X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fmsa_compactor%2FMsaCompactor.java;h=4411fd23c5cd34abe5b33c43a450a9b0ed4510e1;hb=9ccba62f1e15f16ec171ca1db42386e1ad137f06;hp=366d5bd21baca2fad6cb1ec6f64fe4dee17e3f46;hpb=504b2b133e9814ac9ee966dc04a1408c455c6a2f;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 366d5bd..4411fd2 100644 --- a/forester/java/src/org/forester/msa_compactor/MsaCompactor.java +++ b/forester/java/src/org/forester/msa_compactor/MsaCompactor.java @@ -24,6 +24,7 @@ package org.forester.msa_compactor; +import java.awt.Color; import java.io.File; import java.io.IOException; import java.io.Writer; @@ -36,11 +37,16 @@ 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.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; @@ -52,8 +58,15 @@ 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.ForesterUtil; public class MsaCompactor { @@ -61,16 +74,18 @@ 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 String _infile_name = null; private final short _longest_id_length; // private String _maffts_opts = "--auto"; private int _min_length = -1; - // 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 _phylogentic_inference = false; // private boolean _realign = false; private final SortedSet _removed_seq_ids; @@ -91,6 +106,29 @@ public class MsaCompactor { _removed_seqs = new ArrayList(); } + 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 norm ) throws IOException, InterruptedException { final GapContribution stats[] = calcGapContribtionsStats( norm ); @@ -99,17 +137,23 @@ public class MsaCompactor { 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(); + } if ( !_realign ) { _step = -1; } - printTableHeader(); int x = ForesterUtil.roundToInt( _msa.getNumberOfSequences() / 20.0 ); if ( x < 1 ) { x = 1; } - MsaProperties msa_prop = new MsaProperties( _msa, _report_aln_mean_identity ); + MsaProperties msa_prop = new MsaProperties( _msa, "", _report_aln_mean_identity ); msa_props.add( msa_prop ); - printMsaProperties( "", msa_prop ); + printTableHeader(); + printMsaProperties( msa_prop ); System.out.println(); int i = 0; while ( _msa.getNumberOfSequences() > x ) { @@ -118,42 +162,112 @@ public class MsaCompactor { if ( realign && isPrintMsaStatsWriteOutfileAndRealign( i ) ) { removeGapColumns(); realignWithMafft(); - msa_prop = new MsaProperties( _msa, _report_aln_mean_identity ); + msa_prop = new MsaProperties( _msa, id, _report_aln_mean_identity ); 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, _report_aln_mean_identity ); + msa_prop = new MsaProperties( _msa, id, _report_aln_mean_identity ); msa_props.add( msa_prop ); - printMsaProperties( id, msa_prop ); + printMsaProperties( msa_prop ); System.out.println(); } ++i; } + if ( _phylogentic_inference ) { + decorateTree( phy, msa_props, true ); + displayTree( phy ); + } return msa_props; } + public final 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.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 ) ); + 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 ) ); + printMsaProperties( new MsaProperties( _msa, "", _report_aln_mean_identity ) ); System.out.println(); } @@ -165,10 +279,16 @@ public class MsaCompactor { 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(); + } printTableHeader(); - MsaProperties msa_prop = new MsaProperties( _msa, _report_aln_mean_identity ); + MsaProperties msa_prop = new MsaProperties( _msa, "", _report_aln_mean_identity ); msa_props.add( msa_prop ); - printMsaProperties( "", msa_prop ); + printMsaProperties( msa_prop ); System.out.println(); int i = 0; while ( MsaMethods.calcGapRatio( _msa ) > mean_gapiness ) { @@ -183,9 +303,9 @@ public class MsaCompactor { System.out.println(); } else if ( isPrintMsaStats( i ) ) { - msa_prop = new MsaProperties( _msa, _report_aln_mean_identity ); + msa_prop = new MsaProperties( _msa, id, _report_aln_mean_identity ); msa_props.add( msa_prop ); - printMsaProperties( id, msa_prop ); + printMsaProperties( msa_prop ); System.out.println(); } ++i; @@ -195,6 +315,10 @@ public class MsaCompactor { System.out.println(); System.out.println( msg ); } + if ( _phylogentic_inference ) { + decorateTree( phy, msa_props, false ); + displayTree( phy ); + } return msa_props; } @@ -205,10 +329,16 @@ public class MsaCompactor { 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(); + } printTableHeader(); - MsaProperties msa_prop = new MsaProperties( _msa, _report_aln_mean_identity ); + MsaProperties msa_prop = new MsaProperties( _msa, "", _report_aln_mean_identity ); msa_props.add( msa_prop ); - printMsaProperties( "", msa_prop ); + printMsaProperties( msa_prop ); System.out.println(); int i = 0; while ( _msa.getLength() > length ) { @@ -223,8 +353,8 @@ public class MsaCompactor { System.out.println(); } else if ( isPrintMsaStats( i ) ) { - msa_prop = new MsaProperties( _msa, _report_aln_mean_identity ); - printMsaProperties( id, msa_prop ); + msa_prop = new MsaProperties( _msa, id, _report_aln_mean_identity ); + printMsaProperties( msa_prop ); msa_props.add( msa_prop ); System.out.println(); } @@ -235,6 +365,10 @@ public class MsaCompactor { System.out.println(); System.out.println( msg ); } + if ( _phylogentic_inference ) { + decorateTree( phy, msa_props, false ); + displayTree( phy ); + } return msa_props; } @@ -245,12 +379,17 @@ public class MsaCompactor { 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(); } printTableHeader(); - MsaProperties msa_prop = new MsaProperties( _msa, _report_aln_mean_identity ); + MsaProperties msa_prop = new MsaProperties( _msa, "", _report_aln_mean_identity ); 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 ); @@ -264,9 +403,9 @@ public class MsaCompactor { System.out.println(); } else if ( isPrintMsaStats( i ) ) { - msa_prop = new MsaProperties( _msa, _report_aln_mean_identity ); + msa_prop = new MsaProperties( _msa, id, _report_aln_mean_identity ); msa_props.add( msa_prop ); - printMsaProperties( id, msa_prop ); + printMsaProperties( msa_prop ); System.out.println(); } } @@ -275,6 +414,10 @@ public class MsaCompactor { System.out.println(); System.out.println( msg ); } + if ( _phylogentic_inference ) { + decorateTree( phy, msa_props, false ); + displayTree( phy ); + } return msa_props; } @@ -282,6 +425,10 @@ public class MsaCompactor { _gap_ratio = gap_ratio; } + public void setInfileName( final String infile_name ) { + _infile_name = infile_name; + } + public final void setMafftOptions( final String maffts_opts ) { _maffts_opts = maffts_opts; } @@ -306,6 +453,10 @@ 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; } @@ -466,7 +617,7 @@ public class MsaCompactor { return ""; } - private final 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; @@ -484,9 +635,9 @@ public class MsaCompactor { return master_phy; } - 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 ) ); @@ -498,8 +649,8 @@ public class MsaCompactor { if ( realign ) { realignWithMafft(); } - final MsaProperties msa_prop = new MsaProperties( _msa, _report_aln_mean_identity ); - printMsaProperties( id, msa_prop ); + final MsaProperties msa_prop = new MsaProperties( _msa, id, _report_aln_mean_identity ); + printMsaProperties( msa_prop ); final String s = writeOutfile(); System.out.print( "-> " + s + ( realign ? "\t(realigned)" : "" ) ); return msa_prop;