if ( node.isCollapse() ) {
continue;
}
- if ( getControlPanel().isShowNodeNames() ) {
- sum += getFontMetricsForLargeDefaultFont().stringWidth( node.getName() + " " );
- }
- if ( node.getNodeData().isHasSequence() ) {
- if ( getControlPanel().isShowSequenceAcc()
- && ( node.getNodeData().getSequence().getAccession() != null ) ) {
- sum += getFontMetricsForLargeDefaultFont().stringWidth( node.getNodeData().getSequence()
- .getAccession().getValue()
- + " " );
- }
- if ( getControlPanel().isShowSeqNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) {
- sum += getFontMetricsForLargeDefaultFont().stringWidth( node.getNodeData().getSequence().getName()
- + " " );
- }
- if ( getControlPanel().isShowSeqSymbols()
- && ( node.getNodeData().getSequence().getSymbol().length() > 0 ) ) {
- sum += getFontMetricsForLargeDefaultFont().stringWidth( node.getNodeData().getSequence()
- .getSymbol()
- + " " );
- }
- if ( getControlPanel().isShowGeneNames()
- && ( node.getNodeData().getSequence().getGeneName().length() > 0 ) ) {
- sum += getFontMetricsForLargeDefaultFont().stringWidth( node.getNodeData().getSequence()
- .getGeneName()
- + " " );
- }
- if ( getControlPanel().isShowAnnotation()
- && ( node.getNodeData().getSequence().getAnnotations() != null )
- && !node.getNodeData().getSequence().getAnnotations().isEmpty() ) {
- sum += getFontMetricsForLargeDefaultFont().stringWidth( TreePanelUtil.createAnnotationString( node
- .getNodeData().getSequence().getAnnotations(), getOptions().isShowAnnotationRefSource() )
- + " " );
- }
- if ( getControlPanel().isShowDomainArchitectures()
- && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) {
- sum += ( ( RenderableDomainArchitecture ) node.getNodeData().getSequence().getDomainArchitecture() )
- .getRenderingSize().getWidth();
- }
- }
+ final StringBuilder sb = new StringBuilder();
+ nodeDataAsSB( node, sb );
if ( node.getNodeData().isHasTaxonomy() ) {
- final Taxonomy tax = node.getNodeData().getTaxonomy();
- if ( getControlPanel().isShowTaxonomyCode() && !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
- sum += getFontMetricsForLargeDefaultFont().stringWidth( tax.getTaxonomyCode() + " " );
- }
- if ( getControlPanel().isShowTaxonomyScientificNames()
- && !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
- sum += getFontMetricsForLargeDefaultFont().stringWidth( tax.getScientificName() + " " );
- }
- if ( getControlPanel().isShowTaxonomyCommonNames() && !ForesterUtil.isEmpty( tax.getCommonName() ) ) {
- sum += getFontMetricsForLargeDefaultFont().stringWidth( tax.getCommonName() + " ()" );
- }
+ nodeTaxonomyDataAsSB( node.getNodeData().getTaxonomy(), sb );
+ }
+ boolean use_vis = false;
+ final Graphics2D g = ( Graphics2D ) getGraphics();
+ if ( getControlPanel().isUseVisualStyles() ) {
+ use_vis = setFont( g, node, false );
+ }
+ if ( !use_vis ) {
+ sum = getFontMetricsForLargeDefaultFont().stringWidth( sb.toString() );
}
- if ( getControlPanel().isShowProperties() && node.getNodeData().isHasProperties() ) {
- sum += getFontMetricsForLargeDefaultFont().stringWidth( propertiesToString( node ).toString() );
+ else {
+ sum = getFontMetrics( g.getFont() ).stringWidth( sb.toString() );
}
if ( getControlPanel().isShowBinaryCharacters() && node.getNodeData().isHasBinaryCharacters() ) {
sum += getFontMetricsForLargeDefaultFont().stringWidth( node.getNodeData().getBinaryCharacters()
}
}
- private void abbreviateScientificName( final String sn ) {
+ private void abbreviateScientificName( final String sn, final StringBuilder sb ) {
final String[] a = sn.split( "\\s+" );
- _sb.append( a[ 0 ].substring( 0, 1 ) );
- _sb.append( a[ 1 ].substring( 0, 2 ) );
+ sb.append( a[ 0 ].substring( 0, 1 ) );
+ sb.append( a[ 1 ].substring( 0, 2 ) );
if ( a.length > 2 ) {
for( int i = 2; i < a.length; i++ ) {
- _sb.append( " " );
- _sb.append( a[ i ] );
+ sb.append( " " );
+ sb.append( a[ i ] );
}
}
}
g.fill( _ellipse );
}
- final private void drawOvalGradient( final double x,
- final double y,
- final double width,
- final double heigth,
+ final private void drawOvalGradient( final float x,
+ final float y,
+ final float width,
+ final float heigth,
final Graphics2D g,
final Color color_1,
final Color color_2,
final Color color_border ) {
_ellipse.setFrame( x, y, width, heigth );
- g.setPaint( new GradientPaint( ( float ) x,
- ( float ) y,
- color_1,
- ( float ) ( x + width ),
- ( float ) ( y + heigth ),
- color_2,
- false ) );
+ g.setPaint( new GradientPaint( x, y, color_1, ( x + width ), ( y + heigth ), color_2, false ) );
g.fill( _ellipse );
if ( color_border != null ) {
g.setPaint( color_border );
g.fill( _rectangle );
}
- final private void drawRectGradient( final double x,
- final double y,
- final double width,
- final double heigth,
+ final private void drawRectGradient( final float x,
+ final float y,
+ final float width,
+ final float heigth,
final Graphics2D g,
final Color color_1,
final Color color_2,
final Color color_border ) {
_rectangle.setFrame( x, y, width, heigth );
- g.setPaint( new GradientPaint( ( float ) x,
- ( float ) y,
- color_1,
- ( float ) ( x + width ),
- ( float ) ( y + heigth ),
- color_2,
- false ) );
+ g.setPaint( new GradientPaint( x, y, color_1, ( x + width ), ( y + heigth ), color_2, false ) );
g.fill( _rectangle );
if ( color_border != null ) {
g.setPaint( color_border );
}
}
+ private final void nodeDataAsSB( final PhylogenyNode node, final StringBuilder sb ) {
+ if ( getControlPanel().isShowNodeNames() && ( node.getName().length() > 0 ) ) {
+ if ( sb.length() > 0 ) {
+ sb.append( " " );
+ }
+ sb.append( node.getName() );
+ }
+ if ( node.getNodeData().isHasSequence() ) {
+ if ( getControlPanel().isShowSeqSymbols() && ( node.getNodeData().getSequence().getSymbol().length() > 0 ) ) {
+ if ( sb.length() > 0 ) {
+ sb.append( " " );
+ }
+ sb.append( node.getNodeData().getSequence().getSymbol() );
+ }
+ if ( getControlPanel().isShowGeneNames() && ( node.getNodeData().getSequence().getGeneName().length() > 0 ) ) {
+ if ( sb.length() > 0 ) {
+ sb.append( " " );
+ }
+ sb.append( node.getNodeData().getSequence().getGeneName() );
+ }
+ if ( getControlPanel().isShowSeqNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) {
+ if ( sb.length() > 0 ) {
+ sb.append( " " );
+ }
+ sb.append( node.getNodeData().getSequence().getName() );
+ }
+ if ( getControlPanel().isShowSequenceAcc() && ( node.getNodeData().getSequence().getAccession() != null ) ) {
+ if ( sb.length() > 0 ) {
+ sb.append( " " );
+ }
+ if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() ) ) {
+ sb.append( node.getNodeData().getSequence().getAccession().getSource() );
+ sb.append( ":" );
+ }
+ sb.append( node.getNodeData().getSequence().getAccession().getValue() );
+ }
+ }
+ if ( getControlPanel().isShowProperties() && node.getNodeData().isHasProperties() ) {
+ if ( sb.length() > 0 ) {
+ sb.append( " " );
+ }
+ sb.append( propertiesToString( node ) );
+ }
+ }
+
+ private final void nodeTaxonomyDataAsSB( final Taxonomy taxonomy, final StringBuilder sb ) {
+ if ( _control_panel.isShowTaxonomyCode() && !ForesterUtil.isEmpty( taxonomy.getTaxonomyCode() ) ) {
+ sb.append( taxonomy.getTaxonomyCode() );
+ sb.append( " " );
+ }
+ if ( _control_panel.isShowTaxonomyScientificNames() && _control_panel.isShowTaxonomyCommonNames() ) {
+ if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() )
+ && !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
+ if ( getOptions().isAbbreviateScientificTaxonNames()
+ && ( taxonomy.getScientificName().indexOf( ' ' ) > 0 ) ) {
+ abbreviateScientificName( taxonomy.getScientificName(), sb );
+ }
+ else {
+ sb.append( taxonomy.getScientificName() );
+ }
+ sb.append( " (" );
+ sb.append( taxonomy.getCommonName() );
+ sb.append( ") " );
+ }
+ else if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
+ if ( getOptions().isAbbreviateScientificTaxonNames()
+ && ( taxonomy.getScientificName().indexOf( ' ' ) > 0 ) ) {
+ abbreviateScientificName( taxonomy.getScientificName(), sb );
+ }
+ else {
+ sb.append( taxonomy.getScientificName() );
+ }
+ sb.append( " " );
+ }
+ else if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
+ sb.append( taxonomy.getCommonName() );
+ sb.append( " " );
+ }
+ }
+ else if ( _control_panel.isShowTaxonomyScientificNames() ) {
+ if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
+ if ( getOptions().isAbbreviateScientificTaxonNames()
+ && ( taxonomy.getScientificName().indexOf( ' ' ) > 0 ) ) {
+ abbreviateScientificName( taxonomy.getScientificName(), sb );
+ }
+ else {
+ sb.append( taxonomy.getScientificName() );
+ }
+ sb.append( " " );
+ }
+ }
+ else if ( _control_panel.isShowTaxonomyCommonNames() ) {
+ if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
+ sb.append( taxonomy.getCommonName() );
+ sb.append( " " );
+ }
+ }
+ }
+
private final String obtainTitleForExtDescNodeData() {
switch ( getOptions().getExtDescNodeDataToReturn() ) {
case NODE_NAME:
* @param node
* @param g
*/
- final private void paintNodeBox( final double x,
- final double y,
+ final private void paintNodeBox( final float x,
+ final float y,
final PhylogenyNode node,
final Graphics2D g,
final boolean to_pdf,
if ( ( isInFoundNodes( node ) || isInCurrentExternalNodes( node ) )
|| ( getOptions().isShowDefaultNodeShapesExternal() && node.isExternal() )
|| ( getOptions().isShowDefaultNodeShapesInternal() && node.isInternal() )
+ || ( getControlPanel().isUseVisualStyles() && ( ( node.getNodeData().getNodeVisualData() != null ) && ( ( node
+ .getNodeData().getNodeVisualData().getNodeColor() != null )
+ || ( node.getNodeData().getNodeVisualData().getSize() != NodeVisualData.DEFAULT_SIZE )
+ || ( node.getNodeData().getNodeVisualData().getFillType() != NodeFill.DEFAULT ) || ( node
+ .getNodeData().getNodeVisualData().getShape() != NodeShape.DEFAULT ) ) ) )
|| ( getControlPanel().isEvents() && node.isHasAssignedEvent() && ( node.getNodeData().getEvent()
.isDuplication()
|| node.getNodeData().getEvent().isSpeciation() || node.getNodeData().getEvent()
.isSpeciationOrDuplication() ) ) ) {
- final double box_size = getOptions().getDefaultNodeShapeSize();
- final double half_box_size = box_size / 2.0;
+ NodeVisualData vis = null;
+ if ( getControlPanel().isUseVisualStyles() && ( node.getNodeData().getNodeVisualData() != null )
+ && ( !node.getNodeData().getNodeVisualData().isEmpty() ) ) {
+ vis = node.getNodeData().getNodeVisualData();
+ }
+ float box_size = getOptions().getDefaultNodeShapeSize();
+ if ( ( vis != null ) && ( vis.getSize() != NodeVisualData.DEFAULT_SIZE ) ) {
+ box_size = vis.getSize();
+ }
+ final float half_box_size = box_size / 2.0f;
Color outline_color = null;
if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
outline_color = Color.BLACK;
else if ( isInFoundNodes( node ) || isInCurrentExternalNodes( node ) ) {
outline_color = getColorForFoundNode( node );
}
+ else if ( vis != null ) {
+ if ( vis.getNodeColor() != null ) {
+ outline_color = vis.getNodeColor();
+ }
+ else if ( vis.getFontColor() != null ) {
+ outline_color = vis.getFontColor();
+ }
+ }
else if ( getControlPanel().isEvents() && TreePanelUtil.isHasAssignedEvent( node ) ) {
final Event event = node.getNodeData().getEvent();
if ( event.isDuplication() ) {
outline_color = getTreeColorSet().getDuplicationOrSpeciationColor();
}
}
- else {
+ if ( outline_color == null ) {
outline_color = getGraphicsForNodeBoxWithColorForParentBranch( node );
if ( to_pdf && ( outline_color == getTreeColorSet().getBranchColor() ) ) {
outline_color = getTreeColorSet().getBranchColorForPdf();
}
}
- if ( getOptions().getDefaultNodeShape() == NodeShape.CIRCLE ) {
- if ( getOptions().getDefaultNodeFill() == NodeFill.GRADIENT ) {
+ NodeShape shape = null;
+ if ( vis != null ) {
+ if ( vis.getShape() == NodeShape.CIRCLE ) {
+ shape = NodeShape.CIRCLE;
+ }
+ else if ( vis.getShape() == NodeShape.RECTANGLE ) {
+ shape = NodeShape.RECTANGLE;
+ }
+ }
+ if ( shape == null ) {
+ if ( getOptions().getDefaultNodeShape() == NodeShape.CIRCLE ) {
+ shape = NodeShape.CIRCLE;
+ }
+ else if ( getOptions().getDefaultNodeShape() == NodeShape.RECTANGLE ) {
+ shape = NodeShape.RECTANGLE;
+ }
+ }
+ NodeFill fill = null;
+ if ( vis != null ) {
+ if ( vis.getFillType() == NodeFill.SOLID ) {
+ fill = NodeFill.SOLID;
+ }
+ else if ( vis.getFillType() == NodeFill.NONE ) {
+ fill = NodeFill.NONE;
+ }
+ else if ( vis.getFillType() == NodeFill.GRADIENT ) {
+ fill = NodeFill.GRADIENT;
+ }
+ }
+ if ( fill == null ) {
+ if ( getOptions().getDefaultNodeFill() == NodeFill.SOLID ) {
+ fill = NodeFill.SOLID;
+ }
+ else if ( getOptions().getDefaultNodeFill() == NodeFill.NONE ) {
+ fill = NodeFill.NONE;
+ }
+ else if ( getOptions().getDefaultNodeFill() == NodeFill.GRADIENT ) {
+ fill = NodeFill.GRADIENT;
+ }
+ }
+ Color vis_fill_color = null;
+ if ( ( vis != null ) && ( vis.getNodeColor() != null ) ) {
+ vis_fill_color = vis.getNodeColor();
+ }
+ if ( shape == NodeShape.CIRCLE ) {
+ if ( fill == NodeFill.GRADIENT ) {
drawOvalGradient( x - half_box_size, y - half_box_size, box_size, box_size, g, to_pdf ? Color.WHITE
: outline_color, to_pdf ? outline_color : getBackground(), outline_color );
}
- else if ( getOptions().getDefaultNodeFill() == NodeFill.NONE ) {
+ else if ( fill == NodeFill.NONE ) {
Color background = getBackground();
if ( to_pdf ) {
background = Color.WHITE;
background,
outline_color );
}
- else if ( getOptions().getDefaultNodeFill() == NodeVisualData.NodeFill.SOLID ) {
- g.setColor( outline_color );
+ else if ( fill == NodeVisualData.NodeFill.SOLID ) {
+ if ( vis_fill_color != null ) {
+ g.setColor( vis_fill_color );
+ }
+ else {
+ g.setColor( outline_color );
+ }
drawOvalFilled( x - half_box_size, y - half_box_size, box_size, box_size, g );
}
}
- else if ( getOptions().getDefaultNodeShape() == NodeVisualData.NodeShape.RECTANGLE ) {
- if ( getOptions().getDefaultNodeFill() == NodeVisualData.NodeFill.GRADIENT ) {
+ else if ( shape == NodeVisualData.NodeShape.RECTANGLE ) {
+ if ( fill == NodeVisualData.NodeFill.GRADIENT ) {
drawRectGradient( x - half_box_size, y - half_box_size, box_size, box_size, g, to_pdf ? Color.WHITE
: outline_color, to_pdf ? outline_color : getBackground(), outline_color );
}
- else if ( getOptions().getDefaultNodeFill() == NodeVisualData.NodeFill.NONE ) {
+ else if ( fill == NodeVisualData.NodeFill.NONE ) {
Color background = getBackground();
if ( to_pdf ) {
background = Color.WHITE;
background,
outline_color );
}
- else if ( getOptions().getDefaultNodeFill() == NodeVisualData.NodeFill.SOLID ) {
- g.setColor( outline_color );
+ else if ( fill == NodeVisualData.NodeFill.SOLID ) {
+ if ( vis_fill_color != null ) {
+ g.setColor( vis_fill_color );
+ }
+ else {
+ g.setColor( outline_color );
+ }
drawRectFilled( x - half_box_size, y - half_box_size, box_size, box_size, g );
}
}
else {
_sb.setLength( 0 );
}
- if ( getControlPanel().isShowNodeNames() && ( node.getName().length() > 0 ) ) {
- if ( _sb.length() > 0 ) {
- _sb.append( " " );
- }
- _sb.append( node.getName() );
- }
- if ( node.getNodeData().isHasSequence() ) {
- if ( getControlPanel().isShowSeqSymbols() && ( node.getNodeData().getSequence().getSymbol().length() > 0 ) ) {
- if ( _sb.length() > 0 ) {
- _sb.append( " " );
- }
- _sb.append( node.getNodeData().getSequence().getSymbol() );
- }
- if ( getControlPanel().isShowGeneNames() && ( node.getNodeData().getSequence().getGeneName().length() > 0 ) ) {
- if ( _sb.length() > 0 ) {
- _sb.append( " " );
- }
- _sb.append( node.getNodeData().getSequence().getGeneName() );
- }
- if ( getControlPanel().isShowSeqNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) {
- if ( _sb.length() > 0 ) {
- _sb.append( " " );
- }
- _sb.append( node.getNodeData().getSequence().getName() );
- }
- if ( getControlPanel().isShowSequenceAcc() && ( node.getNodeData().getSequence().getAccession() != null ) ) {
- if ( _sb.length() > 0 ) {
- _sb.append( " " );
- }
- if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() ) ) {
- _sb.append( node.getNodeData().getSequence().getAccession().getSource() );
- _sb.append( ":" );
- }
- _sb.append( node.getNodeData().getSequence().getAccession().getValue() );
- }
- }
- if ( getControlPanel().isShowProperties() && node.getNodeData().isHasProperties() ) {
- if ( _sb.length() > 0 ) {
- _sb.append( " " );
- }
- _sb.append( propertiesToString( node ) );
- }
+ nodeDataAsSB( node, _sb );
final boolean using_visual_font = setFont( g, node, is_in_found_nodes );
float down_shift_factor = 3.0f;
if ( !node.isExternal() && ( node.getNumberOfDescendants() == 1 ) ) {
+ ( getFontMetrics( g.getFont() ).getAscent() / ( node.getNumberOfDescendants() == 1 ? 1 : 3.0f ) );
}
_sb.setLength( 0 );
- if ( _control_panel.isShowTaxonomyCode() && !ForesterUtil.isEmpty( taxonomy.getTaxonomyCode() ) ) {
- _sb.append( taxonomy.getTaxonomyCode() );
- _sb.append( " " );
- }
- if ( _control_panel.isShowTaxonomyScientificNames() && _control_panel.isShowTaxonomyCommonNames() ) {
- if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() )
- && !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
- if ( getOptions().isAbbreviateScientificTaxonNames()
- && ( taxonomy.getScientificName().indexOf( ' ' ) > 0 ) ) {
- abbreviateScientificName( taxonomy.getScientificName() );
- }
- else {
- _sb.append( taxonomy.getScientificName() );
- }
- _sb.append( " (" );
- _sb.append( taxonomy.getCommonName() );
- _sb.append( ") " );
- }
- else if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
- if ( getOptions().isAbbreviateScientificTaxonNames()
- && ( taxonomy.getScientificName().indexOf( ' ' ) > 0 ) ) {
- abbreviateScientificName( taxonomy.getScientificName() );
- }
- else {
- _sb.append( taxonomy.getScientificName() );
- }
- _sb.append( " " );
- }
- else if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
- _sb.append( taxonomy.getCommonName() );
- _sb.append( " " );
- }
- }
- else if ( _control_panel.isShowTaxonomyScientificNames() ) {
- if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) {
- if ( getOptions().isAbbreviateScientificTaxonNames()
- && ( taxonomy.getScientificName().indexOf( ' ' ) > 0 ) ) {
- abbreviateScientificName( taxonomy.getScientificName() );
- }
- else {
- _sb.append( taxonomy.getScientificName() );
- }
- _sb.append( " " );
- }
- }
- else if ( _control_panel.isShowTaxonomyCommonNames() ) {
- if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) {
- _sb.append( taxonomy.getCommonName() );
- _sb.append( " " );
- }
- }
+ nodeTaxonomyDataAsSB( taxonomy, _sb );
final String label = _sb.toString();
/* GUILHEM_BEG */
if ( _control_panel.isShowSequenceRelations() && ( label.length() > 0 )
git://source.jalview.org / jalview.git / blobdiff