_main_panel = tjp;
_configuration = configuration;
_phylogeny = t;
- _phy_has_branch_lengths = ForesterUtil.isHasAtLeastOneBranchLengthLargerThanZero( _phylogeny );
+ _phy_has_branch_lengths = Util.isHasAtLeastOneBranchLengthLargerThanZero( _phylogeny );
init();
// if ( !_phylogeny.isEmpty() ) {
_phylogeny.recalculateNumberOfExternalDescendants( true );
sum += getTreeFontSet()._fm_large_italic.stringWidth( tax.getCommonName() + " ()" );
}
}
+ if ( getControlPanel().isShowProperties() && node.getNodeData().isHasProperties() ) {
+ sum += getTreeFontSet()._fm_large.stringWidth( propertiesToString( node ).toString() );
+ }
if ( getControlPanel().isShowBinaryCharacters() && node.getNodeData().isHasBinaryCharacters() ) {
sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getBinaryCharacters()
.getGainedCharactersAsStringBuffer().toString() );
return;
}
setWaitCursor();
+ Util.removeBranchColors( _phylogeny );
Util.colorPhylogenyAccordingToConfidenceValues( _phylogeny, this );
_control_panel.setColorBranches( true );
if ( _control_panel.getColorBranchesCb() != null ) {
return;
}
setWaitCursor();
- Util.colorPhylogenyAccordingToRanks( _phylogeny, rank, this );
- _control_panel.setColorBranches( true );
- if ( _control_panel.getColorBranchesCb() != null ) {
- _control_panel.getColorBranchesCb().setSelected( true );
+ Util.removeBranchColors( _phylogeny );
+ final int colorizations = Util.colorPhylogenyAccordingToRanks( _phylogeny, rank, this );
+ if ( colorizations > 0 ) {
+ _control_panel.setColorBranches( true );
+ if ( _control_panel.getColorBranchesCb() != null ) {
+ _control_panel.getColorBranchesCb().setSelected( true );
+ }
+ if ( _control_panel.getColorAccSpeciesCb() != null ) {
+ _control_panel.getColorAccSpeciesCb().setSelected( false );
+ }
+ _options.setColorLabelsSameAsParentBranch( true );
+ _control_panel.repaint();
}
setArrowCursor();
repaint();
+ if ( colorizations > 0 ) {
+ String msg = "Taxonomy colorization via " + rank + " completed:\n";
+ if ( colorizations > 1 ) {
+ msg += "colorized " + colorizations + " subtrees";
+ }
+ else {
+ msg += "colorized one subtree";
+ }
+ JOptionPane.showMessageDialog( this,
+ msg,
+ "Taxonomy Colorization Completed (" + rank + ")",
+ JOptionPane.INFORMATION_MESSAGE );
+ }
+ else {
+ String msg = "Could not taxonomy colorize any subtree via " + rank + ".\n";
+ msg += "Possible solutions (given that suitable taxonomic information is present):\n";
+ msg += "select a different rank (e.g. phylum, genus, ...)\n";
+ msg += " and/or\n";
+ msg += "execute:\n";
+ msg += "1. \"" + MainFrameApplication.OBTAIN_DETAILED_TAXONOMIC_INFORMATION + "\" (Tools)\n";
+ msg += "2. \"" + MainFrameApplication.INFER_ANCESTOR_TAXONOMIES + "\" (Analysis)";
+ JOptionPane.showMessageDialog( this, msg, "Taxonomy Colorization Failed", JOptionPane.WARNING_MESSAGE );
+ }
}
final private void copySubtree( final PhylogenyNode node ) {
_sb.append( node.getNodeData().getSequence().getAccession().getValue() );
}
}
+ if ( getControlPanel().isShowProperties() && node.getNodeData().isHasProperties() ) {
+ if ( _sb.length() > 0 ) {
+ _sb.append( " " );
+ }
+ _sb.append( propertiesToString( node ) );
+ }
g.setFont( getTreeFontSet().getLargeFont() );
if ( is_in_found_nodes ) {
g.setFont( getTreeFontSet().getLargeFont().deriveFont( Font.BOLD ) );
}
}
+ private StringBuffer propertiesToString( final PhylogenyNode node ) {
+ final PropertiesMap properties = node.getNodeData().getProperties();
+ final StringBuffer sb = new StringBuffer();
+ boolean first = true;
+ for( final String ref : properties.getPropertyRefs() ) {
+ if ( first ) {
+ first = false;
+ }
+ else {
+ sb.append( " " );
+ }
+ sb.append( properties.getProperty( ref ).asText() );
+ }
+ return sb;
+ }
+
private double drawTaxonomyImage( final double x, final double y, final PhylogenyNode node, final Graphics2D g ) {
final List<Uri> us = new ArrayList<Uri>();
for( final Taxonomy t : node.getNodeData().getTaxonomies() ) {