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