X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fmsa_compactor%2FMsaCompactor.java;h=58953a8dc70ce51b9f60d29f2e9b8e2e7f239923;hb=70da437f494b483dac92a488bd3500e5add2e34e;hp=5d3a55c6d229e51887e8800aa308f3a0620fe33c;hpb=6479c35c4734850f517a6ef8de0fce500fdd6693;p=jalview.git diff --git a/forester/java/src/org/forester/msa_compactor/MsaCompactor.java b/forester/java/src/org/forester/msa_compactor/MsaCompactor.java index 5d3a55c..58953a8 100644 --- a/forester/java/src/org/forester/msa_compactor/MsaCompactor.java +++ b/forester/java/src/org/forester/msa_compactor/MsaCompactor.java @@ -1,6 +1,30 @@ +// $Id: +// FORESTER -- software libraries and applications +// for evolutionary biology research and applications. +// +// Copyright (C) 2014 Christian M. Zmasek +// Copyright (C) 2014 Sanford-Burnham Medical Research Institute +// All rights reserved +// +// This library is free software; you can redistribute it and/or +// modify it under the terms of the GNU Lesser General Public +// License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// +// This library is distributed in the hope that it will be useful, +// but WITHOUT ANY WARRANTY; without even the implied warranty of +// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +// Lesser General Public License for more details. +// +// You should have received a copy of the GNU Lesser General Public +// License along with this library; if not, write to the Free Software +// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +// +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.msa_compactor; +import java.awt.Color; import java.io.File; import java.io.IOException; import java.io.Writer; @@ -13,12 +37,19 @@ import java.util.List; import java.util.SortedSet; import java.util.TreeSet; +import org.forester.archaeopteryx.Archaeopteryx; +import org.forester.archaeopteryx.Configuration; import org.forester.evoinference.distance.NeighborJoiningF; import org.forester.evoinference.distance.PairwiseDistanceCalculator; import org.forester.evoinference.distance.PairwiseDistanceCalculator.PWD_DISTANCE_METHOD; import org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix; import org.forester.evoinference.tools.BootstrapResampler; -import org.forester.msa.BasicMsa; +import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION; +import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException; +import org.forester.io.parsers.util.ParserUtils; +import org.forester.io.writers.SequenceWriter; +import org.forester.io.writers.SequenceWriter.SEQ_FORMAT; +import org.forester.msa.DeleteableMsa; import org.forester.msa.Mafft; import org.forester.msa.Msa; import org.forester.msa.Msa.MSA_FORMAT; @@ -27,28 +58,105 @@ import org.forester.msa.MsaMethods; import org.forester.msa.ResampleableMsa; import org.forester.phylogeny.Phylogeny; import org.forester.phylogeny.PhylogenyMethods; +import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY; +import org.forester.phylogeny.PhylogenyNode; +import org.forester.phylogeny.data.NodeVisualData; +import org.forester.phylogeny.data.NodeVisualData.NodeFill; +import org.forester.phylogeny.data.NodeVisualData.NodeShape; +import org.forester.phylogeny.iterators.PhylogenyNodeIterator; import org.forester.sequence.Sequence; import org.forester.tools.ConfidenceAssessor; -import org.forester.util.BasicDescriptiveStatistics; -import org.forester.util.DescriptiveStatistics; import org.forester.util.ForesterUtil; public class MsaCompactor { - final private static NumberFormat NF_3 = new DecimalFormat( "#.###" ); - final private static NumberFormat NF_4 = new DecimalFormat( "#.####" ); - private static final boolean VERBOSE = true; - private Msa _msa; + final private static NumberFormat NF_3 = new DecimalFormat( "#.###" ); + final private static NumberFormat NF_4 = new DecimalFormat( "#.####" ); + private double _gap_ratio = -1; + private final short _longest_id_length; + // + private String _maffts_opts = "--auto"; + private int _min_length = -1; + // + private String _infile_name = null; + private DeleteableMsa _msa = null; + private boolean _norm = true; + private File _out_file_base = null; + private MSA_FORMAT _output_format = MSA_FORMAT.FASTA; + private String _path_to_mafft = null; + // + private boolean _realign = false; private final SortedSet _removed_seq_ids; - private String _path_to_mafft; + private final ArrayList _removed_seqs; + private File _removed_seqs_out_base = null; + private boolean _report_aln_mean_identity = false; + private int _step = -1; + private int _step_for_diagnostics = -1; + private boolean _phylogentic_inference = false; static { NF_4.setRoundingMode( RoundingMode.HALF_UP ); NF_3.setRoundingMode( RoundingMode.HALF_UP ); } - private MsaCompactor( final Msa msa ) { + public MsaCompactor( final DeleteableMsa msa ) { _msa = msa; _removed_seq_ids = new TreeSet(); + _longest_id_length = _msa.determineMaxIdLength(); + _removed_seqs = new ArrayList(); + } + + public final List chart( final int step, final boolean realign, final boolean norm ) + throws IOException, InterruptedException { + final GapContribution stats[] = calcGapContribtionsStats( norm ); + final List to_remove_ids = new ArrayList(); + final List msa_props = new ArrayList(); + for( final GapContribution gap_gontribution : stats ) { + to_remove_ids.add( gap_gontribution.getId() ); + } + if ( !_realign ) { + _step = -1; + } + int x = ForesterUtil.roundToInt( _msa.getNumberOfSequences() / 20.0 ); + if ( x < 1 ) { + x = 1; + } + MsaProperties msa_prop = new MsaProperties( _msa, _report_aln_mean_identity ); + msa_props.add( msa_prop ); + if ( _phylogentic_inference ) { + System.out.println( "calculating phylogentic tree..." ); + System.out.println(); + pi( to_remove_ids ); + } + printTableHeader(); + printMsaProperties( "", msa_prop ); + System.out.println(); + int i = 0; + while ( _msa.getNumberOfSequences() > x ) { + final String id = to_remove_ids.get( i ); + _msa.deleteRow( id, false ); + if ( realign && isPrintMsaStatsWriteOutfileAndRealign( i ) ) { + removeGapColumns(); + realignWithMafft(); + msa_prop = new MsaProperties( _msa, _report_aln_mean_identity ); + msa_props.add( msa_prop ); + printMsaProperties( id, msa_prop ); + System.out.print( "(realigned)" ); + System.out.println(); + } + else if ( isPrintMsaStats( i ) ) { + removeGapColumns(); + msa_prop = new MsaProperties( _msa, _report_aln_mean_identity ); + msa_props.add( msa_prop ); + printMsaProperties( id, msa_prop ); + System.out.println(); + } + ++i; + } + return msa_props; + } + + final public void deleteGapColumns( final double max_allowed_gap_ratio ) { + _msa.deleteGapColumns( max_allowed_gap_ratio ); } final public Msa getMsa() { @@ -59,11 +167,213 @@ public class MsaCompactor { return _removed_seq_ids; } - final public void writeMsa( final File outfile, final MSA_FORMAT format, final String suffix ) throws IOException { + public final void removeSequencesByMinimalLength( final int min_effective_length ) { + printMsaProperties( "", new MsaProperties( _msa, _report_aln_mean_identity ) ); + System.out.println(); + _msa = DeleteableMsa.createInstance( MsaMethods.removeSequencesByMinimalLength( _msa, min_effective_length ) ); + removeGapColumns(); + printMsaProperties( "", new MsaProperties( _msa, _report_aln_mean_identity ) ); + System.out.println(); + } + + public final List removeViaGapAverage( final double mean_gapiness ) throws IOException, + InterruptedException { + final GapContribution stats[] = calcGapContribtionsStats( _norm ); + final List to_remove_ids = new ArrayList(); + final List msa_props = new ArrayList(); + for( final GapContribution gap_gontribution : stats ) { + to_remove_ids.add( gap_gontribution.getId() ); + } + printTableHeader(); + MsaProperties msa_prop = new MsaProperties( _msa, _report_aln_mean_identity ); + msa_props.add( msa_prop ); + printMsaProperties( "", msa_prop ); + System.out.println(); + int i = 0; + while ( MsaMethods.calcGapRatio( _msa ) > mean_gapiness ) { + final String id = to_remove_ids.get( i ); + _removed_seq_ids.add( id ); + final Sequence deleted = _msa.deleteRow( id, true ); + _removed_seqs.add( deleted ); + removeGapColumns(); + if ( isPrintMsaStatsWriteOutfileAndRealign( i ) || ( MsaMethods.calcGapRatio( _msa ) <= mean_gapiness ) ) { + msa_prop = printMsaStatsWriteOutfileAndRealign( _realign, id ); + msa_props.add( msa_prop ); + System.out.println(); + } + else if ( isPrintMsaStats( i ) ) { + msa_prop = new MsaProperties( _msa, _report_aln_mean_identity ); + msa_props.add( msa_prop ); + printMsaProperties( id, msa_prop ); + System.out.println(); + } + ++i; + } + if ( _removed_seqs_out_base != null ) { + final String msg = writeAndAlignRemovedSeqs(); + System.out.println(); + System.out.println( msg ); + } + return msa_props; + } + + public List removeViaLength( final int length ) throws IOException, InterruptedException { + final GapContribution stats[] = calcGapContribtionsStats( _norm ); + final List to_remove_ids = new ArrayList(); + final List msa_props = new ArrayList(); + for( final GapContribution gap_gontribution : stats ) { + to_remove_ids.add( gap_gontribution.getId() ); + } + printTableHeader(); + MsaProperties msa_prop = new MsaProperties( _msa, _report_aln_mean_identity ); + msa_props.add( msa_prop ); + printMsaProperties( "", msa_prop ); + System.out.println(); + int i = 0; + while ( _msa.getLength() > length ) { + final String id = to_remove_ids.get( i ); + _removed_seq_ids.add( id ); + final Sequence deleted = _msa.deleteRow( id, true ); + _removed_seqs.add( deleted ); + removeGapColumns(); + if ( isPrintMsaStatsWriteOutfileAndRealign( i ) || ( _msa.getLength() <= length ) ) { + msa_prop = printMsaStatsWriteOutfileAndRealign( _realign, id ); + msa_props.add( msa_prop ); + System.out.println(); + } + else if ( isPrintMsaStats( i ) ) { + msa_prop = new MsaProperties( _msa, _report_aln_mean_identity ); + printMsaProperties( id, msa_prop ); + msa_props.add( msa_prop ); + System.out.println(); + } + ++i; + } + if ( _removed_seqs_out_base != null ) { + final String msg = writeAndAlignRemovedSeqs(); + System.out.println(); + System.out.println( msg ); + } + return msa_props; + } + + public final List removeWorstOffenders( final int to_remove ) throws IOException, + InterruptedException { + final GapContribution stats[] = calcGapContribtionsStats( _norm ); + final List to_remove_ids = new ArrayList(); + final List msa_props = new ArrayList(); + for( int j = 0; j < to_remove; ++j ) { + to_remove_ids.add( stats[ j ].getId() ); + _removed_seq_ids.add( stats[ j ].getId() ); + } + printTableHeader(); + MsaProperties msa_prop = new MsaProperties( _msa, _report_aln_mean_identity ); + msa_props.add( msa_prop ); + printMsaProperties( "", msa_prop ); + System.out.println(); + for( int i = 0; i < to_remove_ids.size(); ++i ) { + final String id = to_remove_ids.get( i ); + _removed_seq_ids.add( id ); + final Sequence deleted = _msa.deleteRow( id, true ); + _removed_seqs.add( deleted ); + removeGapColumns(); + if ( isPrintMsaStatsWriteOutfileAndRealign( i ) || ( i == ( to_remove_ids.size() - 1 ) ) ) { + msa_prop = printMsaStatsWriteOutfileAndRealign( _realign, id ); + msa_props.add( msa_prop ); + System.out.println(); + } + else if ( isPrintMsaStats( i ) ) { + msa_prop = new MsaProperties( _msa, _report_aln_mean_identity ); + msa_props.add( msa_prop ); + printMsaProperties( id, msa_prop ); + System.out.println(); + } + } + if ( _removed_seqs_out_base != null ) { + final String msg = writeAndAlignRemovedSeqs(); + System.out.println(); + System.out.println( msg ); + } + return msa_props; + } + + public final void setGapRatio( final double gap_ratio ) { + _gap_ratio = gap_ratio; + } + + public final void setMafftOptions( final String maffts_opts ) { + _maffts_opts = maffts_opts; + } + + public final void setMinLength( final int min_length ) { + _min_length = min_length; + } + + public final void setNorm( final boolean norm ) { + _norm = norm; + } + + final public void setOutFileBase( final File out_file_base ) { + _out_file_base = out_file_base; + } + + public final void setOutputFormat( final MSA_FORMAT output_format ) { + _output_format = output_format; + } + + public void setPathToMafft( final String path_to_mafft ) { + _path_to_mafft = path_to_mafft; + } + + public final void setRealign( final boolean realign ) { + _realign = realign; + } + + public final void setRemovedSeqsOutBase( final File removed_seqs_out_base ) { + _removed_seqs_out_base = removed_seqs_out_base; + } + + public final void setReportAlnMeanIdentity( final boolean report_aln_mean_identity ) { + _report_aln_mean_identity = report_aln_mean_identity; + } + + public final void setStep( final int step ) { + _step = step; + } + + public final void setStepForDiagnostics( final int step_for_diagnostics ) { + _step_for_diagnostics = step_for_diagnostics; + } + + final public String writeAndAlignRemovedSeqs() throws IOException, InterruptedException { + final StringBuilder msg = new StringBuilder(); + final String n = _removed_seqs_out_base + "_" + _removed_seqs.size() + ".fasta"; + SequenceWriter.writeSeqs( _removed_seqs, new File( n ), SEQ_FORMAT.FASTA, 100 ); + msg.append( "wrote " + _removed_seqs.size() + " removed sequences to " + "\"" + n + "\"" ); + if ( _realign ) { + final MsaInferrer mafft = Mafft.createInstance( _path_to_mafft ); + final List opts = new ArrayList(); + for( final String o : _maffts_opts.split( "\\s" ) ) { + opts.add( o ); + } + final Msa removed_msa = mafft.infer( _removed_seqs, opts ); + final Double gr = MsaMethods.calcGapRatio( removed_msa ); + String s = _removed_seqs_out_base + "_" + removed_msa.getNumberOfSequences() + "_" + + removed_msa.getLength() + "_" + ForesterUtil.roundToInt( gr * 100 ); + final String suffix = obtainSuffix(); + s += suffix; + writeMsa( removed_msa, s, _output_format ); + msg.append( ", and as MSA of length " + removed_msa.getLength() + " to \"" + s + "\"" ); + } + return msg.toString(); + } + + final public String writeMsa( final File outfile ) throws IOException { final Double gr = MsaMethods.calcGapRatio( _msa ); - writeMsa( outfile + "_" + _msa.getNumberOfSequences() + "_" + _msa.getLength() + "_" - + ForesterUtil.roundToInt( gr * 100 ) + suffix, - format ); + final String s = outfile + "_" + _msa.getNumberOfSequences() + "_" + _msa.getLength() + "_" + + ForesterUtil.roundToInt( gr * 100 ); + writeMsa( _msa, s + obtainSuffix(), _output_format ); + return s; } final int calcNonGapResidues( final Sequence seq ) { @@ -99,28 +409,6 @@ public class MsaCompactor { final private GapContribution[] calcGapContribtionsStats( final boolean norm ) { final GapContribution stats[] = calcGapContribtions( norm ); Arrays.sort( stats ); - // for( final GapContribution stat : stats ) { - // final StringBuilder sb = new StringBuilder(); - // sb.append( stat.getId() ); - // sb.append( "\t" ); - // sb.append( NF_4.format( stat.getValue() ) ); - // sb.append( "\t" ); - // sb.append( NF_4.format( stat.median() ) ); - // sb.append( "\t" ); - // sb.append( NF_4.format( stat.getMin() ) ); - // sb.append( "\t" ); - // sb.append( NF_4.format( stat.getMax() ) ); - //sb.append( "\t" ); - //System.out.println( sb ); - // } - return stats; - } - - private static DescriptiveStatistics calculateIdentityRatio( final int from, final int to, final Msa msa ) { - final DescriptiveStatistics stats = new BasicDescriptiveStatistics(); - for( int c = from; c <= to; ++c ) { - stats.addValue( MsaMethods.calculateIdentityRatio( msa, c ) ); - } return stats; } @@ -134,131 +422,74 @@ public class MsaCompactor { return gappiness; } - // Returns null if not path found. - final public static String guessPathToMafft() { - String path; - if ( ForesterUtil.OS_NAME.toLowerCase().indexOf( "win" ) >= 0 ) { - path = "C:\\Program Files\\mafft-win\\mafft.bat"; - if ( MsaInferrer.isInstalled( path ) ) { - return path; - } - } - path = "/usr/local/bin/mafft"; - if ( MsaInferrer.isInstalled( path ) ) { - return path; - } - path = "/usr/bin/mafft"; - if ( MsaInferrer.isInstalled( path ) ) { - return path; - } - path = "/bin/mafft"; - if ( MsaInferrer.isInstalled( path ) ) { - return path; + private final Phylogeny inferNJphylogeny( final PWD_DISTANCE_METHOD pwd_distance_method, + final Msa msa, + final boolean write_matrix, + final String matrix_name ) { + BasicSymmetricalDistanceMatrix m = null; + switch ( pwd_distance_method ) { + case KIMURA_DISTANCE: + m = PairwiseDistanceCalculator.calcKimuraDistances( msa ); + break; + case POISSON_DISTANCE: + m = PairwiseDistanceCalculator.calcPoissonDistances( msa ); + break; + case FRACTIONAL_DISSIMILARITY: + m = PairwiseDistanceCalculator.calcFractionalDissimilarities( msa ); + break; + default: + throw new IllegalArgumentException( "invalid pwd method" ); } - path = "mafft"; - if ( MsaInferrer.isInstalled( path ) ) { - return path; + if ( write_matrix ) { + try { + m.write( ForesterUtil.createBufferedWriter( matrix_name ) ); + } + catch ( final IOException e ) { + e.printStackTrace(); + } } - return null; + final NeighborJoiningF nj = NeighborJoiningF.createInstance( false, 5 ); + final Phylogeny phy = nj.execute( m ); + return phy; } - final private void mafft() throws IOException, InterruptedException { - // final MsaInferrer mafft = Mafft - // .createInstance( "/home/czmasek/SOFTWARE/MSA/MAFFT/mafft-7.130-without-extensions/scripts/mafft" ); - final MsaInferrer mafft = Mafft.createInstance( _path_to_mafft ); - final List opts = new ArrayList(); - opts.add( "--maxiterate" ); - opts.add( "1000" ); - opts.add( "--localpair" ); - opts.add( "--quiet" ); - _msa = mafft.infer( _msa.asSequenceList(), opts ); + private final boolean isPrintMsaStats( final int i ) { + return ( ( ( _step == 1 ) && ( _step_for_diagnostics == 1 ) ) || ( ( _step_for_diagnostics > 0 ) && ( ( ( i + 1 ) % _step_for_diagnostics ) == 0 ) ) ); } - private StringBuilder msaStatsAsSB() { + private final boolean isPrintMsaStatsWriteOutfileAndRealign( final int i ) { + return ( ( ( _step == 1 ) && ( _step_for_diagnostics == 1 ) ) || ( ( _step > 0 ) && ( ( ( i + 1 ) % _step ) == 0 ) ) ); + } + + private final StringBuilder msaPropertiesAsSB( final MsaProperties msa_properties ) { final StringBuilder sb = new StringBuilder(); - sb.append( _msa.getNumberOfSequences() ); - sb.append( "\t" ); - sb.append( _msa.getLength() ); + sb.append( msa_properties.getNumberOfSequences() ); sb.append( "\t" ); - sb.append( NF_3.format( MsaMethods.calcGapRatio( _msa ) ) ); + sb.append( msa_properties.getLength() ); sb.append( "\t" ); - sb.append( NF_3.format( calculateIdentityRatio( 0, _msa.getLength() - 1, _msa ).arithmeticMean() ) ); - return sb; - } - - final private void removeGapColumns() { - _msa = MsaMethods.createInstance().removeGapColumns( 1, 0, _msa ); - } - - final private void removeViaGapAverage( final double mean_gapiness, - final int step, - final boolean realign, - final File outfile, - final int minimal_effective_length ) throws IOException, - InterruptedException { - if ( step < 1 ) { - throw new IllegalArgumentException( "step cannot be less than 1" ); - } - if ( mean_gapiness < 0 ) { - throw new IllegalArgumentException( "target average gap ratio cannot be less than 0" ); - } - if ( VERBOSE ) { - System.out.println( "orig: " + msaStatsAsSB() ); - } - if ( minimal_effective_length > 1 ) { - _msa = MsaMethods.removeSequencesByMinimalLength( _msa, minimal_effective_length ); - if ( VERBOSE ) { - System.out.println( "short seq removal: " + msaStatsAsSB() ); - } - } - int counter = step; - double gr; - do { - removeWorstOffenders( step, 1, false, false ); - if ( realign ) { - mafft(); - } - gr = MsaMethods.calcGapRatio( _msa ); - if ( VERBOSE ) { - System.out.println( counter + ": " + msaStatsAsSB() ); - } - // write( outfile, gr ); - counter += step; - } while ( gr > mean_gapiness ); - if ( VERBOSE ) { - System.out.println( "final: " + msaStatsAsSB() ); + sb.append( NF_4.format( msa_properties.getGapRatio() ) ); + if ( _report_aln_mean_identity ) { + sb.append( "\t" ); + sb.append( NF_4.format( msa_properties.getAverageIdentityRatio() ) ); } + return sb; } - final private void removeViaLength( final int length, final int step, final boolean realign ) throws IOException, - InterruptedException { - if ( step < 1 ) { - throw new IllegalArgumentException( "step cannot be less than 1" ); + private String obtainSuffix() { + if ( _output_format == MSA_FORMAT.FASTA ) { + return ".fasta"; } - if ( length < 11 ) { - throw new IllegalArgumentException( "target length cannot be less than 1" ); - } - if ( VERBOSE ) { - System.out.println( "orig: " + msaStatsAsSB() ); - } - int counter = step; - while ( _msa.getLength() > length ) { - removeWorstOffenders( step, 1, false, false ); - if ( realign ) { - mafft(); - } - if ( VERBOSE ) { - System.out.println( counter + ": " + msaStatsAsSB() ); - } - counter += step; + else if ( _output_format == MSA_FORMAT.PHYLIP ) { + return ".aln"; } + return ""; } - Phylogeny pi( final String matrix ) { + private final Phylogeny pi( final String matrix, final int boostrap ) { final Phylogeny master_phy = inferNJphylogeny( PWD_DISTANCE_METHOD.KIMURA_DISTANCE, _msa, true, matrix ); final int seed = 15; final int n = 100; - final ResampleableMsa resampleable_msa = new ResampleableMsa( ( BasicMsa ) _msa ); + final ResampleableMsa resampleable_msa = new ResampleableMsa( _msa ); final int[][] resampled_column_positions = BootstrapResampler.createResampledColumnPositions( _msa.getLength(), n, seed ); @@ -272,121 +503,155 @@ public class MsaCompactor { return master_phy; } - private Phylogeny inferNJphylogeny( final PWD_DISTANCE_METHOD pwd_distance_method, - final Msa msa, - final boolean write_matrix, - final String matrix_name ) { - BasicSymmetricalDistanceMatrix m = null; - switch ( pwd_distance_method ) { - case KIMURA_DISTANCE: - m = PairwiseDistanceCalculator.calcKimuraDistances( msa ); - break; - case POISSON_DISTANCE: - m = PairwiseDistanceCalculator.calcPoissonDistances( msa ); - break; - case FRACTIONAL_DISSIMILARITY: - m = PairwiseDistanceCalculator.calcFractionalDissimilarities( msa ); - break; - default: - throw new IllegalArgumentException( "invalid pwd method" ); + private final Phylogeny pi( final List to_remove_ids ) { + final Phylogeny phy = inferNJphylogeny( PWD_DISTANCE_METHOD.KIMURA_DISTANCE, _msa, false, "" ); + for( int i = 0; i < to_remove_ids.size(); ++i ) { + final String id = to_remove_ids.get( i ); + final PhylogenyNode n = phy.getNode( id ); + n.setName( n.getName() + " [" + ( i + 1 ) + "]" ); + final NodeVisualData vis = new NodeVisualData(); + vis.setFillType( NodeFill.SOLID ); + vis.setShape( NodeShape.RECTANGLE ); + vis.setSize( 6 ); + vis.setNodeColor( new Color( i > 255 ? 0 : 255 - i, 0, 0 ) ); + n.getNodeData().setNodeVisualData( vis ); } - if ( write_matrix ) { - try { - m.write( ForesterUtil.createBufferedWriter( matrix_name ) ); - } - catch ( final IOException e ) { - // TODO Auto-generated catch block - e.printStackTrace(); + PhylogenyMethods.midpointRoot( phy ); + PhylogenyMethods.orderAppearance( phy.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME ); + final boolean x = PhylogenyMethods.extractFastaInformation( phy ); + if ( !x ) { + final PhylogenyNodeIterator it = phy.iteratorExternalForward(); + while ( it.hasNext() ) { + final PhylogenyNode n = it.next(); + final String name = n.getName().trim(); + if ( !ForesterUtil.isEmpty( name ) ) { + try { + ParserUtils.extractTaxonomyDataFromNodeName( n, TAXONOMY_EXTRACTION.AGGRESSIVE ); + } + catch ( final PhyloXmlDataFormatException e ) { + // Ignore. + } + } } } - final NeighborJoiningF nj = NeighborJoiningF.createInstance( false, 5 ); - final Phylogeny phy = nj.execute( m ); + final Configuration config = new Configuration(); + config.setDisplayAsPhylogram( true ); + config.setUseStyle( true ); + config.setDisplayTaxonomyCode( false ); + config.setDisplayTaxonomyCommonNames( false ); + config.setDisplayTaxonomyScientificNames( false ); + config.setDisplaySequenceNames( false ); + config.setDisplaySequenceSymbols( false ); + config.setDisplayGeneNames( false ); + config.setShowScale( true ); + config.setAddTaxonomyImagesCB( false ); + config.setBaseFontSize( 9 ); + config.setBaseFontFamilyName( "Arial" ); + Archaeopteryx.createApplication( phy, config, _infile_name ); return phy; } - final private void removeWorstOffenders( final int to_remove, - final int step, - final boolean realign, - final boolean norm ) throws IOException, InterruptedException { - //final Phylogeny a = pi( "a.pwd" ); - //Archaeopteryx.createApplication( a ); - final GapContribution stats[] = calcGapContribtionsStats( norm ); - final List to_remove_ids = new ArrayList(); - for( int j = 0; j < to_remove; ++j ) { - to_remove_ids.add( stats[ j ].getId() ); - _removed_seq_ids.add( stats[ j ].getId() ); - } - //TODO if verbose/interactive - for( final String id : to_remove_ids ) { - _msa = MsaMethods.removeSequence( _msa, id ); - removeGapColumns(); - //System.out.print( id ); - System.out.print( ForesterUtil.pad( id, 20, ' ', false ) ); + private final void printMsaProperties( final String id, final MsaProperties msa_properties ) { + if ( ( _step == 1 ) || ( _step_for_diagnostics == 1 ) ) { + System.out.print( ForesterUtil.pad( id, _longest_id_length, ' ', false ) ); System.out.print( "\t" ); - final StringBuilder sb = msaStatsAsSB(); - System.out.println( sb ); } - //TODO else: - //_msa = MsaMethods.removeSequences( _msa, to_remove_ids ); - //removeGapColumns(); + System.out.print( msaPropertiesAsSB( msa_properties ) ); + System.out.print( "\t" ); + } + + final private MsaProperties printMsaStatsWriteOutfileAndRealign( final boolean realign, final String id ) + throws IOException, InterruptedException { if ( realign ) { - mafft(); + realignWithMafft(); } - //final Phylogeny b = pi( "b.pwd" ); - //Archaeopteryx.createApplication( b ); + final MsaProperties msa_prop = new MsaProperties( _msa, _report_aln_mean_identity ); + printMsaProperties( id, msa_prop ); + final String s = writeOutfile(); + System.out.print( "-> " + s + ( realign ? "\t(realigned)" : "" ) ); + return msa_prop; } - final private void writeMsa( final String outfile, final MSA_FORMAT format ) throws IOException { - final Writer w = ForesterUtil.createBufferedWriter( outfile ); - _msa.write( w, format ); - w.close(); + private final void printTableHeader() { + if ( ( _step == 1 ) || ( _step_for_diagnostics == 1 ) ) { + System.out.print( ForesterUtil.pad( "Id", _longest_id_length, ' ', false ) ); + System.out.print( "\t" ); + } + System.out.print( "Seqs" ); + System.out.print( "\t" ); + System.out.print( "Length" ); + System.out.print( "\t" ); + System.out.print( "Gaps" ); + System.out.print( "\t" ); + if ( _report_aln_mean_identity ) { + System.out.print( "MSA qual" ); + System.out.print( "\t" ); + } + System.out.println(); } - public final static MsaCompactor reduceGapAverage( final Msa msa, - final double max_gap_average, - final int step, - final boolean realign, - final File out, - final int minimal_effective_length, - final String path_to_mafft ) throws IOException, - InterruptedException { - final MsaCompactor mc = new MsaCompactor( msa ); - if ( realign ) { - mc.setPathToMafft( path_to_mafft ); + final private void realignWithMafft() throws IOException, InterruptedException { + final MsaInferrer mafft = Mafft.createInstance( _path_to_mafft ); + final List opts = new ArrayList(); + for( final String o : _maffts_opts.split( "\\s" ) ) { + opts.add( o ); } - mc.removeViaGapAverage( max_gap_average, step, realign, out, minimal_effective_length ); - return mc; + _msa = DeleteableMsa.createInstance( mafft.infer( _msa.asSequenceList(), opts ) ); } - public final static MsaCompactor reduceLength( final Msa msa, - final int length, - final int step, - final boolean realign, - final String path_to_mafft ) throws IOException, - InterruptedException { - final MsaCompactor mc = new MsaCompactor( msa ); - if ( realign ) { - mc.setPathToMafft( path_to_mafft ); - } - mc.removeViaLength( length, step, realign ); - return mc; + final private void removeGapColumns() { + _msa.deleteGapOnlyColumns(); } - public final static MsaCompactor removeWorstOffenders( final Msa msa, - final int worst_offenders_to_remove, - final boolean realign, - final boolean norm, - final String path_to_mafft ) throws IOException, - InterruptedException { - final MsaCompactor mc = new MsaCompactor( msa ); - if ( realign ) { - mc.setPathToMafft( path_to_mafft ); + private final String writeOutfile() throws IOException { + final String s = writeMsa( _out_file_base ); + return s; + } + + // Returns null if not path found. + final public static String guessPathToMafft() { + String path; + if ( ForesterUtil.OS_NAME.toLowerCase().indexOf( "win" ) >= 0 ) { + path = "C:\\Program Files\\mafft-win\\mafft.bat"; + if ( MsaInferrer.isInstalled( path ) ) { + return path; + } + } + path = "/home/czmasek/SOFTWARE/MSA/MAFFT/mafft-7.130-without-extensions/scripts/mafft"; + if ( MsaInferrer.isInstalled( path ) ) { + return path; } - mc.removeWorstOffenders( worst_offenders_to_remove, 1, realign, norm ); - return mc; + path = "/usr/local/bin/mafft"; + if ( MsaInferrer.isInstalled( path ) ) { + return path; + } + path = "/usr/bin/mafft"; + if ( MsaInferrer.isInstalled( path ) ) { + return path; + } + path = "/bin/mafft"; + if ( MsaInferrer.isInstalled( path ) ) { + return path; + } + path = "mafft"; + if ( MsaInferrer.isInstalled( path ) ) { + return path; + } + return null; } - private void setPathToMafft( final String path_to_mafft ) { - _path_to_mafft = path_to_mafft; + final private static void writeMsa( final Msa msa, final String outfile, final MSA_FORMAT format ) + throws IOException { + final Writer w = ForesterUtil.createBufferedWriter( outfile ); + msa.write( w, format ); + w.close(); + } + + public void setPeformPhylogenticInference( final boolean phylogentic_inference ) { + _phylogentic_inference = phylogentic_inference; + } + + public void setInfileName( final String infile_name ) { + _infile_name = infile_name; } }