removed old classes/tools

diff --git a/forester/java/src/org/forester/application/sdix.java b/forester/java/src/org/forester/application/sdix.java
deleted file mode 100644 (file)
index 9375b2d..0000000
--- a/forester/java/src/org/forester/application/sdix.java
+++ /dev/null
@@ -1,196 +0,0 @@
-// $Id:
-// FORESTER -- software libraries and applications
-// for evolutionary biology research and applications.
-//
-// Copyright (C) 2008-2009 Christian M. Zmasek
-// Copyright (C) 2008-2009 Burnham Institute for Medical Research
-// All rights reserved
-//
-// This library is free software; you can redistribute it and/or
-// modify it under the terms of the GNU Lesser General Public
-// License as published by the Free Software Foundation; either
-// version 2.1 of the License, or (at your option) any later version.
-//
-// This library is distributed in the hope that it will be useful,
-// but WITHOUT ANY WARRANTY; without even the implied warranty of
-// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
-// Lesser General Public License for more details.
-//
-// You should have received a copy of the GNU Lesser General Public
-// License along with this library; if not, write to the Free Software
-// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-//
-// Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
-
-package org.forester.application;
-
-import java.io.File;
-import java.io.FilenameFilter;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
-
-import org.forester.io.parsers.phyloxml.PhyloXmlParser;
-import org.forester.phylogeny.Phylogeny;
-import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
-import org.forester.phylogeny.factories.PhylogenyFactory;
-import org.forester.sdi.SDIException;
-import org.forester.sdi.SDIx;
-import org.forester.util.CommandLineArguments;
-import org.forester.util.ForesterUtil;
-
-public class sdix {
-
-    final static private String HELP_OPTION_1 = "help";
-    final static private String HELP_OPTION_2 = "h";
-    final static private String PRG_NAME      = "sdix";
-    final static private String PRG_VERSION   = "0.001 alpha";
-    final static private String PRG_DATE      = "2009.10.14";
-
-    public static void main( final String args[] ) throws SDIException {
-        ForesterUtil.printProgramInformation( PRG_NAME, PRG_VERSION, PRG_DATE );
-        System.out.println();
-        CommandLineArguments cla = null;
-        try {
-            cla = new CommandLineArguments( args );
-        }
-        catch ( final Exception e ) {
-            ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
-        }
-        if ( cla.isOptionSet( HELP_OPTION_1 ) || cla.isOptionSet( HELP_OPTION_2 ) ) {
-            System.out.println();
-            print_help();
-            System.exit( 0 );
-        }
-        else if ( ( args.length != 3 ) ) {
-            System.out.println();
-            System.out.println( "wrong number of arguments" );
-            System.out.println();
-            print_help();
-            System.exit( -1 );
-        }
-        final List<String> allowed_options = new ArrayList<String>();
-        final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options );
-        if ( dissallowed_options.length() > 0 ) {
-            ForesterUtil.fatalError( PRG_NAME, "unknown option(s): " + dissallowed_options );
-        }
-        File gene_trees_dir = null;
-        File species_trees_file = null;
-        //File out_file = null;
-        File out_dir = null;
-        Phylogeny[] species_trees = null;
-        try {
-            gene_trees_dir = cla.getFile( 0 );
-            species_trees_file = cla.getFile( 1 );
-            out_dir = cla.getFile( 2 );
-        }
-        catch ( final IllegalArgumentException e ) {
-            ForesterUtil.fatalError( PRG_NAME, "error in command line: " + e.getMessage() );
-        }
-        if ( ForesterUtil.isReadableFile( species_trees_file ) != null ) {
-            ForesterUtil.fatalError( PRG_NAME, ForesterUtil.isReadableFile( species_trees_file ) );
-        }
-        if ( !gene_trees_dir.isDirectory() || !gene_trees_dir.canRead() ) {
-            ForesterUtil.fatalError( PRG_NAME, "cannot read gene trees from [" + gene_trees_dir + "]" );
-        }
-        // if ( ForesterUtil.isWritableFile( out_file ) != null ) {
-        //     ForesterUtil.fatalError( PRG_NAME, ForesterUtil.isWritableFile( out_file ) );
-        // }
-        if ( !out_dir.exists() ) {
-            boolean success = false;
-            try {
-                success = out_dir.mkdir();
-            }
-            catch ( final Exception e ) {
-                ForesterUtil.fatalError( PRG_NAME, "failed to create [" + out_dir + "] [" + e.getMessage() + "]" );
-            }
-            if ( !success ) {
-                ForesterUtil.fatalError( PRG_NAME, "failed to create [" + out_dir + "]" );
-            }
-        }
-        try {
-            final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
-            species_trees = factory.create( species_trees_file, new PhyloXmlParser() );
-        }
-        catch ( final IOException e ) {
-            ForesterUtil.fatalError( PRG_NAME,
-                                     "failed to read species trees from [" + species_trees_file + "] ["
-                                             + e.getMessage() + "]" );
-        }
-        if ( ( species_trees == null ) || ( species_trees.length < 1 ) ) {
-            ForesterUtil.fatalError( PRG_NAME, "failed to read species trees from [" + species_trees_file + "]" );
-        }
-        ForesterUtil.programMessage( PRG_NAME, "read in " + species_trees.length + " species trees from ["
-                + species_trees_file + "]" );
-        final FilenameFilter filter = new FilenameFilter() {
-
-            @Override
-            public boolean accept( final File dir, final String name ) {
-                return ( !name.startsWith( "." ) && !name.startsWith( "00_" ) && name.endsWith( ".xml" ) );
-            }
-        };
-        final String[] gene_tree_names = gene_trees_dir.list( filter );
-        Arrays.sort( gene_tree_names );
-        final List<File> gene_tree_files = new ArrayList<File>();
-        for( final String gene_tree_name : gene_tree_names ) {
-            final File gene_tree_file = new File( gene_trees_dir + ForesterUtil.FILE_SEPARATOR + gene_tree_name );
-            if ( !gene_tree_file.isDirectory() ) {
-                gene_tree_files.add( gene_tree_file );
-            }
-        }
-        ForesterUtil.programMessage( PRG_NAME, "going to analyze " + gene_tree_files.size() + " gene trees from ["
-                + gene_trees_dir + "]" );
-        final SDIx shin = new SDIx();
-        try {
-            shin.method1( gene_tree_files, species_trees, out_dir );
-        }
-        catch ( final IOException e ) {
-            ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
-            e.printStackTrace();
-        }
-        ForesterUtil.programMessage( PRG_NAME, "OK" );
-        //        System.out.println();
-        //        System.out.println( "Strip species tree: " + strip );
-        //        SDI sdi = null;
-        //        final long start_time = new Date().getTime();
-        //        try {
-        //            if ( use_sdise ) {
-        //                System.out.println();
-        //                System.out.println( "Using SDIse algorithm." );
-        //                sdi = new SDIse( gene_tree, species_tree );
-        //            }
-        //            else {
-        //                System.out.println();
-        //                System.out.println( "Using GSDI algorithm." );
-        //                System.out.println();
-        //                System.out.println( "Use most parsimonous duplication model: " + most_parsimonous_duplication_model );
-        //                sdi = new GSDI( gene_tree, species_tree, most_parsimonous_duplication_model );
-        //            }
-        //        }
-        //        catch ( final Exception e ) {
-        //            ForesterUtil.unexpectedFatalError( PRG_NAME, e );
-        //        }
-        //        System.out.println();
-        //        System.out.println( "Running time (excluding I/O): " + ( new Date().getTime() - start_time ) + "ms" );
-        //        try {
-        //            final PhylogenyWriter writer = new PhylogenyWriter();
-        //            writer.toPhyloXML( out_file, gene_tree, 1 );
-        //        }
-        //        catch ( final IOException e ) {
-        //            ForesterUtil.fatalError( PRG_NAME, "Failed to write to \"" + out_file + "\" [" + e.getMessage() + "]" );
-        //        }
-        //        System.out.println();
-        //        System.out.println( "Successfully wrote resulting gene tree to: " + out_file );
-        //        System.out.println();
-        //        System.out.println();
-    }
-
-    private static void print_help() {
-        System.out.println( "Usage: " + PRG_NAME + " [-options] <gene trees dir> <species tree file name> <outdir>" );
-        System.out.println();
-        System.out.println( "Options:" );
-        System.out.println();
-    }
-}

diff --git a/forester/java/src/org/forester/sdi/SDIx.java b/forester/java/src/org/forester/sdi/SDIx.java
deleted file mode 100644 (file)
index 4667f72..0000000
--- a/forester/java/src/org/forester/sdi/SDIx.java
+++ /dev/null
@@ -1,134 +0,0 @@
-// $Id:
-// FORESTER -- software libraries and applications
-// for evolutionary biology research and applications.
-//
-// Copyright (C) 2008-2009 Christian M. Zmasek
-// Copyright (C) 2008-2009 Burnham Institute for Medical Research
-// All rights reserved
-//
-// This library is free software; you can redistribute it and/or
-// modify it under the terms of the GNU Lesser General Public
-// License as published by the Free Software Foundation; either
-// version 2.1 of the License, or (at your option) any later version.
-//
-// This library is distributed in the hope that it will be useful,
-// but WITHOUT ANY WARRANTY; without even the implied warranty of
-// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
-// Lesser General Public License for more details.
-//
-// You should have received a copy of the GNU Lesser General Public
-// License along with this library; if not, write to the Free Software
-// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-//
-// Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
-
-package org.forester.sdi;
-
-import java.io.File;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
-import org.forester.io.parsers.phyloxml.PhyloXmlParser;
-import org.forester.io.writers.PhylogenyWriter;
-import org.forester.phylogeny.Phylogeny;
-import org.forester.phylogeny.PhylogenyMethods;
-import org.forester.phylogeny.PhylogenyNode;
-import org.forester.phylogeny.data.Taxonomy;
-import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
-import org.forester.phylogeny.factories.PhylogenyFactory;
-import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
-import org.forester.util.ForesterUtil;
-
-public class SDIx {
-
-    public SDIx() {
-    }
-
-    private void analyze( final Phylogeny gene_tree,
-                          final String gene_tree_file_name,
-                          final Phylogeny[] species_trees,
-                          final File out_dir ) throws IOException, SDIException {
-        final boolean minimize_cost = true;
-        final boolean minimize_sum_of_dup = true;
-        final boolean minimize_height = true;
-        final int trees_to_return = 1;
-        System.out.println( gene_tree_file_name + ": " + gene_tree.getName() );
-        final Set<Taxonomy> species_tree_species = getAllExternalSpecies( species_trees[ 0 ] );
-        final PhylogenyWriter w = new PhylogenyWriter();
-        for( final Phylogeny species_tree : species_trees ) {
-            PhylogenyMethods.deleteExternalNodesPositiveSelection( species_tree_species, gene_tree );
-            if ( gene_tree.isEmpty() ) {
-                System.out.println( " >> empty: " + gene_tree_file_name + ": " + gene_tree.getName() );
-                continue;
-            }
-            final File outfile = new File( out_dir + ForesterUtil.FILE_SEPARATOR + gene_tree_file_name );
-            if ( outfile.exists() ) {
-                System.out
-                        .println( " >> already exists, skipping: " + gene_tree_file_name + ": " + gene_tree.getName() );
-            }
-            final SDIR sdir = new SDIR();
-            final Phylogeny[] analyzed_gene_trees = sdir.infer( gene_tree,
-                                                                species_tree,
-                                                                minimize_cost,
-                                                                minimize_sum_of_dup,
-                                                                minimize_height,
-                                                                true,
-                                                                trees_to_return );
-            final int duplications = sdir.getMinimalDuplications();
-            final int mapping_cost = sdir.getMinimalMappingCost();
-            final List<Phylogeny> phys = new ArrayList<Phylogeny>();
-            for( final Phylogeny phy : analyzed_gene_trees ) {
-                phys.add( phy );
-            }
-            w.toPhyloXML( outfile, phys, 0, ForesterUtil.LINE_SEPARATOR );
-        }
-    }
-
-    private void checkSpeciesTreesForEqualNumberOfExtNodes( final Phylogeny[] species_trees ) {
-        int ext_nodes = -1;
-        for( final Phylogeny phylogeny : species_trees ) {
-            if ( ext_nodes < 0 ) {
-                ext_nodes = phylogeny.getNumberOfExternalNodes();
-            }
-            else if ( ext_nodes != phylogeny.getNumberOfExternalNodes() ) {
-                throw new IllegalArgumentException( "species trees must have all the same number of external nodes" );
-            }
-        }
-    }
-
-    public void method1( final List<File> gene_tree_files, final Phylogeny[] species_trees, final File out_dir )
-            throws IOException, SDIException {
-        checkSpeciesTreesForEqualNumberOfExtNodes( species_trees );
-        final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
-        for( final File gene_tree_file : gene_tree_files ) {
-            if ( ForesterUtil.isReadableFile( gene_tree_file ) != null ) {
-                throw new IOException( "[" + gene_tree_file + "] is not readable" );
-            }
-            Phylogeny[] gene_trees = null;
-            gene_trees = factory.create( gene_tree_file, new PhyloXmlParser() );
-            if ( gene_trees.length != 1 ) {
-                throw new IOException( "[" + gene_tree_file + "] contains " + gene_trees.length
-                        + " gene trees, expecting precisely one" );
-            }
-            analyze( gene_trees[ 0 ], gene_tree_file.getName(), species_trees, out_dir );
-        }
-    }
-
-    private static Set<Taxonomy> getAllExternalSpecies( final Phylogeny phy ) {
-        final Set<Taxonomy> specs = new HashSet<Taxonomy>();
-        for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
-            final PhylogenyNode n = it.next();
-            if ( n.getNodeData().isHasTaxonomy() ) {
-                specs.add( n.getNodeData().getTaxonomy() );
-            }
-            else {
-                throw new IllegalArgumentException( "node " + n.getId() + " has no taxonomic data" );
-            }
-        }
-        return specs;
-    }
-}