X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2Ftools%2FPhylogeneticInferrer.java;h=9e651fb227444b1ef1546b9e3cb946f84de73735;hb=72c535142a5e6b0da9c7edb2f605eb835b43e6fb;hp=c5fa04dd2a3fa05dff04490ffd603f23a9903292;hpb=0f295917c869b17a9322af3e738e3527ba9b31d4;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/tools/PhylogeneticInferrer.java b/forester/java/src/org/forester/archaeopteryx/tools/PhylogeneticInferrer.java index c5fa04d..9e651fb2 100644 --- a/forester/java/src/org/forester/archaeopteryx/tools/PhylogeneticInferrer.java +++ b/forester/java/src/org/forester/archaeopteryx/tools/PhylogeneticInferrer.java @@ -26,39 +26,44 @@ package org.forester.archaeopteryx.tools; import java.io.BufferedWriter; -import java.io.File; import java.io.FileWriter; import java.io.IOException; import java.util.ArrayList; import java.util.List; +import java.util.regex.Matcher; import javax.swing.JOptionPane; +import org.forester.archaeopteryx.AptxUtil; import org.forester.archaeopteryx.MainFrameApplication; import org.forester.evoinference.distance.NeighborJoining; import org.forester.evoinference.distance.PairwiseDistanceCalculator; import org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix; import org.forester.evoinference.tools.BootstrapResampler; import org.forester.io.parsers.FastaParser; -import org.forester.io.writers.SequenceWriter; -import org.forester.io.writers.SequenceWriter.SEQ_FORMAT; import org.forester.msa.BasicMsa; +import org.forester.msa.ClustalOmega; import org.forester.msa.Mafft; import org.forester.msa.Msa; +import org.forester.msa.Msa.MSA_FORMAT; import org.forester.msa.MsaInferrer; -import org.forester.msa.MsaTools; +import org.forester.msa.MsaMethods; import org.forester.msa.ResampleableMsa; import org.forester.phylogeny.Phylogeny; +import org.forester.phylogeny.PhylogenyNode; +import org.forester.phylogeny.data.Accession; +import org.forester.phylogeny.iterators.PhylogenyNodeIterator; import org.forester.sequence.Sequence; import org.forester.tools.ConfidenceAssessor; import org.forester.util.ForesterUtil; -public class PhylogeneticInferrer implements Runnable { +public class PhylogeneticInferrer extends RunnableProcess { private Msa _msa; private final MainFrameApplication _mf; private final PhylogeneticInferenceOptions _options; private final List _seqs; + private final boolean DEBUG = true; public final static String MSA_FILE_SUFFIX = ".aln"; public final static String PWD_FILE_SUFFIX = ".pwd"; @@ -80,25 +85,25 @@ public class PhylogeneticInferrer implements Runnable { _options = options; } - private Msa inferMsa() throws IOException { - final File temp_seqs_file = File.createTempFile( "aptx", ".fasta" ); - System.out.println( "temp file: " + temp_seqs_file ); - //final File temp_seqs_file = new File( _options.getTempDir() + ForesterUtil.FILE_SEPARATOR + "s.fasta" ); - final BufferedWriter writer = new BufferedWriter( new FileWriter( temp_seqs_file ) ); - SequenceWriter.writeSeqs( _seqs, writer, SEQ_FORMAT.FASTA, 100 ); - writer.close(); - final List opts = processMafftOptions(); - Msa msa = null; - try { - msa = runMAFFT( temp_seqs_file, opts ); - } - catch ( final InterruptedException e ) { - // TODO Auto-generated catch block - e.printStackTrace(); + private Msa inferMsa( final MSA_PRG msa_prg ) throws IOException, InterruptedException { + // final File temp_seqs_file = File.createTempFile( "__msa__temp__", ".fasta" ); + // if ( DEBUG ) { + // System.out.println(); + // System.out.println( "temp file: " + temp_seqs_file ); + // System.out.println(); + // } + // //final File temp_seqs_file = new File( _options.getTempDir() + ForesterUtil.FILE_SEPARATOR + "s.fasta" ); + // final BufferedWriter writer = new BufferedWriter( new FileWriter( temp_seqs_file ) ); + // SequenceWriter.writeSeqs( _seqs, writer, SEQ_FORMAT.FASTA, 100 ); + // writer.close(); + switch ( msa_prg ) { + case MAFFT: + return runMAFFT( _seqs, processMafftOptions() ); + case CLUSTAL_O: + return runClustalOmega( _seqs, processMafftOptions() ); + default: + return null; } - // copy aln file to intermediate dir file - // delete temp seqs file - return msa; } private List processMafftOptions() { @@ -145,33 +150,53 @@ public class PhylogeneticInferrer implements Runnable { e.printStackTrace(); } } - final NeighborJoining nj = new NeighborJoining(); + final NeighborJoining nj = NeighborJoining.createInstance(); final Phylogeny phy = nj.execute( m ); - FastaParser.extractFastaInformation( phy ); + PhylogeneticInferrer.extractFastaInformation( phy ); return phy; } - private void infer() { + private void infer() throws InterruptedException { //_mf.getMainPanel().getCurrentTreePanel().setWaitCursor(); if ( ( _msa == null ) && ( _seqs == null ) ) { throw new IllegalArgumentException( "cannot run phylogenetic analysis with null msa and seq array" ); } + start( _mf, "phylogenetic inference" ); if ( _msa == null ) { Msa msa = null; try { - msa = inferMsa(); + msa = inferMsa( MSA_PRG.MAFFT ); } catch ( final IOException e ) { + end( _mf ); JOptionPane.showMessageDialog( _mf, - "Could not create multiple sequence alignment with " - + _options.getMsaPrg() + "\nand the following parameters:\n\"" - + _options.getMsaPrgParameters() + "\"\nError:" + "Could not create multiple sequence alignment with \"" + + _options.getMsaPrg() + "\" and the following parameters:\n\"" + + _options.getMsaPrgParameters() + "\"\nError: " + e.getLocalizedMessage(), "Failed to Calculate MSA", JOptionPane.ERROR_MESSAGE ); + if ( DEBUG ) { + e.printStackTrace(); + } + return; + } + catch ( final Exception e ) { + end( _mf ); + JOptionPane.showMessageDialog( _mf, + "Could not create multiple sequence alignment with \"" + + _options.getMsaPrg() + "\" and the following parameters:\n\"" + + _options.getMsaPrgParameters() + "\"\nError: " + + e.getLocalizedMessage(), + "Unexpected Exception During MSA Calculation", + JOptionPane.ERROR_MESSAGE ); + if ( DEBUG ) { + e.printStackTrace(); + } return; } if ( msa == null ) { + end( _mf ); JOptionPane.showMessageDialog( _mf, "Could not create multiple sequence alignment with " + _options.getMsaPrg() + "\nand the following parameters:\n\"" @@ -180,14 +205,17 @@ public class PhylogeneticInferrer implements Runnable { JOptionPane.ERROR_MESSAGE ); return; } - System.out.println( msa.toString() ); - System.out.println( MsaTools.calcBasicGapinessStatistics( msa ).toString() ); - final MsaTools msa_tools = MsaTools.createInstance(); + if ( DEBUG ) { + System.out.println( msa.toString() ); + System.out.println( MsaMethods.calcGapRatio( msa ) ); + } + final MsaMethods msa_tools = MsaMethods.createInstance(); if ( _options.isExecuteMsaProcessing() ) { msa = msa_tools.removeGapColumns( _options.getMsaProcessingMaxAllowedGapRatio(), _options.getMsaProcessingMinAllowedLength(), msa ); if ( msa == null ) { + end( _mf ); JOptionPane.showMessageDialog( _mf, "Less than two sequences longer than " + _options.getMsaProcessingMinAllowedLength() @@ -197,9 +225,11 @@ public class PhylogeneticInferrer implements Runnable { return; } } - System.out.println( msa_tools.getIgnoredSequenceIds() ); - System.out.println( msa.toString() ); - System.out.println( MsaTools.calcBasicGapinessStatistics( msa ).toString() ); + if ( DEBUG ) { + System.out.println( msa_tools.getIgnoredSequenceIds() ); + System.out.println( msa.toString() ); + System.out.println( MsaMethods.calcGapRatio( msa ) ); + } _msa = msa; } final int n = _options.getBootstrapSamples(); @@ -217,7 +247,8 @@ public class PhylogeneticInferrer implements Runnable { ConfidenceAssessor.evaluate( "bootstrap", eval_phys, master_phy, true, 1 ); } _mf.getMainPanel().addPhylogenyInNewTab( master_phy, _mf.getConfiguration(), "nj", "njpath" ); - _mf.getMainPanel().getCurrentTreePanel().setArrowCursor(); + // _mf.getMainPanel().getCurrentTreePanel().setArrowCursor(); + end( _mf ); JOptionPane.showMessageDialog( _mf, "Inference successfully completed", "Inference Completed", @@ -226,14 +257,22 @@ public class PhylogeneticInferrer implements Runnable { @Override public void run() { - infer(); + try { + infer(); + } + catch ( final InterruptedException e ) { + // TODO need to handle this exception SOMEHOW! + // TODO Auto-generated catch block + e.printStackTrace(); + } } - private Msa runMAFFT( final File input_seqs, final List opts ) throws IOException, InterruptedException { + private Msa runMAFFT( final List seqs, final List opts ) throws IOException, InterruptedException { Msa msa = null; - final MsaInferrer mafft = Mafft.createInstance(); + final MsaInferrer mafft = Mafft.createInstance( _mf.getInferenceManager().getPathToLocalMafft() + .getCanonicalPath() ); try { - msa = mafft.infer( input_seqs, opts ); + msa = mafft.infer( seqs, opts ); } catch ( final IOException e ) { System.out.println( mafft.getErrorDescription() ); @@ -241,12 +280,26 @@ public class PhylogeneticInferrer implements Runnable { return msa; } + private Msa runClustalOmega( final List seqs, final List opts ) throws IOException, + InterruptedException { + Msa msa = null; + final MsaInferrer clustalo = ClustalOmega.createInstance( _mf.getInferenceManager().getPathToLocalClustalo() + .getCanonicalPath() ); + try { + msa = clustalo.infer( seqs, opts ); + } + catch ( final IOException e ) { + System.out.println( clustalo.getErrorDescription() ); + } + return msa; + } + private void writeToFiles( final BasicSymmetricalDistanceMatrix m ) { if ( !ForesterUtil.isEmpty( _options.getIntermediateFilesBase() ) ) { try { final BufferedWriter msa_writer = new BufferedWriter( new FileWriter( _options.getIntermediateFilesBase() + MSA_FILE_SUFFIX ) ); - _msa.write( msa_writer ); + _msa.write( msa_writer, MSA_FORMAT.PHYLIP ); msa_writer.close(); final BufferedWriter pwd_writer = new BufferedWriter( new FileWriter( _options.getIntermediateFilesBase() + PWD_FILE_SUFFIX ) ); @@ -258,4 +311,40 @@ public class PhylogeneticInferrer implements Runnable { } } } + + public static void extractFastaInformation( final Phylogeny phy ) { + for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) { + final PhylogenyNode node = iter.next(); + if ( !ForesterUtil.isEmpty( node.getName() ) ) { + final Matcher name_m = FastaParser.FASTA_DESC_LINE.matcher( node.getName() ); + if ( name_m.lookingAt() ) { + System.out.println(); + // System.out.println( name_m.group( 1 ) ); + // System.out.println( name_m.group( 2 ) ); + // System.out.println( name_m.group( 3 ) ); + // System.out.println( name_m.group( 4 ) ); + final String acc_source = name_m.group( 1 ); + final String acc = name_m.group( 2 ); + final String seq_name = name_m.group( 3 ); + final String tax_sn = name_m.group( 4 ); + if ( !ForesterUtil.isEmpty( acc_source ) && !ForesterUtil.isEmpty( acc ) ) { + AptxUtil.ensurePresenceOfSequence( node ); + node.getNodeData().getSequence( 0 ).setAccession( new Accession( acc, acc_source ) ); + } + if ( !ForesterUtil.isEmpty( seq_name ) ) { + AptxUtil.ensurePresenceOfSequence( node ); + node.getNodeData().getSequence( 0 ).setName( seq_name ); + } + if ( !ForesterUtil.isEmpty( tax_sn ) ) { + AptxUtil.ensurePresenceOfTaxonomy( node ); + node.getNodeData().getTaxonomy( 0 ).setScientificName( tax_sn ); + } + } + } + } + } + + public enum MSA_PRG { + MAFFT, CLUSTAL_O; + } }