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