X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2Ftools%2FPhylogeneticInferrer.java;h=1e8f3fc8c4fb36e889cbb240ef1b7c88b4c016ab;hb=10297bd8b8a4b4ab198a17a42fc6ff24ae2ed49b;hp=66fbdbc843b1d10684902c833d85556413125114;hpb=def5f3c9ca461176f1188d0adfd744726a56e6ed;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 66fbdbc..1e8f3fc 100644 --- a/forester/java/src/org/forester/archaeopteryx/tools/PhylogeneticInferrer.java +++ b/forester/java/src/org/forester/archaeopteryx/tools/PhylogeneticInferrer.java @@ -21,29 +21,24 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester 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.NeighborJoiningF; 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.msa.BasicMsa; -import org.forester.msa.ClustalOmega; import org.forester.msa.Mafft; import org.forester.msa.Msa; import org.forester.msa.Msa.MSA_FORMAT; @@ -51,10 +46,8 @@ import org.forester.msa.MsaInferrer; 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.phylogeny.PhylogenyMethods; +import org.forester.sequence.MolecularSequence; import org.forester.tools.ConfidenceAssessor; import org.forester.util.ForesterUtil; @@ -63,12 +56,12 @@ public class PhylogeneticInferrer extends RunnableProcess { private Msa _msa; private final MainFrameApplication _mf; private final PhylogeneticInferenceOptions _options; - private final List _seqs; + 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"; - public PhylogeneticInferrer( final List seqs, + public PhylogeneticInferrer( final List seqs, final PhylogeneticInferenceOptions options, final MainFrameApplication mf ) { _msa = null; @@ -98,16 +91,11 @@ public class PhylogeneticInferrer extends RunnableProcess { // SequenceWriter.writeSeqs( _seqs, writer, SEQ_FORMAT.FASTA, 100 ); // writer.close(); switch ( msa_prg ) { - case MAFFT: + case MAFFT: return runMAFFT( _seqs, processMafftOptions() ); - - case CLUSTAL_O: - return runClustalOmega( _seqs, processMafftOptions() ); default: return null; } - - } private List processMafftOptions() { @@ -154,9 +142,10 @@ public class PhylogeneticInferrer extends RunnableProcess { e.printStackTrace(); } } - final NeighborJoining nj = NeighborJoining.createInstance(); + final NeighborJoiningF nj = NeighborJoiningF.createInstance( false, 5 ); final Phylogeny phy = nj.execute( m ); - PhylogeneticInferrer.extractFastaInformation( phy ); + PhylogenyMethods.addMolecularSeqsToTree( phy, msa ); + PhylogenyMethods.extractFastaInformation( phy ); return phy; } @@ -178,8 +167,8 @@ public class PhylogeneticInferrer extends RunnableProcess { + _options.getMsaPrg() + "\" and the following parameters:\n\"" + _options.getMsaPrgParameters() + "\"\nError: " + e.getLocalizedMessage(), - "Failed to Calculate MSA", - JOptionPane.ERROR_MESSAGE ); + "Failed to Calculate MSA", + JOptionPane.ERROR_MESSAGE ); if ( DEBUG ) { e.printStackTrace(); } @@ -192,8 +181,8 @@ public class PhylogeneticInferrer extends RunnableProcess { + _options.getMsaPrg() + "\" and the following parameters:\n\"" + _options.getMsaPrgParameters() + "\"\nError: " + e.getLocalizedMessage(), - "Unexpected Exception During MSA Calculation", - JOptionPane.ERROR_MESSAGE ); + "Unexpected Exception During MSA Calculation", + JOptionPane.ERROR_MESSAGE ); if ( DEBUG ) { e.printStackTrace(); } @@ -205,8 +194,8 @@ public class PhylogeneticInferrer extends RunnableProcess { "Could not create multiple sequence alignment with " + _options.getMsaPrg() + "\nand the following parameters:\n\"" + _options.getMsaPrgParameters() + "\"", - "Failed to Calculate MSA", - JOptionPane.ERROR_MESSAGE ); + "Failed to Calculate MSA", + JOptionPane.ERROR_MESSAGE ); return; } if ( DEBUG ) { @@ -215,7 +204,7 @@ public class PhylogeneticInferrer extends RunnableProcess { } final MsaMethods msa_tools = MsaMethods.createInstance(); if ( _options.isExecuteMsaProcessing() ) { - msa = msa_tools.removeGapColumns( _options.getMsaProcessingMaxAllowedGapRatio(), + msa = msa_tools.deleteGapColumns( _options.getMsaProcessingMaxAllowedGapRatio(), _options.getMsaProcessingMinAllowedLength(), msa ); if ( msa == null ) { @@ -224,8 +213,8 @@ public class PhylogeneticInferrer extends RunnableProcess { "Less than two sequences longer than " + _options.getMsaProcessingMinAllowedLength() + " residues left after MSA processing", - "MSA Processing Settings Too Stringent", - JOptionPane.ERROR_MESSAGE ); + "MSA Processing Settings Too Stringent", + JOptionPane.ERROR_MESSAGE ); return; } } @@ -242,7 +231,7 @@ public class PhylogeneticInferrer extends RunnableProcess { if ( _options.isPerformBootstrapResampling() && ( n > 0 ) ) { final ResampleableMsa resampleable_msa = new ResampleableMsa( ( BasicMsa ) _msa ); final int[][] resampled_column_positions = BootstrapResampler.createResampledColumnPositions( _msa - .getLength(), n, seed ); + .getLength(), n, seed ); final Phylogeny[] eval_phys = new Phylogeny[ n ]; for( int i = 0; i < n; ++i ) { resampleable_msa.resample( resampled_column_positions[ i ] ); @@ -271,10 +260,11 @@ public class PhylogeneticInferrer extends RunnableProcess { } } - private Msa runMAFFT( final List 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( _mf.getInferenceManager().getPathToLocalMafft() - .getCanonicalPath() ); + .getCanonicalPath() ); try { msa = mafft.infer( seqs, opts ); } @@ -284,29 +274,15 @@ public class PhylogeneticInferrer extends RunnableProcess { 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_FILE_SUFFIX ) ); _msa.write( msa_writer, MSA_FORMAT.PHYLIP ); msa_writer.close(); final BufferedWriter pwd_writer = new BufferedWriter( new FileWriter( _options.getIntermediateFilesBase() - + PWD_FILE_SUFFIX ) ); + + PWD_FILE_SUFFIX ) ); m.write( pwd_writer ); pwd_writer.close(); } @@ -316,39 +292,7 @@ public class PhylogeneticInferrer extends RunnableProcess { } } - 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; + MAFFT; } }