final int colorizations = TreePanelUtil.colorPhylogenyAccordingToRanks( _phylogeny, rank, this );
if ( colorizations > 0 ) {
_control_panel.setColorBranches( true );
- if ( _control_panel.getColorBranchesCb() != null ) {
- _control_panel.getColorBranchesCb().setSelected( true );
+ if ( _control_panel.getUseVisualStylesCb() != null ) {
+ _control_panel.getUseVisualStylesCb().setSelected( true );
}
if ( _control_panel.getColorAccSpeciesCb() != null ) {
_control_panel.getColorAccSpeciesCb().setSelected( false );
AptxUtil.removeBranchColors( _phylogeny );
TreePanelUtil.colorPhylogenyAccordingToConfidenceValues( _phylogeny, this );
_control_panel.setColorBranches( true );
- if ( _control_panel.getColorBranchesCb() != null ) {
- _control_panel.getColorBranchesCb().setSelected( true );
+ if ( _control_panel.getUseVisualStylesCb() != null ) {
+ _control_panel.getUseVisualStylesCb().setSelected( true );
}
setArrowCursor();
repaint();
}
final Color getGraphicsForNodeBoxWithColorForParentBranch( final PhylogenyNode node ) {
- if ( getControlPanel().isColorBranches() && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
+ if ( getControlPanel().isUseVisualStyles() && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
return ( PhylogenyMethods.getBranchColorValue( node ) );
}
else {
setWaitCursor();
TreePanelUtil.colorPhylogenyAccordingToExternalTaxonomy( _phylogeny, this );
_control_panel.setColorBranches( true );
- if ( _control_panel.getColorBranchesCb() != null ) {
- _control_panel.getColorBranchesCb().setSelected( true );
+ if ( _control_panel.getUseVisualStylesCb() != null ) {
+ _control_panel.getUseVisualStylesCb().setSelected( true );
}
setEdited( true );
setArrowCursor();
&& !to_graphics_file && getCopiedAndPastedNodes().contains( node.getId() ) ) {
g.setColor( getTreeColorSet().getFoundColor0() );
}
- else if ( getControlPanel().isColorBranches() && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
+ else if ( getControlPanel().isUseVisualStyles() && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
g.setColor( PhylogenyMethods.getBranchColorValue( node ) );
}
else if ( to_pdf ) {
final PhylogenyNode node,
final List<PhylogenyNode> additional_nodes ) {
_control_panel.setColorBranches( true );
- if ( _control_panel.getColorBranchesCb() != null ) {
- _control_panel.getColorBranchesCb().setSelected( true );
+ if ( _control_panel.getUseVisualStylesCb() != null ) {
+ _control_panel.getUseVisualStylesCb().setSelected( true );
}
if ( node != null ) {
for( final PreorderTreeIterator it = new PreorderTreeIterator( node ); it.hasNext(); ) {
final PhylogenyNode node,
final List<PhylogenyNode> additional_nodes ) {
_control_panel.setColorBranches( true );
- if ( _control_panel.getColorBranchesCb() != null ) {
- _control_panel.getColorBranchesCb().setSelected( true );
+ if ( _control_panel.getUseVisualStylesCb() != null ) {
+ _control_panel.getUseVisualStylesCb().setSelected( true );
}
if ( node != null ) {
colorizeNodesHelper( c, node );
}
private final static void colorizeNodesHelper( final Color c, final PhylogenyNode node ) {
- NodeVisualData v;
- if ( node.getNodeData().getNodeVisualData() != null ) {
- v = node.getNodeData().getNodeVisualData();
+ if ( node.getNodeData().getNodeVisualData() == null ) {
+ node.getNodeData().setNodeVisualData( new NodeVisualData() );
}
- else {
- v = new NodeVisualData();
- }
- v.setFontColor( new Color( c.getRed(), c.getGreen(), c.getBlue() ) );
+ node.getNodeData().getNodeVisualData().setFontColor( new Color( c.getRed(), c.getGreen(), c.getBlue() ) );
}
final private void colorSubtree( final PhylogenyNode node ) {
}
_color_chooser.setPreviewPanel( new JPanel() );
SubtreeColorizationActionListener al;
- if ( ( getFoundNodes0() != null ) && !getFoundNodes0().isEmpty() ) {
- final List<PhylogenyNode> additional_nodes = getFoundNodes0AsListOfPhylogenyNodes();
+ if ( ( getFoundNodes0() != null ) || ( getFoundNodes1() != null ) ) {
+ final List<PhylogenyNode> additional_nodes = getFoundNodesAsListOfPhylogenyNodes();
al = new SubtreeColorizationActionListener( _color_chooser, node, additional_nodes );
}
else {
private void colorNodeFont( final PhylogenyNode node ) {
_color_chooser.setPreviewPanel( new JPanel() );
NodeColorizationActionListener al;
- if ( ( getFoundNodes0() != null ) && !getFoundNodes0().isEmpty() ) {
- final List<PhylogenyNode> additional_nodes = getFoundNodes0AsListOfPhylogenyNodes();
+ if ( ( getFoundNodes0() != null ) || ( getFoundNodes1() != null ) ) {
+ final List<PhylogenyNode> additional_nodes = getFoundNodesAsListOfPhylogenyNodes();
al = new NodeColorizationActionListener( _color_chooser, node, additional_nodes );
}
else {
al = new NodeColorizationActionListener( _color_chooser, node );
}
- final JDialog dialog = JColorChooser
- .createDialog( this, "Subtree colorization", true, _color_chooser, al, null );
+ final JDialog dialog = JColorChooser.createDialog( this, "Node colorization", true, _color_chooser, al, null );
dialog.setVisible( true );
}
}
fc.showDialog( this, "Select Font" );
if ( ( fc.getFont() != null ) && !ForesterUtil.isEmpty( fc.getFont().getFamily().trim() ) ) {
- if ( node.getNodeData().getNodeVisualData() == null ) {
- node.getNodeData().setNodeVisualData( new NodeVisualData() );
+ List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
+ if ( ( getFoundNodes0() != null ) || ( getFoundNodes1() != null ) ) {
+ nodes = getFoundNodesAsListOfPhylogenyNodes();
}
- final NodeVisualData vd = node.getNodeData().getNodeVisualData();
- final Font ff = fc.getFont();
- vd.setFontName( ff.getFamily().trim() );
- int s = ff.getSize();
- if ( s < 0 ) {
- s = 0;
+ nodes.add( node );
+ for( final PhylogenyNode n : nodes ) {
+ if ( n.getNodeData().getNodeVisualData() == null ) {
+ n.getNodeData().setNodeVisualData( new NodeVisualData() );
+ }
+ final NodeVisualData vd = n.getNodeData().getNodeVisualData();
+ final Font ff = fc.getFont();
+ vd.setFontName( ff.getFamily().trim() );
+ int s = ff.getSize();
+ if ( s < 0 ) {
+ s = 0;
+ }
+ if ( s > Byte.MAX_VALUE ) {
+ s = Byte.MAX_VALUE;
+ }
+ vd.setFontSize( s );
+ vd.setFontStyle( ff.getStyle() );
}
- if ( s > Byte.MAX_VALUE ) {
- s = Byte.MAX_VALUE;
+ if ( _control_panel.getUseVisualStylesCb() != null ) {
+ getControlPanel().getUseVisualStylesCb().setSelected( true );
}
- vd.setFontSize( s );
- vd.setFontStyle( ff.getStyle() );
}
+ repaint();
}
final private void copySubtree( final PhylogenyNode node ) {
return getMainPanel().getCutOrCopiedTree();
}
- private List<PhylogenyNode> getFoundNodes0AsListOfPhylogenyNodes() {
+ private List<PhylogenyNode> getFoundNodesAsListOfPhylogenyNodes() {
final List<PhylogenyNode> additional_nodes = new ArrayList<PhylogenyNode>();
- for( final Long id : getFoundNodes0() ) {
- additional_nodes.add( _phylogeny.getNode( id ) );
+ if ( getFoundNodes0() != null ) {
+ for( final Long id : getFoundNodes0() ) {
+ additional_nodes.add( _phylogeny.getNode( id ) );
+ }
}
- return additional_nodes;
- }
-
- private List<PhylogenyNode> getFoundNodes1AsListOfPhylogenyNodes() {
- final List<PhylogenyNode> additional_nodes = new ArrayList<PhylogenyNode>();
- for( final Long id : getFoundNodes1() ) {
- additional_nodes.add( _phylogeny.getNode( id ) );
+ if ( getFoundNodes1() != null ) {
+ for( final Long id : getFoundNodes1() ) {
+ if ( ( getFoundNodes0() == null ) || !getFoundNodes0().contains( id ) ) {
+ additional_nodes.add( _phylogeny.getNode( id ) );
+ }
+ }
}
return additional_nodes;
}
else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
c = getTaxonomyBasedColor( node );
}
- else if ( getOptions().isColorLabelsSameAsParentBranch() && getControlPanel().isColorBranches()
+ else if ( getOptions().isColorLabelsSameAsParentBranch() && getControlPanel().isUseVisualStyles()
&& ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
c = PhylogenyMethods.getBranchColorValue( node );
}
else if ( is_in_found_nodes ) {
g.setColor( getColorForFoundNode( node ) );
}
+ else if ( getControlPanel().isUseVisualStyles() && ( node.getNodeData().getNodeVisualData() != null )
+ && ( node.getNodeData().getNodeVisualData().getFontColor() != null ) ) {
+ g.setColor( node.getNodeData().getNodeVisualData().getFontColor() );
+ }
else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
g.setColor( getTaxonomyBasedColor( node ) );
}
.getNodeData().getSequence().getAnnotations().isEmpty() ) ) ) {
g.setColor( calculateColorForAnnotation( node.getNodeData().getSequence().getAnnotations() ) );
}
- else if ( getOptions().isColorLabelsSameAsParentBranch() && getControlPanel().isColorBranches()
+ else if ( getOptions().isColorLabelsSameAsParentBranch() && getControlPanel().isUseVisualStyles()
&& ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
g.setColor( PhylogenyMethods.getBranchColorValue( node ) );
}
}
_sb.append( propertiesToString( node ) );
}
- if ( getControlPanel().isColorBranches() && ( node.getNodeData().getNodeVisualData() != null ) ) {
+ if ( getControlPanel().isUseVisualStyles() && ( node.getNodeData().getNodeVisualData() != null ) ) {
final Font f = node.getNodeData().getNodeVisualData().getFont();
g.setFont( f != null ? f : getTreeFontSet().getLargeFont() );
}
else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
g.setColor( getTaxonomyBasedColor( node ) );
}
- else if ( getOptions().isColorLabelsSameAsParentBranch() && getControlPanel().isColorBranches()
+ else if ( getOptions().isColorLabelsSameAsParentBranch() && getControlPanel().isUseVisualStyles()
&& ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
g.setColor( PhylogenyMethods.getBranchColorValue( node ) );
}
private void showExtDescNodeData( final PhylogenyNode node ) {
final List<String> data = new ArrayList<String>();
final List<PhylogenyNode> nodes = node.getAllExternalDescendants();
- if ( ( getFoundNodes0() != null ) && !getFoundNodes0().isEmpty() ) {
- for( final PhylogenyNode n : getFoundNodes0AsListOfPhylogenyNodes() ) {
- if ( !nodes.contains( n ) ) {
- nodes.add( n );
- }
- }
- }
- if ( ( getFoundNodes1() != null ) && !getFoundNodes1().isEmpty() ) {
- for( final PhylogenyNode n : getFoundNodes1AsListOfPhylogenyNodes() ) {
+ if ( ( getFoundNodes0() != null ) || ( getFoundNodes1() != null ) ) {
+ for( final PhylogenyNode n : getFoundNodesAsListOfPhylogenyNodes() ) {
if ( !nodes.contains( n ) ) {
nodes.add( n );
}