moved classes into different project

diff --git a/forester/java/src/org/forester/application/get_distances.java b/forester/java/src/org/forester/application/get_distances.java
deleted file mode 100644 (file)
index 87d9918..0000000
--- a/forester/java/src/org/forester/application/get_distances.java
+++ /dev/null
@@ -1,92 +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.BufferedReader;
-import java.io.BufferedWriter;
-import java.io.File;
-import java.io.FileReader;
-import java.io.FileWriter;
-import java.io.IOException;
-import java.util.StringTokenizer;
-
-import org.forester.io.parsers.PhylogenyParser;
-import org.forester.phylogeny.Phylogeny;
-import org.forester.phylogeny.PhylogenyMethods;
-import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
-import org.forester.phylogeny.factories.PhylogenyFactory;
-import org.forester.util.ForesterUtil;
-
-public class get_distances {
-
-    public static void main( final String args[] ) {
-        if ( args.length != 3 ) {
-            System.out.println( "\nget_distances: Wrong number of arguments.\n" );
-            System.out.println( "Usage: \"get_distances <phylogeny file> <file with node names> <outfile>\"\n" );
-            System.exit( -1 );
-        }
-        final File phylogeny_infile = new File( args[ 0 ] );
-        final File names_infile = new File( args[ 1 ] );
-        final File outfile = new File( args[ 2 ] );
-        Phylogeny p = null;
-        try {
-            final PhylogenyParser pp = ForesterUtil.createParserDependingOnFileType( phylogeny_infile, true );
-            final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
-            p = factory.create( phylogeny_infile, pp )[ 0 ];
-        }
-        catch ( final Exception e ) {
-            System.out.println( "\nCould not read \"" + phylogeny_infile + "\" [" + e.getMessage() + "]\n" );
-            System.exit( -1 );
-        }
-        String line = "";
-        try {
-            final BufferedReader in = new BufferedReader( new FileReader( names_infile ) );
-            final BufferedWriter out = new BufferedWriter( new FileWriter( outfile ) );
-            while ( ( line = in.readLine() ) != null ) {
-                if ( line.length() < 3 ) {
-                    continue;
-                }
-                final StringTokenizer st = new StringTokenizer( line );
-                if ( st.countTokens() < 2 ) {
-                    continue;
-                }
-                final double d = PhylogenyMethods.getInstance().calculateDistance( p.getNode( st.nextToken() ),
-                                                                                   p.getNode( st.nextToken() ) );
-                out.write( line + " " + d );
-                out.newLine();
-            }
-            out.flush();
-            out.close();
-            in.close();
-        }
-        catch ( final IOException e ) {
-            System.out.println( "\nError during processing of \"" + names_infile + "\" [" + e.getMessage()
-                    + "] at line \"" + line + "\"\n" );
-            System.exit( -1 );
-        }
-        System.out.println( "\nDone.\n" );
-    }
-}