private void writeCladeSeparator() { setSawComma( true ); if ( ( getOutputFormt() == FORMAT.NHX ) || ( getOutputFormt() == FORMAT.NH ) ) { getBuffer().append( "," ); } }
private void reset( final Phylogeny tree ) { setBuffer( new StringBuffer() ); setWriter( null ); setSawComma( false ); setHasNext( true ); setRoot( tree.getRoot() ); setStack( new Stack<PostOrderStackObject>() ); getStack().push( new PostOrderStackObject( tree.getRoot(), 1 ) ); setNodeLevel( 1 ); }
private void reset( final Writer writer, final Phylogeny tree ) { setBuffer( null ); setWriter( writer ); setSawComma( false ); setHasNext( true ); setRoot( tree.getRoot() ); setStack( new Stack<PostOrderStackObject>() ); getStack().push( new PostOrderStackObject( tree.getRoot(), 1 ) ); setNodeLevel( 1 ); }
private void writeOpenClade( final PhylogenyNode node ) throws IOException { if ( !isSawComma() ) { if ( !node.isRoot() && node.isFirstChildNode() ) { increaseNodeLevel(); } if ( getOutputFormt() == FORMAT.PHYLO_XML ) { getWriter().write( ForesterUtil.LINE_SEPARATOR ); if ( isIndentPhyloxml() ) { getWriter().write( createIndentation().toString() ); } if ( node.isCollapse() ) { PhylogenyDataUtil.appendOpen( getWriter(), PhyloXmlMapping.CLADE, PhyloXmlMapping.NODE_COLLAPSE, "true" ); } else { PhylogenyDataUtil.appendOpen( getWriter(), PhyloXmlMapping.CLADE ); } } else if ( ( getOutputFormt() == FORMAT.NHX ) || ( getOutputFormt() == FORMAT.NH ) ) { getBuffer().append( "(" ); } } setSawComma( false ); }