//
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;
return phy;
}
- public final List<MsaProperties> chart( final int step, final boolean realign, final boolean norm )
+ public final List<MsaProperties> 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<String> to_remove_ids = new ArrayList<String>();
final List<MsaProperties> msa_props = new ArrayList<MsaProperties>();
for( final GapContribution gap_gontribution : stats ) {
}
++i;
}
+
if ( _phylogentic_inference ) {
decorateTree( phy, msa_props, true );
displayTree( phy );
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 ) {
config.setDisplaySequenceNames( false );
config.setDisplaySequenceSymbols( false );
config.setDisplayGeneNames( false );
+ config.setDisplayMultipleSequenceAlignment( true );
config.setShowScale( true );
config.setAddTaxonomyImagesCB( false );
config.setBaseFontSize( 9 );
public final List<MsaProperties> removeViaGapAverage( final double mean_gapiness ) throws IOException,
InterruptedException {
- final GapContribution stats[] = calcGapContribtionsStats( _norm );
+ final GapContribution stats[] = calcGapContribtionsStats( _normalize_for_effective_seq_length );
final List<String> to_remove_ids = new ArrayList<String>();
final List<MsaProperties> msa_props = new ArrayList<MsaProperties>();
for( final GapContribution gap_gontribution : stats ) {
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<MsaProperties> removeViaLength( final int length ) throws IOException, InterruptedException {
- final GapContribution stats[] = calcGapContribtionsStats( _norm );
+ final GapContribution stats[] = calcGapContribtionsStats( _normalize_for_effective_seq_length );
final List<String> to_remove_ids = new ArrayList<String>();
final List<MsaProperties> msa_props = new ArrayList<MsaProperties>();
for( final GapContribution gap_gontribution : stats ) {
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<MsaProperties> removeWorstOffenders( final int to_remove ) throws IOException,
InterruptedException {
- final GapContribution stats[] = calcGapContribtionsStats( _norm );
+ final GapContribution stats[] = calcGapContribtionsStats( _normalize_for_effective_seq_length );
final List<String> to_remove_ids = new ArrayList<String>();
final List<MsaProperties> msa_props = new ArrayList<MsaProperties>();
for( int j = 0; j < to_remove; ++j ) {
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;
}
_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 ) {
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;
}
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() ) );
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 ) {