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.MolecularSequence;
  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<MolecularSequence>      _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<MolecularSequence> 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.addMolecularSeqsToTree( phy, msa );
 148         PhylogenyMethods.extractFastaInformation( phy );
 149         return phy;
 150     }
 151
 152     private void infer() throws InterruptedException {
 153         //_mf.getMainPanel().getCurrentTreePanel().setWaitCursor();
 154         if ( ( _msa == null ) && ( _seqs == null ) ) {
 155             throw new IllegalArgumentException( "cannot run phylogenetic analysis with null msa and seq array" );
 156         }
 157         start( _mf, "phylogenetic inference" );
 158         if ( _msa == null ) {
 159             Msa msa = null;
 160             try {
 161                 msa = inferMsa( MSA_PRG.MAFFT );
 162             }
 163             catch ( final IOException e ) {
 164                 end( _mf );
 165                 JOptionPane.showMessageDialog( _mf,
 166                                                "Could not create multiple sequence alignment with \""
 167                                                        + _options.getMsaPrg() + "\" and the following parameters:\n\""
 168                                                        + _options.getMsaPrgParameters() + "\"\nError: "
 169                                                        + e.getLocalizedMessage(),
 170                                                "Failed to Calculate MSA",
 171                                                JOptionPane.ERROR_MESSAGE );
 172                 if ( DEBUG ) {
 173                     e.printStackTrace();
 174                 }
 175                 return;
 176             }
 177             catch ( final Exception e ) {
 178                 end( _mf );
 179                 JOptionPane.showMessageDialog( _mf,
 180                                                "Could not create multiple sequence alignment with \""
 181                                                        + _options.getMsaPrg() + "\" and the following parameters:\n\""
 182                                                        + _options.getMsaPrgParameters() + "\"\nError: "
 183                                                        + e.getLocalizedMessage(),
 184                                                "Unexpected Exception During MSA Calculation",
 185                                                JOptionPane.ERROR_MESSAGE );
 186                 if ( DEBUG ) {
 187                     e.printStackTrace();
 188                 }
 189                 return;
 190             }
 191             if ( msa == null ) {
 192                 end( _mf );
 193                 JOptionPane.showMessageDialog( _mf,
 194                                                "Could not create multiple sequence alignment with "
 195                                                        + _options.getMsaPrg() + "\nand the following parameters:\n\""
 196                                                        + _options.getMsaPrgParameters() + "\"",
 197                                                "Failed to Calculate MSA",
 198                                                JOptionPane.ERROR_MESSAGE );
 199                 return;
 200             }
 201             if ( DEBUG ) {
 202                 System.out.println( msa.toString() );
 203                 System.out.println( MsaMethods.calcGapRatio( msa ) );
 204             }
 205             final MsaMethods msa_tools = MsaMethods.createInstance();
 206             if ( _options.isExecuteMsaProcessing() ) {
 207                 msa = msa_tools.deleteGapColumns( _options.getMsaProcessingMaxAllowedGapRatio(),
 208                                                   _options.getMsaProcessingMinAllowedLength(),
 209                                                   msa );
 210                 if ( msa == null ) {
 211                     end( _mf );
 212                     JOptionPane.showMessageDialog( _mf,
 213                                                    "Less than two sequences longer than "
 214                                                            + _options.getMsaProcessingMinAllowedLength()
 215                                                            + " residues left after MSA processing",
 216                                                    "MSA Processing Settings Too Stringent",
 217                                                    JOptionPane.ERROR_MESSAGE );
 218                     return;
 219                 }
 220             }
 221             if ( DEBUG ) {
 222                 System.out.println( msa_tools.getIgnoredSequenceIds() );
 223                 System.out.println( msa.toString() );
 224                 System.out.println( MsaMethods.calcGapRatio( msa ) );
 225             }
 226             _msa = msa;
 227         }
 228         final int n = _options.getBootstrapSamples();
 229         final long seed = _options.getRandomNumberGeneratorSeed();
 230         final Phylogeny master_phy = inferPhylogeny( _msa );
 231         if ( _options.isPerformBootstrapResampling() && ( n > 0 ) ) {
 232             final ResampleableMsa resampleable_msa = new ResampleableMsa( ( BasicMsa ) _msa );
 233             final int[][] resampled_column_positions = BootstrapResampler.createResampledColumnPositions( _msa
 234                     .getLength(), n, seed );
 235             final Phylogeny[] eval_phys = new Phylogeny[ n ];
 236             for( int i = 0; i < n; ++i ) {
 237                 resampleable_msa.resample( resampled_column_positions[ i ] );
 238                 eval_phys[ i ] = inferPhylogeny( resampleable_msa );
 239             }
 240             ConfidenceAssessor.evaluate( "bootstrap", eval_phys, master_phy, true, 1 );
 241         }
 242         _mf.getMainPanel().addPhylogenyInNewTab( master_phy, _mf.getConfiguration(), "nj", "njpath" );
 243         //  _mf.getMainPanel().getCurrentTreePanel().setArrowCursor();
 244         end( _mf );
 245         JOptionPane.showMessageDialog( _mf,
 246                                        "Inference successfully completed",
 247                                        "Inference Completed",
 248                                        JOptionPane.INFORMATION_MESSAGE );
 249     }
 250
 251     @Override
 252     public void run() {
 253         try {
 254             infer();
 255         }
 256         catch ( final InterruptedException e ) {
 257             // TODO need to handle this exception SOMEHOW!
 258             // TODO Auto-generated catch block
 259             e.printStackTrace();
 260         }
 261     }
 262
 263     private Msa runMAFFT( final List<MolecularSequence> seqs, final List<String> opts ) throws IOException,
 264             InterruptedException {
 265         Msa msa = null;
 266         final MsaInferrer mafft = Mafft.createInstance( _mf.getInferenceManager().getPathToLocalMafft()
 267                 .getCanonicalPath() );
 268         try {
 269             msa = mafft.infer( seqs, opts );
 270         }
 271         catch ( final IOException e ) {
 272             System.out.println( mafft.getErrorDescription() );
 273         }
 274         return msa;
 275     }
 276
 277     private void writeToFiles( final BasicSymmetricalDistanceMatrix m ) {
 278         if ( !ForesterUtil.isEmpty( _options.getIntermediateFilesBase() ) ) {
 279             try {
 280                 final BufferedWriter msa_writer = new BufferedWriter( new FileWriter( _options.getIntermediateFilesBase()
 281                         + MSA_FILE_SUFFIX ) );
 282                 _msa.write( msa_writer, MSA_FORMAT.PHYLIP );
 283                 msa_writer.close();
 284                 final BufferedWriter pwd_writer = new BufferedWriter( new FileWriter( _options.getIntermediateFilesBase()
 285                         + PWD_FILE_SUFFIX ) );
 286                 m.write( pwd_writer );
 287                 pwd_writer.close();
 288             }
 289             catch ( final Exception e ) {
 290                 System.out.println( "Error: " + e.getMessage() );
 291             }
 292         }
 293     }
 294
 295     public enum MSA_PRG {
 296         MAFFT;
 297     }
 298 }