-
- 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 ) );