2 // forester -- software libraries and applications
3 // for genomics and evolutionary biology research.
5 // Copyright (C) 2010 Christian M Zmasek
6 // Copyright (C) 2010 Sanford-Burnham Medical Research Institute
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.
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.
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
23 // Contact: phylosoft @ gmail . com
24 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
26 package org.forester.archaeopteryx.tools;
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 import java.util.regex.Matcher;
35 import javax.swing.JOptionPane;
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.msa.BasicMsa;
44 import org.forester.msa.ClustalOmega;
45 import org.forester.msa.Mafft;
46 import org.forester.msa.Msa;
47 import org.forester.msa.Msa.MSA_FORMAT;
48 import org.forester.msa.MsaInferrer;
49 import org.forester.msa.MsaMethods;
50 import org.forester.msa.ResampleableMsa;
51 import org.forester.phylogeny.Phylogeny;
52 import org.forester.phylogeny.PhylogenyNode;
53 import org.forester.phylogeny.data.Accession;
54 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
55 import org.forester.sequence.Sequence;
56 import org.forester.tools.ConfidenceAssessor;
57 import org.forester.util.ForesterUtil;
59 public class PhylogeneticInferrer extends RunnableProcess {
62 private final MainFrameApplication _mf;
63 private final PhylogeneticInferenceOptions _options;
64 private final List<Sequence> _seqs;
65 private final boolean DEBUG = true;
66 public final static String MSA_FILE_SUFFIX = ".aln";
67 public final static String PWD_FILE_SUFFIX = ".pwd";
69 public PhylogeneticInferrer( final List<Sequence> seqs,
70 final PhylogeneticInferenceOptions options,
71 final MainFrameApplication mf ) {
78 public PhylogeneticInferrer( final Msa msa,
79 final PhylogeneticInferenceOptions options,
80 final MainFrameApplication mf ) {
87 private Msa inferMsa( final MSA_PRG msa_prg ) throws IOException, InterruptedException {
88 // final File temp_seqs_file = File.createTempFile( "__msa__temp__", ".fasta" );
90 // System.out.println();
91 // System.out.println( "temp file: " + temp_seqs_file );
92 // System.out.println();
94 // //final File temp_seqs_file = new File( _options.getTempDir() + ForesterUtil.FILE_SEPARATOR + "s.fasta" );
95 // final BufferedWriter writer = new BufferedWriter( new FileWriter( temp_seqs_file ) );
96 // SequenceWriter.writeSeqs( _seqs, writer, SEQ_FORMAT.FASTA, 100 );
100 return runMAFFT( _seqs, processMafftOptions() );
102 return runClustalOmega( _seqs, processMafftOptions() );
108 private List<String> processMafftOptions() {
109 final String opts_str = _options.getMsaPrgParameters().trim().toLowerCase();
110 final String[] opts_ary = opts_str.split( " " );
111 final List<String> opts = new ArrayList<String>();
112 boolean saw_quiet = false;
113 for( final String opt : opts_ary ) {
115 if ( opt.equals( "--quiet" ) ) {
120 opts.add( "--quiet" );
125 private Phylogeny inferPhylogeny( final Msa msa ) {
126 BasicSymmetricalDistanceMatrix m = null;
127 switch ( _options.getPwdDistanceMethod() ) {
128 case KIMURA_DISTANCE:
129 m = PairwiseDistanceCalculator.calcKimuraDistances( msa );
131 case POISSON_DISTANCE:
132 m = PairwiseDistanceCalculator.calcPoissonDistances( msa );
134 case FRACTIONAL_DISSIMILARITY:
135 m = PairwiseDistanceCalculator.calcFractionalDissimilarities( msa );
138 throw new RuntimeException( "invalid pwd method" );
140 if ( !ForesterUtil.isEmpty( _options.getIntermediateFilesBase() ) ) {
141 BufferedWriter pwd_writer;
143 pwd_writer = new BufferedWriter( new FileWriter( _options.getIntermediateFilesBase() + PWD_FILE_SUFFIX ) );
144 m.write( pwd_writer );
147 catch ( final IOException e ) {
148 // TODO Auto-generated catch block
152 final NeighborJoining nj = NeighborJoining.createInstance();
153 final Phylogeny phy = nj.execute( m );
154 PhylogeneticInferrer.extractFastaInformation( phy );
158 private void infer() throws InterruptedException {
159 //_mf.getMainPanel().getCurrentTreePanel().setWaitCursor();
160 if ( ( _msa == null ) && ( _seqs == null ) ) {
161 throw new IllegalArgumentException( "cannot run phylogenetic analysis with null msa and seq array" );
163 start( _mf, "phylogenetic inference" );
164 if ( _msa == null ) {
167 msa = inferMsa( MSA_PRG.MAFFT );
169 catch ( final IOException e ) {
171 JOptionPane.showMessageDialog( _mf,
172 "Could not create multiple sequence alignment with \""
173 + _options.getMsaPrg() + "\" and the following parameters:\n\""
174 + _options.getMsaPrgParameters() + "\"\nError: "
175 + e.getLocalizedMessage(),
176 "Failed to Calculate MSA",
177 JOptionPane.ERROR_MESSAGE );
183 catch ( final Exception e ) {
185 JOptionPane.showMessageDialog( _mf,
186 "Could not create multiple sequence alignment with \""
187 + _options.getMsaPrg() + "\" and the following parameters:\n\""
188 + _options.getMsaPrgParameters() + "\"\nError: "
189 + e.getLocalizedMessage(),
190 "Unexpected Exception During MSA Calculation",
191 JOptionPane.ERROR_MESSAGE );
199 JOptionPane.showMessageDialog( _mf,
200 "Could not create multiple sequence alignment with "
201 + _options.getMsaPrg() + "\nand the following parameters:\n\""
202 + _options.getMsaPrgParameters() + "\"",
203 "Failed to Calculate MSA",
204 JOptionPane.ERROR_MESSAGE );
208 System.out.println( msa.toString() );
209 System.out.println( MsaMethods.calcGapRatio( msa ) );
211 final MsaMethods msa_tools = MsaMethods.createInstance();
212 if ( _options.isExecuteMsaProcessing() ) {
213 msa = msa_tools.removeGapColumns( _options.getMsaProcessingMaxAllowedGapRatio(),
214 _options.getMsaProcessingMinAllowedLength(),
218 JOptionPane.showMessageDialog( _mf,
219 "Less than two sequences longer than "
220 + _options.getMsaProcessingMinAllowedLength()
221 + " residues left after MSA processing",
222 "MSA Processing Settings Too Stringent",
223 JOptionPane.ERROR_MESSAGE );
228 System.out.println( msa_tools.getIgnoredSequenceIds() );
229 System.out.println( msa.toString() );
230 System.out.println( MsaMethods.calcGapRatio( msa ) );
234 final int n = _options.getBootstrapSamples();
235 final long seed = _options.getRandomNumberGeneratorSeed();
236 final Phylogeny master_phy = inferPhylogeny( _msa );
237 if ( _options.isPerformBootstrapResampling() && ( n > 0 ) ) {
238 final ResampleableMsa resampleable_msa = new ResampleableMsa( ( BasicMsa ) _msa );
239 final int[][] resampled_column_positions = BootstrapResampler.createResampledColumnPositions( _msa
240 .getLength(), n, seed );
241 final Phylogeny[] eval_phys = new Phylogeny[ n ];
242 for( int i = 0; i < n; ++i ) {
243 resampleable_msa.resample( resampled_column_positions[ i ] );
244 eval_phys[ i ] = inferPhylogeny( resampleable_msa );
246 ConfidenceAssessor.evaluate( "bootstrap", eval_phys, master_phy, true, 1 );
248 _mf.getMainPanel().addPhylogenyInNewTab( master_phy, _mf.getConfiguration(), "nj", "njpath" );
249 // _mf.getMainPanel().getCurrentTreePanel().setArrowCursor();
251 JOptionPane.showMessageDialog( _mf,
252 "Inference successfully completed",
253 "Inference Completed",
254 JOptionPane.INFORMATION_MESSAGE );
262 catch ( final InterruptedException e ) {
263 // TODO need to handle this exception SOMEHOW!
264 // TODO Auto-generated catch block
269 private Msa runMAFFT( final List<Sequence> seqs, final List<String> opts ) throws IOException, InterruptedException {
271 final MsaInferrer mafft = Mafft.createInstance( _mf.getInferenceManager().getPathToLocalMafft()
272 .getCanonicalPath() );
274 msa = mafft.infer( seqs, opts );
276 catch ( final IOException e ) {
277 System.out.println( mafft.getErrorDescription() );
282 private Msa runClustalOmega( final List<Sequence> seqs, final List<String> opts ) throws IOException,
283 InterruptedException {
285 final MsaInferrer clustalo = ClustalOmega.createInstance( _mf.getInferenceManager().getPathToLocalClustalo()
286 .getCanonicalPath() );
288 msa = clustalo.infer( seqs, opts );
290 catch ( final IOException e ) {
291 System.out.println( clustalo.getErrorDescription() );
296 private void writeToFiles( final BasicSymmetricalDistanceMatrix m ) {
297 if ( !ForesterUtil.isEmpty( _options.getIntermediateFilesBase() ) ) {
299 final BufferedWriter msa_writer = new BufferedWriter( new FileWriter( _options.getIntermediateFilesBase()
300 + MSA_FILE_SUFFIX ) );
301 _msa.write( msa_writer, MSA_FORMAT.PHYLIP );
303 final BufferedWriter pwd_writer = new BufferedWriter( new FileWriter( _options.getIntermediateFilesBase()
304 + PWD_FILE_SUFFIX ) );
305 m.write( pwd_writer );
308 catch ( final Exception e ) {
309 System.out.println( "Error: " + e.getMessage() );
314 public static void extractFastaInformation( final Phylogeny phy ) {
315 for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {
316 final PhylogenyNode node = iter.next();
317 if ( !ForesterUtil.isEmpty( node.getName() ) ) {
318 final Matcher name_m = FastaParser.FASTA_DESC_LINE.matcher( node.getName() );
319 if ( name_m.lookingAt() ) {
320 System.out.println();
321 // System.out.println( name_m.group( 1 ) );
322 // System.out.println( name_m.group( 2 ) );
323 // System.out.println( name_m.group( 3 ) );
324 // System.out.println( name_m.group( 4 ) );
325 final String acc_source = name_m.group( 1 );
326 final String acc = name_m.group( 2 );
327 final String seq_name = name_m.group( 3 );
328 final String tax_sn = name_m.group( 4 );
329 if ( !ForesterUtil.isEmpty( acc_source ) && !ForesterUtil.isEmpty( acc ) ) {
330 ForesterUtil.ensurePresenceOfSequence( node );
331 node.getNodeData().getSequence( 0 ).setAccession( new Accession( acc, acc_source ) );
333 if ( !ForesterUtil.isEmpty( seq_name ) ) {
334 ForesterUtil.ensurePresenceOfSequence( node );
335 node.getNodeData().getSequence( 0 ).setName( seq_name );
337 if ( !ForesterUtil.isEmpty( tax_sn ) ) {
338 ForesterUtil.ensurePresenceOfTaxonomy( node );
339 node.getNodeData().getTaxonomy( 0 ).setScientificName( tax_sn );
346 public enum MSA_PRG {