old version...

diff --git a/forester/java/src/org/forester/application/cladinatorOLD.java b/forester/java/src/org/forester/application/cladinatorOLD.java
new file mode 100644 (file)
index 0000000..23fe98a
--- /dev/null
+++ b/forester/java/src/org/forester/application/cladinatorOLD.java
@@ -0,0 +1,181 @@
+// $Id:
+// FORESTER -- software libraries and applications
+// for evolutionary biology research and applications.
+//
+// Copyright (C) 2017 Christian M. Zmasek
+// Copyright (C) 2017 J. Craig Venter Institute
+// 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: phyloxml @ gmail . com
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
+
+package org.forester.application;
+
+import java.io.File;
+import java.io.IOException;
+import java.text.DecimalFormat;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.forester.clade_analysis.AnalysisSingle;
+import org.forester.clade_analysis.ResultSingle;
+import org.forester.io.parsers.PhylogenyParser;
+import org.forester.io.parsers.util.ParserUtils;
+import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
+import org.forester.phylogeny.factories.PhylogenyFactory;
+import org.forester.util.CommandLineArguments;
+import org.forester.util.ForesterUtil;
+
+public final class cladinatorOLD {
+
+    final static private String        PRG_NAME      = "cladinator";
+    final static private String        PRG_VERSION   = "0.101";
+    final static private String        PRG_DATE      = "170810";
+    final static private String        PRG_DESC      = "clades within clades -- analysis of pplacer type outputs";
+    final static private String        E_MAIL        = "phyloxml@gmail.com";
+    final static private String        WWW           = "https://sites.google.com/site/cmzmasek/home/software/forester";
+    final static private String        HELP_OPTION_1 = "help";
+    final static private String        HELP_OPTION_2 = "h";
+    final static private String        SEP_OPTION    = "s";
+    private final static DecimalFormat df2           = new DecimalFormat( "0.0#" );
+
+    public static void main( final String args[] ) {
+        try {
+            ForesterUtil.printProgramInformation( PRG_NAME,
+                                                  PRG_DESC,
+                                                  PRG_VERSION,
+                                                  PRG_DATE,
+                                                  E_MAIL,
+                                                  WWW,
+                                                  ForesterUtil.getForesterLibraryInformation() );
+            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 != 2 && 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>();
+            allowed_options.add( SEP_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 separator;
+            if ( cla.isOptionSet( SEP_OPTION ) ) {
+                separator = cla.getOptionValue( SEP_OPTION );
+            }
+            else {
+                separator = null;
+            }
+            final File intreefile = cla.getFile( 0 );
+            final String query = cla.getName( 1 );
+            System.out.println( "Input tree: " + intreefile );
+            System.out.println( "Query     : " + query );
+            if ( !ForesterUtil.isEmpty( separator ) ) {
+                System.out.println( "Separator : " + separator );
+            }
+            else {
+                System.out.println( "Separator : none" );
+            }
+            Phylogeny p = null;
+            try {
+                final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+                final PhylogenyParser pp = ParserUtils.createParserDependingOnFileType( intreefile, true );
+                p = factory.create( intreefile, pp )[ 0 ];
+            }
+            catch ( final IOException e ) {
+                System.out.println( "\nCould not read \"" + intreefile + "\" [" + e.getMessage() + "]\n" );
+                System.exit( -1 );
+            }
+            final ResultSingle res = AnalysisSingle.execute( p, query, separator );
+            System.out.println();
+            System.out.println( "Result:" );
+            System.out.println( "Query                        : " + query );
+            System.out.print( "Greatest Common Prefix       : " + res.getGreatestCommonPrefix() );
+            if ( !ForesterUtil.isEmpty( res.getGreatestCommonPrefix() )
+                    && !ForesterUtil.isEmpty( res.getGreatestCommonCladeSubtreeConfidence() ) ) {
+                System.out.println( "\t(" + res.getGreatestCommonCladeSubtreeConfidence() + ")" );
+            }
+            else {
+                System.out.println();
+            }
+            System.out.print( "Greatest Common Prefix Up    : " + res.getGreatestCommonPrefixUp() );
+            if ( !ForesterUtil.isEmpty( res.getGreatestCommonPrefixUp() )
+                    && !ForesterUtil.isEmpty( res.getGreatestCommonCladeUpSubtreeConfidence() ) ) {
+                System.out.println( "\t(" + res.getGreatestCommonCladeUpSubtreeConfidence() + ")" );
+            }
+            else {
+                System.out.println();
+            }
+            System.out.print( "Greatest Common Prefix Down  : " + res.getGreatestCommonPrefixDown() );
+            if ( !ForesterUtil.isEmpty( res.getGreatestCommonPrefixDown() )
+                    && !ForesterUtil.isEmpty( res.getGreatestCommonCladeDownSubtreeConfidence() ) ) {
+                System.out.println( "\t(" + res.getGreatestCommonCladeDownSubtreeConfidence() + ")" );
+            }
+            else {
+                System.out.println();
+            }
+            System.out.println( "Least Encompassing Clade size: " + res.getLeastEncompassingCladeSize()
+                    + " external nodes" );
+            final double lec_ratio = ( 100.0 * res.getLeastEncompassingCladeSize() ) / res.getTreeSize();
+            System.out.println( "Least Encompassing Clade size: " + df2.format( lec_ratio ) + "%" );
+            System.out.println( "Total tree size              : " + res.getTreeSize() + " external nodes" );
+            if ( res.getWarnings().size() > 0 ) {
+                System.out.println( "Warnings:" );
+                for( final String s : res.getWarnings() ) {
+                    System.out.println( s );
+                }
+            }
+            System.out.println();
+        }
+        catch ( final IllegalArgumentException e ) {
+            ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
+        }
+        catch ( final Exception e ) {
+            e.printStackTrace();
+            ForesterUtil.fatalError( PRG_NAME, "Unexpected errror!" );
+        }
+    }
+
+    private final static void print_help() {
+        System.out.println( "Usage:" );
+        System.out.println();
+        System.out.println( PRG_NAME + " [options] <gene tree file> <query>" );
+        System.out.println();
+        System.out.println( " options:" );
+        System.out.println( "  -" + SEP_OPTION + "=<separator>: the separator to be used" );
+        System.out.println();
+        System.out.println( "Example:" );
+        System.out.println();
+        System.out.println( " " + PRG_NAME + " -s=. my_tree.xml A.1.1.1" );
+        System.out.println();
+    }
+}