forester/java/src/org/forester/application/cladinator.java

   1 // $Id:
   2 // FORESTER -- software libraries and applications
   3 // for evolutionary biology research and applications.
   4 //
   5 // Copyright (C) 2017 Christian M. Zmasek
   6 // Copyright (C) 2017 J. Craig Venter Institute
   7 // All rights reserved
   8 //
   9 // This library is free software; you can redistribute it and/or
  10 // modify it under the terms of the GNU Lesser General Public
  11 // License as published by the Free Software Foundation; either
  12 // version 2.1 of the License, or (at your option) any later version.
  13 //
  14 // This library is distributed in the hope that it will be useful,
  15 // but WITHOUT ANY WARRANTY; without even the implied warranty of
  16 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
  17 // Lesser General Public License for more details.
  18 //
  19 // You should have received a copy of the GNU Lesser General Public
  20 // License along with this library; if not, write to the Free Software
  21 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
  22 //
  23 // Contact: phyloxml @ gmail . com
  24 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
  25
  26 package org.forester.application;
  27
  28 import java.io.File;
  29 import java.io.IOException;
  30 import java.text.DecimalFormat;
  31 import java.util.ArrayList;
  32 import java.util.List;
  33
  34 import org.forester.clade_analysis.Analysis;
  35 import org.forester.clade_analysis.Result;
  36 import org.forester.io.parsers.PhylogenyParser;
  37 import org.forester.io.parsers.util.ParserUtils;
  38 import org.forester.phylogeny.Phylogeny;
  39 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
  40 import org.forester.phylogeny.factories.PhylogenyFactory;
  41 import org.forester.util.CommandLineArguments;
  42 import org.forester.util.ForesterUtil;
  43
  44 public final class cladinator {
  45
  46     final static private String        PRG_NAME      = "cladinator";
  47     final static private String        PRG_VERSION   = "0.101";
  48     final static private String        PRG_DATE      = "170810";
  49     final static private String        PRG_DESC      = "clades within clades -- analysis of pplacer type outputs";
  50     final static private String        E_MAIL        = "phyloxml@gmail.com";
  51     final static private String        WWW           = "https://sites.google.com/site/cmzmasek/home/software/forester";
  52     final static private String        HELP_OPTION_1 = "help";
  53     final static private String        HELP_OPTION_2 = "h";
  54     final static private String        SEP_OPTION    = "s";
  55     private final static DecimalFormat df2           = new DecimalFormat( ".##" );
  56
  57     public static void main( final String args[] ) {
  58         try {
  59             ForesterUtil.printProgramInformation( PRG_NAME,
  60                                                   PRG_DESC,
  61                                                   PRG_VERSION,
  62                                                   PRG_DATE,
  63                                                   E_MAIL,
  64                                                   WWW,
  65                                                   ForesterUtil.getForesterLibraryInformation() );
  66             CommandLineArguments cla = null;
  67             try {
  68                 cla = new CommandLineArguments( args );
  69             }
  70             catch ( final Exception e ) {
  71                 ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
  72             }
  73             if ( cla.isOptionSet( HELP_OPTION_1 ) || cla.isOptionSet( HELP_OPTION_2 ) ) {
  74                 System.out.println();
  75                 print_help();
  76                 System.exit( 0 );
  77             }
  78             else if ( ( args.length != 2 && args.length != 3 ) ) {
  79                 System.out.println();
  80                 System.out.println( "Wrong number of arguments." );
  81                 System.out.println();
  82                 print_help();
  83                 System.exit( -1 );
  84             }
  85             final List<String> allowed_options = new ArrayList<String>();
  86             allowed_options.add( SEP_OPTION );
  87             final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options );
  88             if ( dissallowed_options.length() > 0 ) {
  89                 ForesterUtil.fatalError( PRG_NAME, "unknown option(s): " + dissallowed_options );
  90             }
  91             final String separator;
  92             if ( cla.isOptionSet( SEP_OPTION ) ) {
  93                 separator = cla.getOptionValue( SEP_OPTION );
  94             }
  95             else {
  96                 separator = null;
  97             }
  98             final File intreefile = cla.getFile( 0 );
  99             final String query = cla.getName( 1 );
 100             System.out.println( "Input tree: " + intreefile );
 101             System.out.println( "Query     : " + query );
 102             if ( !ForesterUtil.isEmpty( separator ) ) {
 103                 System.out.println( "Separator : " + separator );
 104             }
 105             else {
 106                 System.out.println( "Separator : none" );
 107             }
 108             Phylogeny p = null;
 109             try {
 110                 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
 111                 final PhylogenyParser pp = ParserUtils.createParserDependingOnFileType( intreefile, true );
 112                 p = factory.create( intreefile, pp )[ 0 ];
 113             }
 114             catch ( final IOException e ) {
 115                 System.out.println( "\nCould not read \"" + intreefile + "\" [" + e.getMessage() + "]\n" );
 116                 System.exit( -1 );
 117             }
 118             final Result res = Analysis.execute( p, query, separator );
 119             System.out.println();
 120             System.out.println( "Result:" );
 121             System.out.println( "Query                        : " + query );
 122             System.out.print( "Greatest Common Prefix       : " + res.getGreatestCommonPrefix() );
 123             if ( !ForesterUtil.isEmpty( res.getGreatestCommonPrefix() )
 124                     && !ForesterUtil.isEmpty( res.getGreatestCommonCladeSubtreeConfidence() ) ) {
 125                 System.out.println( "\t(" + res.getGreatestCommonCladeSubtreeConfidence() + ")" );
 126             }
 127             else {
 128                 System.out.println();
 129             }
 130             System.out.print( "Greatest Common Prefix Up    : " + res.getGreatestCommonPrefixUp() );
 131             if ( !ForesterUtil.isEmpty( res.getGreatestCommonPrefixUp() )
 132                     && !ForesterUtil.isEmpty( res.getGreatestCommonCladeUpSubtreeConfidence() ) ) {
 133                 System.out.println( "\t(" + res.getGreatestCommonCladeUpSubtreeConfidence() + ")" );
 134             }
 135             else {
 136                 System.out.println();
 137             }
 138             System.out.print( "Greatest Common Prefix Down  : " + res.getGreatestCommonPrefixDown() );
 139             if ( !ForesterUtil.isEmpty( res.getGreatestCommonPrefixDown() )
 140                     && !ForesterUtil.isEmpty( res.getGreatestCommonCladeDownSubtreeConfidence() ) ) {
 141                 System.out.println( "\t(" + res.getGreatestCommonCladeDownSubtreeConfidence() + ")" );
 142             }
 143             else {
 144                 System.out.println();
 145             }
 146             System.out.println( "Least Encompassing Clade size: " + res.getLeastEncompassingCladeSize()
 147                     + " external nodes" );
 148             final double lec_ratio = ( 100.0 * res.getLeastEncompassingCladeSize() ) / res.getTreeSize();
 149             System.out.println( "Least Encompassing Clade size: " + df2.format( lec_ratio ) + "%" );
 150             System.out.println( "Total tree size              : " + res.getTreeSize() + " external nodes" );
 151             if ( res.getWarnings().size() > 0 ) {
 152                 System.out.println( "Warnings:" );
 153                 for( final String s : res.getWarnings() ) {
 154                     System.out.println( s );
 155                 }
 156             }
 157             System.out.println();
 158         }
 159         catch ( final IllegalArgumentException e ) {
 160             ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
 161         }
 162         catch ( final Exception e ) {
 163             e.printStackTrace();
 164             ForesterUtil.fatalError( PRG_NAME, "Unexpected errror!" );
 165         }
 166     }
 167
 168     private final static void print_help() {
 169         System.out.println( "Usage:" );
 170         System.out.println();
 171         System.out.println( PRG_NAME + " [options] <gene tree file> <query>" );
 172         System.out.println();
 173         System.out.println( " options:" );
 174         System.out.println( "  -" + SEP_OPTION + "=<separator>: the separator to be used" );
 175         System.out.println();
 176         System.out.println( "Example:" );
 177         System.out.println();
 178         System.out.println( " " + PRG_NAME + " -s=. my_tree.xml A.1.1.1" );
 179         System.out.println();
 180     }
 181 }