forester/java/src/org/forester/archaeopteryx/tools/PhylogeneticInferrer.java

   1 // $Id:
   2 // forester -- software libraries and applications
   3 // for genomics and evolutionary biology research.
   4 //
   5 // Copyright (C) 2010 Christian M Zmasek
   6 // Copyright (C) 2010 Sanford-Burnham Medical Research 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: phylosoft @ gmail . com
  24 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
  25
  26 package org.forester.archaeopteryx.tools;
  27
  28 import java.io.BufferedWriter;
  29 import java.io.FileWriter;
  30 import java.io.IOException;
  31 import java.util.ArrayList;
  32 import java.util.List;
  33
  34 import javax.swing.JOptionPane;
  35
  36 import org.forester.archaeopteryx.MainFrameApplication;
  37 import org.forester.evoinference.distance.NeighborJoiningF;
  38 import org.forester.evoinference.distance.PairwiseDistanceCalculator;
  39 import org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix;
  40 import org.forester.evoinference.tools.BootstrapResampler;
  41 import org.forester.msa.BasicMsa;
  42 import org.forester.msa.Mafft;
  43 import org.forester.msa.Msa;
  44 import org.forester.msa.Msa.MSA_FORMAT;
  45 import org.forester.msa.MsaInferrer;
  46 import org.forester.msa.MsaMethods;
  47 import org.forester.msa.ResampleableMsa;
  48 import org.forester.phylogeny.Phylogeny;
  49 import org.forester.phylogeny.PhylogenyMethods;
  50 import org.forester.sequence.Sequence;
  51 import org.forester.tools.ConfidenceAssessor;
  52 import org.forester.util.ForesterUtil;
  53
  54 public class PhylogeneticInferrer extends RunnableProcess {
  55
  56     private Msa                                _msa;
  57     private final MainFrameApplication         _mf;
  58     private final PhylogeneticInferenceOptions _options;
  59     private final List<Sequence>               _seqs;
  60     private final boolean                      DEBUG           = true;
  61     public final static String                 MSA_FILE_SUFFIX = ".aln";
  62     public final static String                 PWD_FILE_SUFFIX = ".pwd";
  63
  64     public PhylogeneticInferrer( final List<Sequence> seqs,
  65                                  final PhylogeneticInferenceOptions options,
  66                                  final MainFrameApplication mf ) {
  67         _msa = null;
  68         _seqs = seqs;
  69         _mf = mf;
  70         _options = options;
  71     }
  72
  73     public PhylogeneticInferrer( final Msa msa,
  74                                  final PhylogeneticInferenceOptions options,
  75                                  final MainFrameApplication mf ) {
  76         _msa = msa;
  77         _seqs = null;
  78         _mf = mf;
  79         _options = options;
  80     }
  81
  82     private Msa inferMsa( final MSA_PRG msa_prg ) throws IOException, InterruptedException {
  83         //        final File temp_seqs_file = File.createTempFile( "__msa__temp__", ".fasta" );
  84         //        if ( DEBUG ) {
  85         //            System.out.println();
  86         //            System.out.println( "temp file: " + temp_seqs_file );
  87         //            System.out.println();
  88         //        }
  89         //        //final File temp_seqs_file = new File( _options.getTempDir() + ForesterUtil.FILE_SEPARATOR + "s.fasta" );
  90         //        final BufferedWriter writer = new BufferedWriter( new FileWriter( temp_seqs_file ) );
  91         //        SequenceWriter.writeSeqs( _seqs, writer, SEQ_FORMAT.FASTA, 100 );
  92         //        writer.close();
  93         switch ( msa_prg ) {
  94             case MAFFT:
  95                 return runMAFFT( _seqs, processMafftOptions() );
  96             default:
  97                 return null;
  98         }
  99     }
 100
 101     private List<String> processMafftOptions() {
 102         final String opts_str = _options.getMsaPrgParameters().trim().toLowerCase();
 103         final String[] opts_ary = opts_str.split( " " );
 104         final List<String> opts = new ArrayList<String>();
 105         boolean saw_quiet = false;
 106         for( final String opt : opts_ary ) {
 107             opts.add( opt );
 108             if ( opt.equals( "--quiet" ) ) {
 109                 saw_quiet = true;
 110             }
 111         }
 112         if ( !saw_quiet ) {
 113             opts.add( "--quiet" );
 114         }
 115         return opts;
 116     }
 117
 118     private Phylogeny inferPhylogeny( final Msa msa ) {
 119         BasicSymmetricalDistanceMatrix m = null;
 120         switch ( _options.getPwdDistanceMethod() ) {
 121             case KIMURA_DISTANCE:
 122                 m = PairwiseDistanceCalculator.calcKimuraDistances( msa );
 123                 break;
 124             case POISSON_DISTANCE:
 125                 m = PairwiseDistanceCalculator.calcPoissonDistances( msa );
 126                 break;
 127             case FRACTIONAL_DISSIMILARITY:
 128                 m = PairwiseDistanceCalculator.calcFractionalDissimilarities( msa );
 129                 break;
 130             default:
 131                 throw new RuntimeException( "invalid pwd method" );
 132         }
 133         if ( !ForesterUtil.isEmpty( _options.getIntermediateFilesBase() ) ) {
 134             BufferedWriter pwd_writer;
 135             try {
 136                 pwd_writer = new BufferedWriter( new FileWriter( _options.getIntermediateFilesBase() + PWD_FILE_SUFFIX ) );
 137                 m.write( pwd_writer );
 138                 pwd_writer.close();
 139             }
 140             catch ( final IOException e ) {
 141                 // TODO Auto-generated catch block
 142                 e.printStackTrace();
 143             }
 144         }
 145         final NeighborJoiningF nj = NeighborJoiningF.createInstance( false, 5 );
 146         final Phylogeny phy = nj.execute( m );
 147         PhylogenyMethods.extractFastaInformation( phy );
 148         return phy;
 149     }
 150
 151     private void infer() throws InterruptedException {
 152         //_mf.getMainPanel().getCurrentTreePanel().setWaitCursor();
 153         if ( ( _msa == null ) && ( _seqs == null ) ) {
 154             throw new IllegalArgumentException( "cannot run phylogenetic analysis with null msa and seq array" );
 155         }
 156         start( _mf, "phylogenetic inference" );
 157         if ( _msa == null ) {
 158             Msa msa = null;
 159             try {
 160                 msa = inferMsa( MSA_PRG.MAFFT );
 161             }
 162             catch ( final IOException e ) {
 163                 end( _mf );
 164                 JOptionPane.showMessageDialog( _mf,
 165                                                "Could not create multiple sequence alignment with \""
 166                                                        + _options.getMsaPrg() + "\" and the following parameters:\n\""
 167                                                        + _options.getMsaPrgParameters() + "\"\nError: "
 168                                                        + e.getLocalizedMessage(),
 169                                                "Failed to Calculate MSA",
 170                                                JOptionPane.ERROR_MESSAGE );
 171                 if ( DEBUG ) {
 172                     e.printStackTrace();
 173                 }
 174                 return;
 175             }
 176             catch ( final Exception e ) {
 177                 end( _mf );
 178                 JOptionPane.showMessageDialog( _mf,
 179                                                "Could not create multiple sequence alignment with \""
 180                                                        + _options.getMsaPrg() + "\" and the following parameters:\n\""
 181                                                        + _options.getMsaPrgParameters() + "\"\nError: "
 182                                                        + e.getLocalizedMessage(),
 183                                                "Unexpected Exception During MSA Calculation",
 184                                                JOptionPane.ERROR_MESSAGE );
 185                 if ( DEBUG ) {
 186                     e.printStackTrace();
 187                 }
 188                 return;
 189             }
 190             if ( msa == null ) {
 191                 end( _mf );
 192                 JOptionPane.showMessageDialog( _mf,
 193                                                "Could not create multiple sequence alignment with "
 194                                                        + _options.getMsaPrg() + "\nand the following parameters:\n\""
 195                                                        + _options.getMsaPrgParameters() + "\"",
 196                                                "Failed to Calculate MSA",
 197                                                JOptionPane.ERROR_MESSAGE );
 198                 return;
 199             }
 200             if ( DEBUG ) {
 201                 System.out.println( msa.toString() );
 202                 System.out.println( MsaMethods.calcGapRatio( msa ) );
 203             }
 204             final MsaMethods msa_tools = MsaMethods.createInstance();
 205             if ( _options.isExecuteMsaProcessing() ) {
 206                 msa = msa_tools.removeGapColumns( _options.getMsaProcessingMaxAllowedGapRatio(),
 207                                                   _options.getMsaProcessingMinAllowedLength(),
 208                                                   msa );
 209                 if ( msa == null ) {
 210                     end( _mf );
 211                     JOptionPane.showMessageDialog( _mf,
 212                                                    "Less than two sequences longer than "
 213                                                            + _options.getMsaProcessingMinAllowedLength()
 214                                                            + " residues left after MSA processing",
 215                                                    "MSA Processing Settings Too Stringent",
 216                                                    JOptionPane.ERROR_MESSAGE );
 217                     return;
 218                 }
 219             }
 220             if ( DEBUG ) {
 221                 System.out.println( msa_tools.getIgnoredSequenceIds() );
 222                 System.out.println( msa.toString() );
 223                 System.out.println( MsaMethods.calcGapRatio( msa ) );
 224             }
 225             _msa = msa;
 226         }
 227         final int n = _options.getBootstrapSamples();
 228         final long seed = _options.getRandomNumberGeneratorSeed();
 229         final Phylogeny master_phy = inferPhylogeny( _msa );
 230         if ( _options.isPerformBootstrapResampling() && ( n > 0 ) ) {
 231             final ResampleableMsa resampleable_msa = new ResampleableMsa( ( BasicMsa ) _msa );
 232             final int[][] resampled_column_positions = BootstrapResampler.createResampledColumnPositions( _msa
 233                     .getLength(), n, seed );
 234             final Phylogeny[] eval_phys = new Phylogeny[ n ];
 235             for( int i = 0; i < n; ++i ) {
 236                 resampleable_msa.resample( resampled_column_positions[ i ] );
 237                 eval_phys[ i ] = inferPhylogeny( resampleable_msa );
 238             }
 239             ConfidenceAssessor.evaluate( "bootstrap", eval_phys, master_phy, true, 1 );
 240         }
 241         _mf.getMainPanel().addPhylogenyInNewTab( master_phy, _mf.getConfiguration(), "nj", "njpath" );
 242         //  _mf.getMainPanel().getCurrentTreePanel().setArrowCursor();
 243         end( _mf );
 244         JOptionPane.showMessageDialog( _mf,
 245                                        "Inference successfully completed",
 246                                        "Inference Completed",
 247                                        JOptionPane.INFORMATION_MESSAGE );
 248     }
 249
 250     @Override
 251     public void run() {
 252         try {
 253             infer();
 254         }
 255         catch ( final InterruptedException e ) {
 256             // TODO need to handle this exception SOMEHOW!
 257             // TODO Auto-generated catch block
 258             e.printStackTrace();
 259         }
 260     }
 261
 262     private Msa runMAFFT( final List<Sequence> seqs, final List<String> opts ) throws IOException, InterruptedException {
 263         Msa msa = null;
 264         final MsaInferrer mafft = Mafft.createInstance( _mf.getInferenceManager().getPathToLocalMafft()
 265                 .getCanonicalPath() );
 266         try {
 267             msa = mafft.infer( seqs, opts );
 268         }
 269         catch ( final IOException e ) {
 270             System.out.println( mafft.getErrorDescription() );
 271         }
 272         return msa;
 273     }
 274
 275     private void writeToFiles( final BasicSymmetricalDistanceMatrix m ) {
 276         if ( !ForesterUtil.isEmpty( _options.getIntermediateFilesBase() ) ) {
 277             try {
 278                 final BufferedWriter msa_writer = new BufferedWriter( new FileWriter( _options.getIntermediateFilesBase()
 279                         + MSA_FILE_SUFFIX ) );
 280                 _msa.write( msa_writer, MSA_FORMAT.PHYLIP );
 281                 msa_writer.close();
 282                 final BufferedWriter pwd_writer = new BufferedWriter( new FileWriter( _options.getIntermediateFilesBase()
 283                         + PWD_FILE_SUFFIX ) );
 284                 m.write( pwd_writer );
 285                 pwd_writer.close();
 286             }
 287             catch ( final Exception e ) {
 288                 System.out.println( "Error: " + e.getMessage() );
 289             }
 290         }
 291     }
 292
 293     public enum MSA_PRG {
 294         MAFFT;
 295     }
 296 }