X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fmsa_compactor%2FMsaCompactor.java;h=8a13b5cc6bdb2ff28954e78fdb04751ad8c850d9;hb=cb49ee5684c6907b3161db82ff9aea72961b8548;hp=da74deca96393c08c7d8bacaeff66303316c07d7;hpb=5e3ce382cc99a6edab8efbfb2877b8a17d463e75;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 da74dec..8a13b5c 100644 --- a/forester/java/src/org/forester/msa_compactor/MsaCompactor.java +++ b/forester/java/src/org/forester/msa_compactor/MsaCompactor.java @@ -82,7 +82,7 @@ public class MsaCompactor { // private String _maffts_opts = "--auto"; private DeleteableMsa _msa = null; - private boolean _norm = true; + 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; @@ -130,9 +130,9 @@ public class MsaCompactor { return phy; } - public final List chart( final int step, final boolean realign, final boolean norm ) + 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 ) { @@ -179,6 +179,7 @@ public class MsaCompactor { } ++i; } + if ( _phylogentic_inference ) { decorateTree( phy, msa_props, true ); displayTree( phy ); @@ -230,34 +231,32 @@ public class MsaCompactor { 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 ) ); - } - } - + 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 ) { @@ -274,6 +273,7 @@ public class MsaCompactor { config.setDisplaySequenceNames( false ); config.setDisplaySequenceSymbols( false ); config.setDisplayGeneNames( false ); + config.setDisplayMultipleSequenceAlignment( true ); config.setShowScale( true ); config.setAddTaxonomyImagesCB( false ); config.setBaseFontSize( 9 ); @@ -305,7 +305,7 @@ public class MsaCompactor { public final List removeViaGapAverage( final double mean_gapiness ) 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 ) { @@ -349,14 +349,21 @@ public class MsaCompactor { System.out.println( msg ); } if ( _phylogentic_inference ) { - decorateTree( phy, msa_props, false ); + 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 ) { @@ -400,15 +407,21 @@ public class MsaCompactor { System.out.println( msg ); } if ( _phylogentic_inference ) { - decorateTree( phy, msa_props, false ); + 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 ); + 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 ) { @@ -450,17 +463,15 @@ public class MsaCompactor { System.out.println( msg ); } if ( _phylogentic_inference ) { - decorateTree( phy, msa_props, false ); + decorateTree( phy, msa_props, false ); displayTree( phy ); - - - System.out.println( "calculating phylogentic tree..." ); - System.out.println(); - Phylogeny phy2 = calcTree(); - addSeqs2Tree( _msa, phy2 ); - displayTree( phy2 ); - - } + System.out.println( "calculating phylogentic tree..." ); + System.out.println(); + final Phylogeny phy2 = calcTree(); + addSeqs2Tree( _msa, phy2 ); + displayTree( phy2 ); + } + return msa_props; } @@ -476,8 +487,8 @@ public class MsaCompactor { _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 ) { @@ -573,8 +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; } @@ -641,6 +652,8 @@ public class MsaCompactor { sb.append( msa_properties.getLength() ); sb.append( "\t" ); sb.append( NF_4.format( msa_properties.getGapRatio() ) ); + 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() ) ); @@ -708,6 +721,8 @@ 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 ( _calculate_shannon_entropy ) {