X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fmsa_compactor%2FMsaCompactor.java;h=8a13b5cc6bdb2ff28954e78fdb04751ad8c850d9;hb=8aadbec1b0627ebd71e57e60e06621d4038bb79a;hp=0b7f8ed47370fe99c9524da3164074b051c41719;hpb=861cf1ba9d6eb76eeb499fa59d7ffc961e5288e1;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 0b7f8ed..8a13b5c 100644 --- a/forester/java/src/org/forester/msa_compactor/MsaCompactor.java +++ b/forester/java/src/org/forester/msa_compactor/MsaCompactor.java @@ -64,37 +64,38 @@ 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.sequence.MolecularSequence; 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 double _gap_ratio = -1; - private final short _longest_id_length; + final private static NumberFormat NF_1 = new DecimalFormat( "0.#" ); + final private static NumberFormat NF_3 = new DecimalFormat( "0.###" ); + final private static NumberFormat NF_4 = new DecimalFormat( "0.####" ); + private boolean _calculate_shannon_entropy = false; // - private String _maffts_opts = "--auto"; - private int _min_length = -1; + private String _infile_name = null; + private final short _longest_id_length; // - 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 String _maffts_opts = "--auto"; + private DeleteableMsa _msa = null; + private boolean _normalize_for_effective_seq_length = true; + private File _out_file_base = null; + private MSA_FORMAT _output_format = MSA_FORMAT.FASTA; + private String _path_to_mafft = null; + private boolean _phylogentic_inference = false; // - private boolean _realign = false; - private final SortedSet _removed_seq_ids; - 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; + private boolean _realign = false; + private final SortedSet _removed_seq_ids; + private final ArrayList _removed_seqs; + private File _removed_seqs_out_base = null; + private int _step = -1; + private int _step_for_diagnostics = -1; static { + NF_1.setRoundingMode( RoundingMode.HALF_UP ); NF_4.setRoundingMode( RoundingMode.HALF_UP ); NF_3.setRoundingMode( RoundingMode.HALF_UP ); } @@ -103,34 +104,58 @@ public class MsaCompactor { _msa = msa; _removed_seq_ids = new TreeSet(); _longest_id_length = _msa.determineMaxIdLength(); - _removed_seqs = new ArrayList(); + _removed_seqs = new ArrayList(); } - public final List chart( final int step, final boolean realign, final boolean norm ) + public final Phylogeny calcTree() { + final Phylogeny phy = inferNJphylogeny( PWD_DISTANCE_METHOD.KIMURA_DISTANCE, _msa, false, "" ); + 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. + } + } + } + } + return phy; + } + + public final List chart( final int step, final boolean realign, final boolean normalize_for_effective_seq_length ) throws IOException, InterruptedException { - final GapContribution stats[] = calcGapContribtionsStats( norm ); + final GapContribution stats[] = calcGapContribtionsStats( normalize_for_effective_seq_length ); 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 ); Phylogeny phy = null; if ( _phylogentic_inference ) { System.out.println( "calculating phylogentic tree..." ); System.out.println(); phy = calcTree(); + addSeqs2Tree( _msa, phy ); } + if ( !_realign ) { + _step = -1; + } + int x = ForesterUtil.roundToInt( _msa.getNumberOfSequences() / 10.0 ); + if ( x < 2 ) { + x = 2; + } + MsaProperties msa_prop = new MsaProperties( _msa, "", _calculate_shannon_entropy ); + msa_props.add( msa_prop ); printTableHeader(); - printMsaProperties( "", msa_prop ); + printMsaProperties( msa_prop ); System.out.println(); int i = 0; while ( _msa.getNumberOfSequences() > x ) { @@ -139,70 +164,170 @@ public class MsaCompactor { if ( realign && isPrintMsaStatsWriteOutfileAndRealign( i ) ) { removeGapColumns(); realignWithMafft(); - msa_prop = new MsaProperties( _msa, id, _report_aln_mean_identity ); + msa_prop = new MsaProperties( _msa, id, _calculate_shannon_entropy ); msa_props.add( msa_prop ); - printMsaProperties( id, msa_prop ); + printMsaProperties( msa_prop ); System.out.print( "(realigned)" ); System.out.println(); } else if ( isPrintMsaStats( i ) ) { removeGapColumns(); - msa_prop = new MsaProperties( _msa, id, _report_aln_mean_identity ); + msa_prop = new MsaProperties( _msa, id, _calculate_shannon_entropy ); msa_props.add( msa_prop ); - printMsaProperties( id, msa_prop ); + printMsaProperties( msa_prop ); System.out.println(); } ++i; } + if ( _phylogentic_inference ) { - final Phylogeny p2 = phy.copy(); - decorateTree( p2, to_remove_ids ); - decorateTree2( phy, msa_props ); - displayTree( p2 ); + decorateTree( phy, msa_props, true ); displayTree( phy ); } return msa_props; } + private final static void addSeqs2Tree( final Msa msa, final Phylogeny phy ) { + for( int i = 0; i < msa.getNumberOfSequences(); ++i ) { + final MolecularSequence seq = msa.getSequence( i ); + final String seq_name = seq.getIdentifier(); + final PhylogenyNode n = phy.getNode( seq_name ); + if ( !n.getNodeData().isHasSequence() ) { + n.getNodeData().addSequence( new org.forester.phylogeny.data.Sequence() ); + } + else { + throw new IllegalArgumentException( "this should not have happened" ); + } + n.getNodeData().getSequence().setMolecularSequence( seq.getMolecularSequenceAsString() ); + n.getNodeData().getSequence().setMolecularSequenceAligned( true ); + n.getNodeData().getSequence().setName( seq_name ); + } + } + + private final static void decorateTree( final Phylogeny phy, + final List msa_props, + final boolean chart_only ) { + final BasicDescriptiveStatistics length_stats = new BasicDescriptiveStatistics(); + for( int i = 0; i < msa_props.size(); ++i ) { + final MsaProperties msa_prop = msa_props.get( i ); + final String id = msa_prop.getRemovedSeq(); + if ( !ForesterUtil.isEmpty( id ) ) { + length_stats.addValue( msa_prop.getLength() ); + } + } + final double mean = length_stats.arithmeticMean(); + final double min = length_stats.getMin(); + final double max = length_stats.getMax(); + final Color min_color = new Color( 0, 255, 0 ); + final Color max_color = new Color( 255, 0, 0 ); + final Color mean_color = new Color( 255, 255, 0 ); + final PhylogenyNodeIterator it = phy.iteratorExternalForward(); + if ( chart_only ) { + while ( it.hasNext() ) { + final NodeVisualData vis = new NodeVisualData(); + vis.setFillType( NodeFill.SOLID ); + vis.setShape( NodeShape.RECTANGLE ); + vis.setNodeColor( min_color ); + it.next().getNodeData().setNodeVisualData( vis ); + } + } + for( int i = 0; i < msa_props.size(); ++i ) { + final MsaProperties msa_prop = msa_props.get( i ); + final String id = msa_prop.getRemovedSeq(); + if ( !ForesterUtil.isEmpty( id ) ) { + final PhylogenyNode n = phy.getNode( id ); + n.setName( n.getName() + " [" + i + "]" ); + if ( !chart_only ) { + final NodeVisualData vis = new NodeVisualData(); + vis.setFillType( NodeFill.SOLID ); + vis.setShape( NodeShape.RECTANGLE ); + vis.setNodeColor( ForesterUtil.calcColor( msa_prop.getLength(), min, max, mean_color, max_color ) ); + n.getNodeData().setNodeVisualData( vis ); + } + else { + n.getNodeData() + .getNodeVisualData() + .setNodeColor( ForesterUtil.calcColor( msa_prop.getLength(), + min, + max, + mean, + min_color, + max_color, + mean_color ) ); + } + } + } + } + final public void deleteGapColumns( final double max_allowed_gap_ratio ) { _msa.deleteGapColumns( max_allowed_gap_ratio ); } - final public Msa getMsa() { - return _msa; + public final void displayTree( final Phylogeny phy ) { + 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.setDisplayMultipleSequenceAlignment( true ); + config.setShowScale( true ); + config.setAddTaxonomyImagesCB( false ); + config.setBaseFontSize( 9 ); + config.setBaseFontFamilyName( "Arial" ); + Archaeopteryx.createApplication( phy, config, _infile_name ); } - final public SortedSet getRemovedSeqIds() { - return _removed_seq_ids; + final public Msa getMsa() { + return _msa; } - public final void removeSequencesByMinimalLength( final int min_effective_length ) { - printMsaProperties( "", new MsaProperties( _msa, "", _report_aln_mean_identity ) ); - System.out.println(); + public final void removeSequencesByMinimalLength( final int min_effective_length ) throws IOException { _msa = DeleteableMsa.createInstance( MsaMethods.removeSequencesByMinimalLength( _msa, min_effective_length ) ); removeGapColumns(); - printMsaProperties( "", new MsaProperties( _msa, "", _report_aln_mean_identity ) ); + final String s = writeOutfile(); + final DescriptiveStatistics msa_stats = MsaMethods.calculateEffectiveLengthStatistics( _msa ); + System.out.println( "Output MSA : " + s ); + System.out.println( " MSA length : " + _msa.getLength() ); + System.out.println( " Number of sequences : " + _msa.getNumberOfSequences() ); + System.out.println( " Median sequence length : " + NF_1.format( msa_stats.median() ) ); + System.out.println( " Mean sequence length : " + NF_1.format( msa_stats.arithmeticMean() ) ); + System.out.println( " Max sequence length : " + ( ( int ) msa_stats.getMax() ) ); + System.out.println( " Min sequence length : " + ( ( int ) msa_stats.getMin() ) ); + System.out.println( " Gap ratio : " + NF_4.format( MsaMethods.calcGapRatio( _msa ) ) ); + System.out.println( " Normalized Shannon Entropy (entn21): " + + NF_4.format( MsaMethods.calcNormalizedShannonsEntropy( 21, _msa ) ) ); System.out.println(); } public final List removeViaGapAverage( final double mean_gapiness ) throws IOException, - InterruptedException { - final GapContribution stats[] = calcGapContribtionsStats( _norm ); + InterruptedException { + final GapContribution stats[] = calcGapContribtionsStats( _normalize_for_effective_seq_length ); 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() ); } + Phylogeny phy = null; + if ( _phylogentic_inference ) { + System.out.println( "calculating phylogentic tree..." ); + System.out.println(); + phy = calcTree(); + addSeqs2Tree( _msa, phy ); + } printTableHeader(); - MsaProperties msa_prop = new MsaProperties( _msa, "", _report_aln_mean_identity ); + MsaProperties msa_prop = new MsaProperties( _msa, "", _calculate_shannon_entropy ); msa_props.add( msa_prop ); - printMsaProperties( "", 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 ); + final MolecularSequence deleted = _msa.deleteRow( id, true ); _removed_seqs.add( deleted ); removeGapColumns(); if ( isPrintMsaStatsWriteOutfileAndRealign( i ) || ( MsaMethods.calcGapRatio( _msa ) <= mean_gapiness ) ) { @@ -211,9 +336,9 @@ public class MsaCompactor { System.out.println(); } else if ( isPrintMsaStats( i ) ) { - msa_prop = new MsaProperties( _msa, id, _report_aln_mean_identity ); + msa_prop = new MsaProperties( _msa, id, _calculate_shannon_entropy ); msa_props.add( msa_prop ); - printMsaProperties( id, msa_prop ); + printMsaProperties( msa_prop ); System.out.println(); } ++i; @@ -223,26 +348,44 @@ public class MsaCompactor { System.out.println(); System.out.println( msg ); } + if ( _phylogentic_inference ) { + decorateTree( phy, msa_props, false ); + displayTree( phy ); + System.out.println( "calculating phylogentic tree..." ); + System.out.println(); + final Phylogeny phy2 = calcTree(); + addSeqs2Tree( _msa, phy2 ); + displayTree( phy2 ); + } + + return msa_props; } public List removeViaLength( final int length ) throws IOException, InterruptedException { - final GapContribution stats[] = calcGapContribtionsStats( _norm ); + final GapContribution stats[] = calcGapContribtionsStats( _normalize_for_effective_seq_length ); 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() ); } + Phylogeny phy = null; + if ( _phylogentic_inference ) { + System.out.println( "calculating phylogentic tree..." ); + System.out.println(); + phy = calcTree(); + addSeqs2Tree( _msa, phy ); + } printTableHeader(); - MsaProperties msa_prop = new MsaProperties( _msa, "", _report_aln_mean_identity ); + MsaProperties msa_prop = new MsaProperties( _msa, "", _calculate_shannon_entropy ); msa_props.add( msa_prop ); - printMsaProperties( "", 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 ); + final MolecularSequence deleted = _msa.deleteRow( id, true ); _removed_seqs.add( deleted ); removeGapColumns(); if ( isPrintMsaStatsWriteOutfileAndRealign( i ) || ( _msa.getLength() <= length ) ) { @@ -251,8 +394,8 @@ public class MsaCompactor { System.out.println(); } else if ( isPrintMsaStats( i ) ) { - msa_prop = new MsaProperties( _msa, id, _report_aln_mean_identity ); - printMsaProperties( id, msa_prop ); + msa_prop = new MsaProperties( _msa, id, _calculate_shannon_entropy ); + printMsaProperties( msa_prop ); msa_props.add( msa_prop ); System.out.println(); } @@ -263,27 +406,43 @@ public class MsaCompactor { System.out.println(); System.out.println( msg ); } + if ( _phylogentic_inference ) { + decorateTree( phy, msa_props, false ); + displayTree( phy ); + System.out.println( "calculating phylogentic tree..." ); + System.out.println(); + final Phylogeny phy2 = calcTree(); + addSeqs2Tree( _msa, phy2 ); + displayTree( phy2 ); + } + return msa_props; } public final List removeWorstOffenders( final int to_remove ) throws IOException, - InterruptedException { - final GapContribution stats[] = calcGapContribtionsStats( _norm ); + InterruptedException { + final GapContribution stats[] = calcGapContribtionsStats( _normalize_for_effective_seq_length ); 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() ); + } + Phylogeny phy = null; + if ( _phylogentic_inference ) { + System.out.println( "calculating phylogentic tree..." ); + System.out.println(); + phy = calcTree(); + addSeqs2Tree( _msa, phy ); } printTableHeader(); - MsaProperties msa_prop = new MsaProperties( _msa, "", _report_aln_mean_identity ); + MsaProperties msa_prop = new MsaProperties( _msa, "", _calculate_shannon_entropy ); msa_props.add( msa_prop ); - printMsaProperties( "", 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 ); + final MolecularSequence deleted = _msa.deleteRow( id, true ); _removed_seqs.add( deleted ); removeGapColumns(); if ( isPrintMsaStatsWriteOutfileAndRealign( i ) || ( i == ( to_remove_ids.size() - 1 ) ) ) { @@ -292,9 +451,9 @@ public class MsaCompactor { System.out.println(); } else if ( isPrintMsaStats( i ) ) { - msa_prop = new MsaProperties( _msa, id, _report_aln_mean_identity ); + msa_prop = new MsaProperties( _msa, id, _calculate_shannon_entropy ); msa_props.add( msa_prop ); - printMsaProperties( id, msa_prop ); + printMsaProperties( msa_prop ); System.out.println(); } } @@ -303,23 +462,33 @@ public class MsaCompactor { System.out.println(); System.out.println( msg ); } + if ( _phylogentic_inference ) { + decorateTree( phy, msa_props, false ); + displayTree( phy ); + System.out.println( "calculating phylogentic tree..." ); + System.out.println(); + final Phylogeny phy2 = calcTree(); + addSeqs2Tree( _msa, phy2 ); + displayTree( phy2 ); + } + return msa_props; } - public final void setGapRatio( final double gap_ratio ) { - _gap_ratio = gap_ratio; + public final void setCalculateNormalizedShannonEntropy( final boolean calculate_shannon_entropy ) { + _calculate_shannon_entropy = calculate_shannon_entropy; } - public final void setMafftOptions( final String maffts_opts ) { - _maffts_opts = maffts_opts; + public void setInfileName( final String infile_name ) { + _infile_name = infile_name; } - public final void setMinLength( final int min_length ) { - _min_length = min_length; + public final void setMafftOptions( final String maffts_opts ) { + _maffts_opts = maffts_opts; } - public final void setNorm( final boolean norm ) { - _norm = norm; + public final void setNorm( final boolean normalize_for_effective_seq_length ) { + _normalize_for_effective_seq_length = normalize_for_effective_seq_length; } final public void setOutFileBase( final File out_file_base ) { @@ -334,6 +503,10 @@ public class MsaCompactor { _path_to_mafft = path_to_mafft; } + public void setPeformPhylogenticInference( final boolean phylogentic_inference ) { + _phylogentic_inference = phylogentic_inference; + } + public final void setRealign( final boolean realign ) { _realign = realign; } @@ -342,10 +515,6 @@ public class MsaCompactor { _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; } @@ -385,7 +554,7 @@ public class MsaCompactor { return s; } - final int calcNonGapResidues( final Sequence seq ) { + final int calcNonGapResidues( final MolecularSequence seq ) { int ng = 0; for( int i = 0; i < seq.getLength(); ++i ) { if ( !seq.isGapAt( i ) ) { @@ -415,8 +584,8 @@ public class MsaCompactor { return stats; } - final private GapContribution[] calcGapContribtionsStats( final boolean norm ) { - final GapContribution stats[] = calcGapContribtions( norm ); + final private GapContribution[] calcGapContribtionsStats( final boolean normalize_for_effective_seq_length ) { + final GapContribution stats[] = calcGapContribtions( normalize_for_effective_seq_length ); Arrays.sort( stats ); return stats; } @@ -431,6 +600,12 @@ public class MsaCompactor { return gappiness; } + private final Phylogeny collapse( final Msa msa, final int threshold ) { + final BasicSymmetricalDistanceMatrix m = PairwiseDistanceCalculator.calcFractionalDissimilarities( msa ); + //TODO + return null; + } + private final Phylogeny inferNJphylogeny( final PWD_DISTANCE_METHOD pwd_distance_method, final Msa msa, final boolean write_matrix, @@ -477,9 +652,13 @@ public class MsaCompactor { sb.append( msa_properties.getLength() ); sb.append( "\t" ); sb.append( NF_4.format( msa_properties.getGapRatio() ) ); - if ( _report_aln_mean_identity ) { + sb.append( "\t" ); + sb.append( NF_1.format( msa_properties.getAvgNumberOfGaps() ) ); + if ( _calculate_shannon_entropy ) { + sb.append( "\t" ); + sb.append( NF_4.format( msa_properties.getEntropy7() ) ); sb.append( "\t" ); - sb.append( NF_4.format( msa_properties.getAverageIdentityRatio() ) ); + sb.append( NF_4.format( msa_properties.getEntropy21() ) ); } return sb; } @@ -512,106 +691,9 @@ public class MsaCompactor { return master_phy; } - public final Phylogeny calcTree() { - final Phylogeny phy = inferNJphylogeny( PWD_DISTANCE_METHOD.KIMURA_DISTANCE, _msa, false, "" ); - 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. - } - } - } - } - return phy; - } - - public final void decorateTree( final Phylogeny phy, final List to_remove_ids ) { - 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 ); - } - } - - public final void decorateTree2( final Phylogeny phy, final List msa_props ) { - final BasicDescriptiveStatistics length_stats = new BasicDescriptiveStatistics(); - for( int i = 0; i < msa_props.size(); ++i ) { - final MsaProperties msa_prop = msa_props.get( i ); - final String id = msa_prop.getRemovedSeq(); - if ( !ForesterUtil.isEmpty( id ) ) { - length_stats.addValue( msa_prop.getLength() ); - } - } - final double mean = length_stats.arithmeticMean(); - final double min = length_stats.getMin(); - final double max = length_stats.getMax(); - final Color min_color = new Color( 0, 255, 0 ); - final Color max_color = new Color( 255, 0, 0 ); - final Color mean_color = new Color( 255, 255, 0 ); - final PhylogenyNodeIterator it = phy.iteratorExternalForward(); - while ( it.hasNext() ) { - final NodeVisualData vis = new NodeVisualData(); - vis.setFillType( NodeFill.SOLID ); - vis.setShape( NodeShape.RECTANGLE ); - vis.setSize( 6 ); - vis.setNodeColor( min_color ); - it.next().getNodeData().setNodeVisualData( vis ); - } - for( int i = 0; i < msa_props.size(); ++i ) { - final MsaProperties msa_prop = msa_props.get( i ); - final String id = msa_prop.getRemovedSeq(); - if ( !ForesterUtil.isEmpty( id ) ) { - final PhylogenyNode n = phy.getNode( id ); - n.setName( n.getName() + " [" + i + "]" ); - n.getNodeData() - .getNodeVisualData() - .setNodeColor( ForesterUtil.calcColor( msa_prop.getLength(), - min, - max, - mean, - min_color, - max_color, - mean_color ) ); - } - } - } - - public final void displayTree( final Phylogeny phy ) { - 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 ); - } - - private final void printMsaProperties( final String id, final MsaProperties msa_properties ) { + private final void printMsaProperties( final MsaProperties msa_properties ) { if ( ( _step == 1 ) || ( _step_for_diagnostics == 1 ) ) { - System.out.print( ForesterUtil.pad( id, _longest_id_length, ' ', false ) ); + System.out.print( ForesterUtil.pad( msa_properties.getRemovedSeq(), _longest_id_length, ' ', false ) ); System.out.print( "\t" ); } System.out.print( msaPropertiesAsSB( msa_properties ) ); @@ -623,8 +705,8 @@ public class MsaCompactor { if ( realign ) { realignWithMafft(); } - final MsaProperties msa_prop = new MsaProperties( _msa, id, _report_aln_mean_identity ); - printMsaProperties( id, msa_prop ); + final MsaProperties msa_prop = new MsaProperties( _msa, id, _calculate_shannon_entropy ); + printMsaProperties( msa_prop ); final String s = writeOutfile(); System.out.print( "-> " + s + ( realign ? "\t(realigned)" : "" ) ); return msa_prop; @@ -639,10 +721,14 @@ public class MsaCompactor { System.out.print( "\t" ); System.out.print( "Length" ); System.out.print( "\t" ); + System.out.print( "Gap R" ); + System.out.print( "\t" ); System.out.print( "Gaps" ); System.out.print( "\t" ); - if ( _report_aln_mean_identity ) { - System.out.print( "MSA qual" ); + if ( _calculate_shannon_entropy ) { + System.out.print( "entn7" ); + System.out.print( "\t" ); + System.out.print( "entn21" ); System.out.print( "\t" ); } System.out.println(); @@ -704,12 +790,4 @@ public class MsaCompactor { 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; - } }