phylogeny species_tree,
         }
         setNumberOfSamples( gene_trees.length );
     }
 
     private final Phylogeny performOrthologInference( final Phylogeny gene_tree,
                                                       final Phylogeny species_tree,

-                                                      final String query ) throws SDIException, RIOException {
-        final SDIR sdiunrooted = new SDIR();
-        final Phylogeny assigned_tree = sdiunrooted.infer( gene_tree,
-                                                           species_tree,
-                                                           false,
-                                                           RIO.ROOT_BY_MINIMIZING_SUM_OF_DUPS,
-                                                           RIO.ROOT_BY_MINIMIZING_TREE_HEIGHT,
-                                                           true,
-                                                           1 )[ 0 ];
+                                                      final String query,
+                                                      final SDI.ALGORITHM algorithm ) throws SDIException, RIOException {
+        final Phylogeny assigned_tree;
+        switch ( algorithm ) {
+            case SDIR: {
+                final SDIR sdir = new SDIR();
+                assigned_tree = sdir.infer( gene_tree,
+                                            species_tree,
+                                            false,
+                                            RIO.ROOT_BY_MINIMIZING_SUM_OF_DUPS,
+                                            RIO.ROOT_BY_MINIMIZING_TREE_HEIGHT,
+                                            true,
+                                            1 )[ 0 ];
+                break;
+            }
+            case GSDIR: {
+                final GSDIR gsdir = new GSDIR( gene_tree, species_tree, true, 1 );
+                assigned_tree = gsdir.getMinDuplicationsSumGeneTrees().get( 1 );
+                break;
+            }
+            default: {
+                throw new IllegalArgumentException( "illegal algorithm: " + algorithm );
+            }
+        }

         setExtNodesOfAnalyzedGeneTrees( assigned_tree.getNumberOfExternalNodes() );
         if ( !ForesterUtil.isEmpty( query ) ) {
             final List<PhylogenyNode> nodes = getNodesViaSequenceName( assigned_tree, query );
         setExtNodesOfAnalyzedGeneTrees( assigned_tree.getNumberOfExternalNodes() );
         if ( !ForesterUtil.isEmpty( query ) ) {
             final List<PhylogenyNode> nodes = getNodesViaSequenceName( assigned_tree, query );

@@ -513,7 +536,8 @@ public final class RIO {
         }
     }
 
         }
     }
 

-    public final static IntMatrix calculateOrthologTable( final Phylogeny[] analyzed_gene_trees ) throws RIOException {
+    public final static IntMatrix calculateOrthologTable( final Phylogeny[] analyzed_gene_trees, final boolean sort )
+            throws RIOException {

         final List<String> labels = new ArrayList<String>();
         final Set<String> labels_set = new HashSet<String>();
         String label;
         final List<String> labels = new ArrayList<String>();
         final Set<String> labels_set = new HashSet<String>();
         String label;

@@ -537,6 +561,9 @@ public final class RIO {
             labels_set.add( label );
             labels.add( label );
         }
             labels_set.add( label );
             labels.add( label );
         }

+        if ( sort ) {
+            Collections.sort( labels );
+        }

         final IntMatrix m = new IntMatrix( labels );
         int counter = 0;
         for( final Phylogeny gt : analyzed_gene_trees ) {
         final IntMatrix m = new IntMatrix( labels );
         int counter = 0;
         for( final Phylogeny gt : analyzed_gene_trees ) {

diff --git a/forester/java/src/org/forester/sdi/GSDIR.java b/forester/java/src/org/forester/sdi/GSDIR.java
index dc3fcae..8179811 100644 (file)
--- a/forester/java/src/org/forester/sdi/GSDIR.java
+++ b/forester/java/src/org/forester/sdi/GSDIR.java
@@ -28,6 +28,7 @@ import java.util.ArrayList;
 import java.util.List;\r
 \r
 import org.forester.phylogeny.Phylogeny;\r
 import java.util.List;\r
 \r
 import org.forester.phylogeny.Phylogeny;\r

+import org.forester.phylogeny.PhylogenyBranch;\r

 import org.forester.phylogeny.PhylogenyMethods;\r
 import org.forester.phylogeny.PhylogenyNode;\r
 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;\r
 import org.forester.phylogeny.PhylogenyMethods;\r
 import org.forester.phylogeny.PhylogenyNode;\r
 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;\r

@@ -41,20 +42,23 @@ public class GSDIR extends GSDI {
 \r
     public GSDIR( final Phylogeny gene_tree, final Phylogeny species_tree, final boolean strip_gene_tree, final int x )\r
             throws SDIException {\r
 \r
     public GSDIR( final Phylogeny gene_tree, final Phylogeny species_tree, final boolean strip_gene_tree, final int x )\r
             throws SDIException {\r

-        super( gene_tree, species_tree, true, strip_gene_tree, true, 1 );\r
+        super( gene_tree.copy(), species_tree, true, strip_gene_tree, true, 1 );\r

         _min_duplications_sum = Integer.MAX_VALUE;\r
         _min_duplications_sum_gene_trees = new ArrayList<Phylogeny>();\r
         _duplications_sum_stats = new BasicDescriptiveStatistics();\r
         linkNodesOfG();\r
         _min_duplications_sum = Integer.MAX_VALUE;\r
         _min_duplications_sum_gene_trees = new ArrayList<Phylogeny>();\r
         _duplications_sum_stats = new BasicDescriptiveStatistics();\r
         linkNodesOfG();\r

-        final List<PhylogenyNode> gene_tree_nodes_post_order = new ArrayList<PhylogenyNode>();\r
-        for( final PhylogenyNodeIterator it = gene_tree.iteratorPostorder(); it.hasNext(); ) {\r
-            gene_tree_nodes_post_order.add( it.next() );\r
+        final List<PhylogenyBranch> gene_tree_branches_post_order = new ArrayList<PhylogenyBranch>();\r
+        for( final PhylogenyNodeIterator it = _gene_tree.iteratorPostorder(); it.hasNext(); ) {\r
+            final PhylogenyNode n = it.next();\r
+            if ( !n.isRoot() ) {\r
+                gene_tree_branches_post_order.add( new PhylogenyBranch( n, n.getParent() ) );\r
+            }\r

         }\r
         }\r

-        for( final PhylogenyNode root : gene_tree_nodes_post_order ) {\r
+        for( final PhylogenyBranch branch : gene_tree_branches_post_order ) {\r

             _duplications_sum = 0;\r
             _speciation_or_duplication_events_sum = 0;\r
             _speciations_sum = 0;\r
             _duplications_sum = 0;\r
             _speciation_or_duplication_events_sum = 0;\r
             _speciations_sum = 0;\r

-            _gene_tree.reRoot( root.getId() ); //TODO reRoot( root )\r
+            _gene_tree.reRoot( branch );\r

             PhylogenyMethods.preOrderReId( getSpeciesTree() );\r
             //TEST, remove later\r
             for( final PhylogenyNodeIterator it = _gene_tree.iteratorPostorder(); it.hasNext(); ) {\r
             PhylogenyMethods.preOrderReId( getSpeciesTree() );\r
             //TEST, remove later\r
             for( final PhylogenyNodeIterator it = _gene_tree.iteratorPostorder(); it.hasNext(); ) {\r

@@ -72,9 +76,9 @@ public class GSDIR extends GSDI {
             else if ( _duplications_sum == _min_duplications_sum ) {\r
                 _min_duplications_sum_gene_trees.add( getGeneTree().copy() );\r
             }\r
             else if ( _duplications_sum == _min_duplications_sum ) {\r
                 _min_duplications_sum_gene_trees.add( getGeneTree().copy() );\r
             }\r

-            System.out.println( getDuplicationsSum() );\r

             _duplications_sum_stats.addValue( _duplications_sum );\r
         }\r
             _duplications_sum_stats.addValue( _duplications_sum );\r
         }\r

+        System.out.println( _duplications_sum_stats.getSummaryAsString() );\r

     }\r
 \r
     public int getMinDuplicationsSum() {\r
     }\r
 \r
     public int getMinDuplicationsSum() {\r

diff --git a/forester/java/src/org/forester/sdi/SDI.java b/forester/java/src/org/forester/sdi/SDI.java
index 1f1e163..fbc3c65 100644 (file)
--- a/forester/java/src/org/forester/sdi/SDI.java
+++ b/forester/java/src/org/forester/sdi/SDI.java
@@ -39,6 +39,9 @@ import org.forester.util.ForesterUtil;
 
 public abstract class SDI {
 
 
 public abstract class SDI {
 

+    public enum ALGORITHM {
+        GSDIR, GSDI, SDI, SDIR
+    }

     final Phylogeny _gene_tree;
     final Phylogeny _species_tree;
     int             _duplications_sum; // Sum of duplications.
     final Phylogeny _gene_tree;
     final Phylogeny _species_tree;
     int             _duplications_sum; // Sum of duplications.

@@ -76,9 +79,6 @@ public abstract class SDI {
         if ( species_tree.isEmpty() || gene_tree.isEmpty() ) {
             throw new IllegalArgumentException( "attempt to infer duplications using empty tree(s)" );
         }
         if ( species_tree.isEmpty() || gene_tree.isEmpty() ) {
             throw new IllegalArgumentException( "attempt to infer duplications using empty tree(s)" );
         }

-        if ( !gene_tree.isRooted() ) {
-            throw new IllegalArgumentException( "attempt to infer duplications on unrooted gene tree" );
-        }

         if ( !species_tree.isRooted() ) {
             throw new IllegalArgumentException( "attempt to infer duplications on unrooted species tree" );
         }
         if ( !species_tree.isRooted() ) {
             throw new IllegalArgumentException( "attempt to infer duplications on unrooted species tree" );
         }

diff --git a/forester/java/src/org/forester/sdi/SDIR.java b/forester/java/src/org/forester/sdi/SDIR.java
index c9224da..ce7fc00 100644 (file)
--- a/forester/java/src/org/forester/sdi/SDIR.java
+++ b/forester/java/src/org/forester/sdi/SDIR.java
@@ -266,20 +266,17 @@ public class SDIR {
             final PhylogenyNode n = iter.next();
             if ( n.isRoot() ) {
                 if ( ( n.getNumberOfDescendants() != 2 ) && ( n.getNumberOfDescendants() != 3 ) ) {
             final PhylogenyNode n = iter.next();
             if ( n.isRoot() ) {
                 if ( ( n.getNumberOfDescendants() != 2 ) && ( n.getNumberOfDescendants() != 3 ) ) {

-                    throw new IllegalArgumentException( "attempt to run SDI on gene tree with "
-                            + n.getNumberOfDescendants() + " child nodes at its root" );
+                    throw new SDIException( "gene tree has " + n.getNumberOfDescendants() + " descendents at its root" );

                 }
             }
             else if ( !n.isExternal() && ( n.getNumberOfDescendants() != 2 ) ) {
                 }
             }
             else if ( !n.isExternal() && ( n.getNumberOfDescendants() != 2 ) ) {

-                throw new IllegalArgumentException( "attempt to run SDI on gene tree which is not completely binary [found node with "
-                        + n.getNumberOfDescendants() + " child nodes]" );
+                throw new SDIException( "gene tree is not completely binary" );

             }
         }
         for( final PhylogenyNodeIterator iter = species_tree.iteratorPostorder(); iter.hasNext(); ) {
             final PhylogenyNode n = iter.next();
             if ( !n.isExternal() && ( n.getNumberOfDescendants() != 2 ) ) {
             }
         }
         for( final PhylogenyNodeIterator iter = species_tree.iteratorPostorder(); iter.hasNext(); ) {
             final PhylogenyNode n = iter.next();
             if ( !n.isExternal() && ( n.getNumberOfDescendants() != 2 ) ) {

-                throw new IllegalArgumentException( "attempt to run SDI with a species tree which is not completely binary (after stripping) [found node with "
-                        + n.getNumberOfDescendants() + " child nodes]" );
+                throw new SDIException( "species tree (after stripping) is not completely binary" );

             }
         }
         g.reRoot( g.getFirstExternalNode() );
             }
         }
         g.reRoot( g.getFirstExternalNode() );

diff --git a/forester/java/src/org/forester/test/Test.java b/forester/java/src/org/forester/test/Test.java
index 19d01c1..be7bee3 100644 (file)
--- a/forester/java/src/org/forester/test/Test.java
+++ b/forester/java/src/org/forester/test/Test.java
@@ -6888,7 +6888,7 @@ public final class Test {
                 gt.setRooted( true );
                 final GSDI sdi = new GSDI( gt, s1, true, true, true );
             }
                 gt.setRooted( true );
                 final GSDI sdi = new GSDI( gt, s1, true, true, true );
             }

-            final IntMatrix m = RIO.calculateOrthologTable( g1 );
+            final IntMatrix m = RIO.calculateOrthologTable( g1, true );

             // System.out.println( m.toString() );
         }
         catch ( final Exception e ) {
             // System.out.println( m.toString() );
         }
         catch ( final Exception e ) {

diff --git a/forester/java/src/org/forester/util/BasicDescriptiveStatistics.java b/forester/java/src/org/forester/util/BasicDescriptiveStatistics.java
index 0818951..dbb1db9 100644 (file)
--- a/forester/java/src/org/forester/util/BasicDescriptiveStatistics.java
+++ b/forester/java/src/org/forester/util/BasicDescriptiveStatistics.java
@@ -50,9 +50,6 @@ public class BasicDescriptiveStatistics implements DescriptiveStatistics {
         setDescription( desc );
     }
 
         setDescription( desc );
     }
 

-    /* (non-Javadoc)
-     * @see org.forester.util.DescriptiveStatisticsI#addValue(double)
-     */

     @Override
     public void addValue( final double d ) {
         _recalc_sigma = true;
     @Override
     public void addValue( final double d ) {
         _recalc_sigma = true;

@@ -66,18 +63,12 @@ public class BasicDescriptiveStatistics implements DescriptiveStatistics {
         }
     }
 
         }
     }
 

-    /* (non-Javadoc)
-     * @see org.forester.util.DescriptiveStatisticsI#arithmeticMean()
-     */

     @Override
     public double arithmeticMean() {
         validate();
         return getSum() / getN();
     }
 
     @Override
     public double arithmeticMean() {
         validate();
         return getSum() / getN();
     }
 

-    /* (non-Javadoc)
-     * @see org.forester.util.DescriptiveStatisticsI#asSummary()
-     */

     @Override
     public String asSummary() {
         if ( getN() > 1 ) {
     @Override
     public String asSummary() {
         if ( getN() > 1 ) {

@@ -89,18 +80,17 @@ public class BasicDescriptiveStatistics implements DescriptiveStatistics {
         }
     }
 
         }
     }
 

-    /* (non-Javadoc)
-     * @see org.forester.util.DescriptiveStatisticsI#coefficientOfVariation()
-     */

     @Override
     public double coefficientOfVariation() {
         validate();
         return ( sampleStandardDeviation() / arithmeticMean() );
     }
 
     @Override
     public double coefficientOfVariation() {
         validate();
         return ( sampleStandardDeviation() / arithmeticMean() );
     }
 

-    /* (non-Javadoc)
-     * @see org.forester.util.DescriptiveStatisticsI#getDataAsDoubleArray()
-     */
+    @Override
+    public List<Double> getData() {
+        return _data;
+    }
+

     @Override
     public double[] getDataAsDoubleArray() {
         validate();
     @Override
     public double[] getDataAsDoubleArray() {
         validate();

@@ -111,35 +101,28 @@ public class BasicDescriptiveStatistics implements DescriptiveStatistics {
         return data_array;
     }
 
         return data_array;
     }
 

-    /* (non-Javadoc)
-     * @see org.forester.util.DescriptiveStatisticsI#getMax()
-     */
+    @Override
+    public String getDescription() {
+        return _desc;
+    }
+

     @Override
     public double getMax() {
         validate();
         return _max;
     }
 
     @Override
     public double getMax() {
         validate();
         return _max;
     }
 

-    /* (non-Javadoc)
-     * @see org.forester.util.DescriptiveStatisticsI#getMin()
-     */

     @Override
     public double getMin() {
         validate();
         return _min;
     }
 
     @Override
     public double getMin() {
         validate();
         return _min;
     }
 

-    /* (non-Javadoc)
-     * @see org.forester.util.DescriptiveStatisticsI#getN()
-     */

     @Override
     public int getN() {
         return _data.size();
     }
 
     @Override
     public int getN() {
         return _data.size();
     }
 

-    /* (non-Javadoc)
-     * @see org.forester.util.DescriptiveStatisticsI#getSum()
-     */

     @Override
     public double getSum() {
         validate();
     @Override
     public double getSum() {
         validate();

@@ -151,7 +134,7 @@ public class BasicDescriptiveStatistics implements DescriptiveStatistics {
         validate();
         final double mean = arithmeticMean();
         final double sd = sampleStandardDeviation();
         validate();
         final double mean = arithmeticMean();
         final double sd = sampleStandardDeviation();

-        return "" + mean + ( ( char ) 177 ) + sd + " [" + getMin() + "..." + getMax() + "]";
+        return "" + mean + ( ( char ) 177 ) + sd + " [" + getN() + "] [" + getMin() + "-" + getMax() + "]";

     }
 
     @Override
     }
 
     @Override

@@ -160,19 +143,6 @@ public class BasicDescriptiveStatistics implements DescriptiveStatistics {
         return ( ( ( _data.get( index ) ) ).doubleValue() );
     }
 
         return ( ( ( _data.get( index ) ) ).doubleValue() );
     }
 

-    private void init() {
-        _data = new ArrayList<Double>();
-        _sum = 0.0;
-        _min = Double.MAX_VALUE;
-        _max = -Double.MAX_VALUE;
-        _sigma = 0.0;
-        _recalc_sigma = true;
-        _desc = "";
-    }
-
-    /* (non-Javadoc)
-     * @see org.forester.util.DescriptiveStatisticsI#median()
-     */

     @Override
     public double median() {
         validate();
     @Override
     public double median() {
         validate();

@@ -195,18 +165,12 @@ public class BasicDescriptiveStatistics implements DescriptiveStatistics {
         return median;
     }
 
         return median;
     }
 

-    /* (non-Javadoc)
-     * @see org.forester.util.DescriptiveStatisticsI#midrange()
-     */

     @Override
     public double midrange() {
         validate();
         return ( _min + _max ) / 2.0;
     }
 
     @Override
     public double midrange() {
         validate();
         return ( _min + _max ) / 2.0;
     }
 

-    /* (non-Javadoc)
-     * @see org.forester.util.DescriptiveStatisticsI#pearsonianSkewness()
-     */

     @Override
     public double pearsonianSkewness() {
         validate();
     @Override
     public double pearsonianSkewness() {
         validate();

@@ -216,26 +180,17 @@ public class BasicDescriptiveStatistics implements DescriptiveStatistics {
         return ( ( 3 * ( mean - median ) ) / sd );
     }
 
         return ( ( 3 * ( mean - median ) ) / sd );
     }
 

-    /* (non-Javadoc)
-     * @see org.forester.util.DescriptiveStatisticsI#sampleStandardDeviation()
-     */

     @Override
     public double sampleStandardDeviation() {
         return Math.sqrt( sampleVariance() );
     }
 
     @Override
     public double sampleStandardDeviation() {
         return Math.sqrt( sampleVariance() );
     }
 

-    /* (non-Javadoc)
-     * @see org.forester.util.DescriptiveStatisticsI#sampleStandardUnit(double)
-     */

     @Override
     public double sampleStandardUnit( final double value ) {
         validate();
         return BasicDescriptiveStatistics.sampleStandardUnit( value, arithmeticMean(), sampleStandardDeviation() );
     }
 
     @Override
     public double sampleStandardUnit( final double value ) {
         validate();
         return BasicDescriptiveStatistics.sampleStandardUnit( value, arithmeticMean(), sampleStandardDeviation() );
     }
 

-    /* (non-Javadoc)
-     * @see org.forester.util.DescriptiveStatisticsI#sampleVariance()
-     */

     @Override
     public double sampleVariance() {
         validate();
     @Override
     public double sampleVariance() {
         validate();

@@ -245,18 +200,17 @@ public class BasicDescriptiveStatistics implements DescriptiveStatistics {
         return ( sumDeviations() / ( getN() - 1 ) );
     }
 
         return ( sumDeviations() / ( getN() - 1 ) );
     }
 

-    /* (non-Javadoc)
-     * @see org.forester.util.DescriptiveStatisticsI#standardErrorOfMean()
-     */
+    @Override
+    public void setDescription( final String desc ) {
+        _desc = desc;
+    }
+

     @Override
     public double standardErrorOfMean() {
         validate();
         return ( sampleStandardDeviation() / Math.sqrt( getN() ) );
     }
 
     @Override
     public double standardErrorOfMean() {
         validate();
         return ( sampleStandardDeviation() / Math.sqrt( getN() ) );
     }
 

-    /* (non-Javadoc)
-     * @see org.forester.util.DescriptiveStatisticsI#sumDeviations()
-     */

     @Override
     public double sumDeviations() {
         validate();
     @Override
     public double sumDeviations() {
         validate();

@@ -271,9 +225,6 @@ public class BasicDescriptiveStatistics implements DescriptiveStatistics {
         return _sigma;
     }
 
         return _sigma;
     }
 

-    /* (non-Javadoc)
-     * @see org.forester.util.DescriptiveStatisticsI#toString()
-     */

     @Override
     public String toString() {
         if ( getN() < 1 ) {
     @Override
     public String toString() {
         if ( getN() < 1 ) {

@@ -308,6 +259,16 @@ public class BasicDescriptiveStatistics implements DescriptiveStatistics {
         return sb.toString();
     }
 
         return sb.toString();
     }
 

+    private void init() {
+        _data = new ArrayList<Double>();
+        _sum = 0.0;
+        _min = Double.MAX_VALUE;
+        _max = -Double.MAX_VALUE;
+        _sigma = 0.0;
+        _recalc_sigma = true;
+        _desc = "";
+    }
+

     private void validate() throws ArithmeticException {
         if ( getN() < 1 ) {
             throw new ArithmeticException( "attempt to get a result from empty data set statistics" );
     private void validate() throws ArithmeticException {
         if ( getN() < 1 ) {
             throw new ArithmeticException( "attempt to get a result from empty data set statistics" );

@@ -357,19 +318,4 @@ public class BasicDescriptiveStatistics implements DescriptiveStatistics {
     public static double sampleStandardUnit( final double value, final double mean, final double sd ) {
         return ( value - mean ) / sd;
     }
     public static double sampleStandardUnit( final double value, final double mean, final double sd ) {
         return ( value - mean ) / sd;
     }

-
-    @Override
-    public List<Double> getData() {
-        return _data;
-    }
-
-    @Override
-    public void setDescription( final String desc ) {
-        _desc = desc;
-    }
-
-    @Override
-    public String getDescription() {
-        return _desc;
-    }

 }
 }