@Override public StringBuffer asText() { final StringBuffer sb = new StringBuffer(); if ( !ForesterUtil.isEmpty( getType() ) ) { sb.append( "[" ); sb.append( getType() ); sb.append( "] " ); } sb.append( ForesterUtil.FORMATTER_6.format( getValue() ) ); if ( getStandardDeviation() != CONFIDENCE_DEFAULT_VALUE ) { sb.append( " (sd=" ); sb.append( getStandardDeviation() ); sb.append( ")" ); } return sb; }
@Override public PhylogenyData copy() { return new Confidence( getValue(), getType(), getStandardDeviation() ); }
@Override public void toPhyloXML( final Writer writer, final int level, final String indentation ) throws IOException { if ( getValue() == CONFIDENCE_DEFAULT_VALUE ) { return; } writer.write( ForesterUtil.LINE_SEPARATOR ); writer.write( indentation ); if ( getStandardDeviation() != CONFIDENCE_DEFAULT_VALUE ) { PhylogenyDataUtil .appendElement( writer, PhyloXmlMapping.CONFIDENCE, FORMATTER.format( ForesterUtil .round( getValue(), PhyloXmlUtil.ROUNDING_DIGITS_FOR_PHYLOXML_DOUBLE_OUTPUT ) ), PhyloXmlMapping.CONFIDENCE_TYPE_ATTR, ForesterUtil.isEmpty( getType() ) ? "unknown" : getType(), PhyloXmlMapping.CONFIDENCE_SD_ATTR, String.valueOf( ForesterUtil .round( getStandardDeviation(), PhyloXmlUtil.ROUNDING_DIGITS_FOR_PHYLOXML_DOUBLE_OUTPUT ) ) ); } else { PhylogenyDataUtil .appendElement( writer, PhyloXmlMapping.CONFIDENCE, FORMATTER.format( ForesterUtil .round( getValue(), PhyloXmlUtil.ROUNDING_DIGITS_FOR_PHYLOXML_DOUBLE_OUTPUT ) ), PhyloXmlMapping.CONFIDENCE_TYPE_ATTR, ForesterUtil.isEmpty( getType() ) ? "unknown" : getType() ); } }
final static public boolean isHasAtLeastOneBranchWithSupportSD( final Phylogeny phy ) { final PhylogenyNodeIterator it = phy.iteratorPostorder(); while ( it.hasNext() ) { final PhylogenyNode n = it.next(); if ( n.getBranchData().isHasConfidences() ) { final List<Confidence> c = n.getBranchData().getConfidences(); for( final Confidence confidence : c ) { if ( confidence.getStandardDeviation() > 0 ) { return true; } } } } return false; }
.getNumberOfDigitsAfterCommaForConfidenceValues() ) ) ); if ( getOptions().isShowConfidenceStddev() ) { if ( confidence.getStandardDeviation() != Confidence.CONFIDENCE_DEFAULT_VALUE ) { sb.append( "(" ); sb.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence .getStandardDeviation(), getOptions() .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) ); sb.append( ")" );
getOptions() .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) ); if ( confidence.getStandardDeviation() != Confidence.CONFIDENCE_DEFAULT_VALUE ) { _popup_buffer.append( " (sd=" ); _popup_buffer.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence .getStandardDeviation(), getOptions() .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) ); _popup_buffer.append( ")" );
return false; if ( !isEqual( p1.getNode( "1" ).getBranchData().getConfidence( 0 ).getStandardDeviation(), 0.1100000000000000e+00 ) ) { return false;
final double sd = getMyNode().getBranchData().getConfidences().get( number ).getStandardDeviation(); getMyNode().getBranchData().getConfidences().set( number, new Confidence( confidence, type, sd ) ); final double sd = getMyNode().getBranchData().getConfidences().get( number ).getStandardDeviation(); getMyNode().getBranchData().getConfidences().set( number, new Confidence( v, value, sd ) );