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=4f17c699089435402b151b7ffdc7e26e786e1395;hpb=eb07e696db878b45a4738f95e58eaef347d719c3;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 4f17c69..9e651fb2 100644 --- a/forester/java/src/org/forester/archaeopteryx/tools/PhylogeneticInferrer.java +++ b/forester/java/src/org/forester/archaeopteryx/tools/PhylogeneticInferrer.java @@ -26,7 +26,6 @@ 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; @@ -42,11 +41,11 @@ 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.MsaMethods; import org.forester.msa.ResampleableMsa; @@ -58,7 +57,7 @@ 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; @@ -86,19 +85,25 @@ public class PhylogeneticInferrer implements Runnable { _options = options; } - private Msa inferMsa() 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(); + 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; } - //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(); - return runMAFFT( temp_seqs_file, opts ); } private List processMafftOptions() { @@ -145,7 +150,7 @@ public class PhylogeneticInferrer implements Runnable { e.printStackTrace(); } } - final NeighborJoining nj = new NeighborJoining(); + final NeighborJoining nj = NeighborJoining.createInstance(); final Phylogeny phy = nj.execute( m ); PhylogeneticInferrer.extractFastaInformation( phy ); return phy; @@ -156,12 +161,14 @@ public class PhylogeneticInferrer implements Runnable { 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() + "\" and the following parameters:\n\"" @@ -175,6 +182,7 @@ public class PhylogeneticInferrer implements Runnable { return; } catch ( final Exception e ) { + end( _mf ); JOptionPane.showMessageDialog( _mf, "Could not create multiple sequence alignment with \"" + _options.getMsaPrg() + "\" and the following parameters:\n\"" @@ -188,6 +196,7 @@ public class PhylogeneticInferrer implements Runnable { return; } if ( msa == null ) { + end( _mf ); JOptionPane.showMessageDialog( _mf, "Could not create multiple sequence alignment with " + _options.getMsaPrg() + "\nand the following parameters:\n\"" @@ -198,7 +207,7 @@ public class PhylogeneticInferrer implements Runnable { } if ( DEBUG ) { System.out.println( msa.toString() ); - System.out.println( MsaMethods.calcBasicGapinessStatistics( msa ).toString() ); + System.out.println( MsaMethods.calcGapRatio( msa ) ); } final MsaMethods msa_tools = MsaMethods.createInstance(); if ( _options.isExecuteMsaProcessing() ) { @@ -206,6 +215,7 @@ public class PhylogeneticInferrer implements Runnable { _options.getMsaProcessingMinAllowedLength(), msa ); if ( msa == null ) { + end( _mf ); JOptionPane.showMessageDialog( _mf, "Less than two sequences longer than " + _options.getMsaProcessingMinAllowedLength() @@ -218,7 +228,7 @@ public class PhylogeneticInferrer implements Runnable { if ( DEBUG ) { System.out.println( msa_tools.getIgnoredSequenceIds() ); System.out.println( msa.toString() ); - System.out.println( MsaMethods.calcBasicGapinessStatistics( msa ).toString() ); + System.out.println( MsaMethods.calcGapRatio( msa ) ); } _msa = msa; } @@ -237,7 +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", @@ -256,11 +267,12 @@ public class PhylogeneticInferrer implements Runnable { } } - 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() ); @@ -268,12 +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 ) ); @@ -317,4 +343,8 @@ public class PhylogeneticInferrer implements Runnable { } } } + + public enum MSA_PRG { + MAFFT, CLUSTAL_O; + } }