}
++i;
}
+
if ( _phylogentic_inference ) {
decorateTree( phy, msa_props, true );
displayTree( phy );
}
else {
n.getNodeData()
- .getNodeVisualData()
- .setNodeColor( ForesterUtil.calcColor( msa_prop.getLength(),
- min,
- max,
- mean,
- min_color,
- max_color,
- mean_color ) );
+ .getNodeVisualData()
+ .setNodeColor( ForesterUtil.calcColor( msa_prop.getLength(),
+ min,
+ max,
+ mean,
+ min_color,
+ max_color,
+ mean_color ) );
}
}
}
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 {
+ InterruptedException {
final GapContribution stats[] = calcGapContribtionsStats( _norm );
final List<String> to_remove_ids = new ArrayList<String>();
final List<MsaProperties> msa_props = new ArrayList<MsaProperties>();
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;
}
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<MsaProperties> removeWorstOffenders( final int to_remove ) throws IOException,
- InterruptedException {
+ InterruptedException {
final GapContribution stats[] = calcGapContribtionsStats( _norm );
final List<String> to_remove_ids = new ArrayList<String>();
final List<MsaProperties> msa_props = new ArrayList<MsaProperties>();
final Phylogeny phy2 = calcTree();
addSeqs2Tree( _msa, phy2 );
displayTree( phy2 );
- }
+ }
+
return msa_props;
}
sb.append( "\t" );
sb.append( NF_4.format( msa_properties.getGapRatio() ) );
sb.append( "\t" );
- sb.append( NF_1.format( msa_properties.getAvgNumberOfGapsPer100() ) );
+ sb.append( NF_1.format( msa_properties.getAvgNumberOfGaps() ) );
if ( _calculate_shannon_entropy ) {
sb.append( "\t" );
sb.append( NF_4.format( msa_properties.getEntropy7() ) );