import java.awt.Cursor;
import java.awt.Dimension;
import java.awt.Font;
+import java.awt.FontMetrics;
import java.awt.GradientPaint;
import java.awt.Graphics;
import java.awt.Graphics2D;
private final static String NODE_POPMENU_NODE_CLIENT_PROPERTY = "node";
private static final float ONEHALF_PI = ( float ) ( 1.5 * Math.PI );
private static final short OV_BORDER = 10;
+ private final static double OVERVIEW_FOUND_NODE_BOX_SIZE = 2;
+ private final static double OVERVIEW_FOUND_NODE_BOX_SIZE_HALF = 1;
private static final float PI = ( float ) ( Math.PI );
final private static Font POPUP_FONT = new Font( Configuration.getDefaultFontFamilyName(),
Font.PLAIN,
private static final BasicStroke STROKE_2 = new BasicStroke( 2f );
private static final double TWO_PI = 2 * Math.PI;
private final static int WIGGLE = 2;
- private final static double OVERVIEW_FOUND_NODE_BOX_SIZE = 2;
- private final static double OVERVIEW_FOUND_NODE_BOX_SIZE_HALF = 1;
HashMap<Long, Short> _nodeid_dist_to_leaf = new HashMap<Long, Short>();
final private Arc2D _arc = new Arc2D.Double();
private AffineTransform _at;
if ( node.isCollapse() ) {
continue;
}
- if ( getControlPanel().isShowNodeNames() ) {
- sum += getTreeFontSet()._fm_large.stringWidth( node.getName() + " " );
+ final StringBuilder sb = new StringBuilder();
+ nodeDataAsSB( node, sb );
+ if ( node.getNodeData().isHasTaxonomy() ) {
+ nodeTaxonomyDataAsSB( node.getNodeData().getTaxonomy(), sb );
}
- if ( node.getNodeData().isHasSequence() ) {
- if ( getControlPanel().isShowSequenceAcc()
- && ( node.getNodeData().getSequence().getAccession() != null ) ) {
- sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getAccession()
- .getValue()
- + " " );
- }
- if ( getControlPanel().isShowSeqNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) {
- sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getName() + " " );
- }
- if ( getControlPanel().isShowSeqSymbols()
- && ( node.getNodeData().getSequence().getSymbol().length() > 0 ) ) {
- sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getSymbol() + " " );
- }
- if ( getControlPanel().isShowGeneNames()
- && ( node.getNodeData().getSequence().getGeneName().length() > 0 ) ) {
- sum += getTreeFontSet()._fm_large
- .stringWidth( node.getNodeData().getSequence().getGeneName() + " " );
- }
- if ( getControlPanel().isShowAnnotation()
- && ( node.getNodeData().getSequence().getAnnotations() != null )
- && !node.getNodeData().getSequence().getAnnotations().isEmpty() ) {
- sum += getTreeFontSet()._fm_large.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();
- }
+ boolean use_vis = false;
+ final Graphics2D g = ( Graphics2D ) getGraphics();
+ if ( getControlPanel().isUseVisualStyles() ) {
+ use_vis = setFont( g, node, false );
}
- if ( node.getNodeData().isHasTaxonomy() ) {
- final Taxonomy tax = node.getNodeData().getTaxonomy();
- if ( getControlPanel().isShowTaxonomyCode() && !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
- sum += getTreeFontSet()._fm_large_italic.stringWidth( tax.getTaxonomyCode() + " " );
- }
- if ( getControlPanel().isShowTaxonomyScientificNames()
- && !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
- sum += getTreeFontSet()._fm_large_italic.stringWidth( tax.getScientificName() + " " );
- }
- if ( getControlPanel().isShowTaxonomyCommonNames() && !ForesterUtil.isEmpty( tax.getCommonName() ) ) {
- sum += getTreeFontSet()._fm_large_italic.stringWidth( tax.getCommonName() + " ()" );
- }
+ if ( !use_vis ) {
+ sum = getFontMetricsForLargeDefaultFont().stringWidth( sb.toString() );
}
- if ( getControlPanel().isShowProperties() && node.getNodeData().isHasProperties() ) {
- sum += getTreeFontSet()._fm_large.stringWidth( propertiesToString( node ).toString() );
+ else {
+ sum = getFontMetrics( g.getFont() ).stringWidth( sb.toString() );
}
if ( getControlPanel().isShowBinaryCharacters() && node.getNodeData().isHasBinaryCharacters() ) {
- sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getBinaryCharacters()
+ sum += getFontMetricsForLargeDefaultFont().stringWidth( node.getNodeData().getBinaryCharacters()
.getGainedCharactersAsStringBuffer().toString() );
}
if ( sum >= max_length ) {
return c;
}
}
+
+ final Color calculateSequenceBasedColor( final Sequence seq ) {
+ if ( ForesterUtil.isEmpty( seq.getName() ) ) {
+ return getTreeColorSet().getSequenceColor();
+ }
+ Color c = null;
+ final String seq_name = seq.getName();
+ c = getControlPanel().getSequenceColors().get( seq_name );
+ if ( c == null ) {
+ c = TreePanelUtil.calculateColorFromString( seq_name, false );
+ getControlPanel().getSequenceColors().put( seq_name, c );
+ }
+ return c;
+ }
void checkForVectorProperties( final Phylogeny phy ) {
final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
if ( _control_panel.getColorAccSpeciesCb() != null ) {
_control_panel.getColorAccSpeciesCb().setSelected( false );
}
+
_options.setColorLabelsSameAsParentBranch( true );
_control_panel.repaint();
}
return _statistics_for_vector_data;
}
- /**
- * Find a color for this species name.
- *
- * @param species
- * @return the species color
- */
+
final Color getTaxonomyBasedColor( final PhylogenyNode node ) {
if ( node.getNodeData().isHasTaxonomy() ) {
return calculateTaxonomyBasedColor( node.getNodeData().getTaxonomy() );
// return non-colorized color
return getTreeColorSet().getTaxonomyColor();
}
+
+
+ final Color getSequenceBasedColor( final PhylogenyNode node ) {
+ if ( node.getNodeData().isHasSequence() ) {
+ return calculateSequenceBasedColor( node.getNodeData().getSequence() );
+ }
+ // return non-colorized color
+ return getTreeColorSet().getSequenceColor();
+ }
+
/**
* @return pointer to colorset for tree drawing
final boolean radial_labels = getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL;
_dynamic_hiding_factor = 0;
if ( getControlPanel().isDynamicallyHideData() ) {
- _dynamic_hiding_factor = ( int ) ( ( getTreeFontSet()._fm_large.getHeight() * 1.5 * getPhylogeny()
+ _dynamic_hiding_factor = ( int ) ( ( getFontMetricsForLargeDefaultFont().getHeight() * 1.5 * getPhylogeny()
.getNumberOfExternalNodes() ) / ( TWO_PI * 10 ) );
}
if ( getControlPanel().getDynamicallyHideData() != null ) {
final int d = radius + MOVE + getLongestExtNodeInfo();
_dynamic_hiding_factor = 0;
if ( getControlPanel().isDynamicallyHideData() && ( radius > 0 ) ) {
- _dynamic_hiding_factor = ( int ) ( ( getTreeFontSet()._fm_large.getHeight() * 1.5 * getPhylogeny()
+ _dynamic_hiding_factor = ( int ) ( ( getFontMetricsForLargeDefaultFont().getHeight() * 1.5 * getPhylogeny()
.getNumberOfExternalNodes() ) / ( TWO_PI * radius ) );
}
if ( getControlPanel().getDynamicallyHideData() != null ) {
}
}
- 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 ] );
}
}
}
}
private final int calcDynamicHidingFactor() {
- return ( int ) ( 0.5 + ( getTreeFontSet()._fm_large.getHeight() / ( 1.5 * getYdistance() ) ) );
+ return ( int ) ( 0.5 + ( getFontMetricsForLargeDefaultFont().getHeight() / ( 1.5 * getYdistance() ) ) );
}
/**
}
}
}
+
return c;
}
JOptionPane.WARNING_MESSAGE );
}
- final private void colorizeSubtree( final Color c,
- final PhylogenyNode node,
- final List<PhylogenyNode> additional_nodes ) {
- _control_panel.setColorBranches( true );
- if ( _control_panel.getUseVisualStylesCb() != null ) {
- _control_panel.getUseVisualStylesCb().setSelected( true );
+ private void changeNodeFont( final PhylogenyNode node ) {
+ final FontChooser fc = new FontChooser();
+ Font f = null;
+ if ( ( node.getNodeData().getNodeVisualData() != null ) && !node.getNodeData().getNodeVisualData().isEmpty() ) {
+ f = node.getNodeData().getNodeVisualData().getFont();
}
- if ( node != null ) {
- for( final PreorderTreeIterator it = new PreorderTreeIterator( node ); it.hasNext(); ) {
- it.next().getBranchData().setBranchColor( new BranchColor( c ) );
- }
+ if ( f != null ) {
+ fc.setFont( f );
}
- if ( additional_nodes != null ) {
- for( final PhylogenyNode n : additional_nodes ) {
- n.getBranchData().setBranchColor( new BranchColor( c ) );
+ else {
+ fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );
+ }
+ fc.showDialog( this, "Select Font" );
+ if ( ( fc.getFont() != null ) && !ForesterUtil.isEmpty( fc.getFont().getFamily().trim() ) ) {
+ List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
+ if ( ( getFoundNodes0() != null ) || ( getFoundNodes1() != null ) ) {
+ nodes = getFoundNodesAsListOfPhylogenyNodes();
+ }
+ 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 ( _control_panel.getUseVisualStylesCb() != null ) {
+ getControlPanel().getUseVisualStylesCb().setSelected( true );
}
}
repaint();
repaint();
}
- private final static void colorizeNodesHelper( final Color c, final PhylogenyNode node ) {
- if ( node.getNodeData().getNodeVisualData() == null ) {
- node.getNodeData().setNodeVisualData( new NodeVisualData() );
- }
- node.getNodeData().getNodeVisualData().setFontColor( new Color( c.getRed(), c.getGreen(), c.getBlue() ) );
- }
-
- final private void colorSubtree( final PhylogenyNode node ) {
- if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
- JOptionPane.showMessageDialog( this,
- "Cannot colorize subtree in unrooted display type",
- "Attempt to colorize subtree in unrooted display",
- JOptionPane.WARNING_MESSAGE );
- return;
+ final private void colorizeSubtree( final Color c,
+ final PhylogenyNode node,
+ final List<PhylogenyNode> additional_nodes ) {
+ _control_panel.setColorBranches( true );
+ if ( _control_panel.getUseVisualStylesCb() != null ) {
+ _control_panel.getUseVisualStylesCb().setSelected( true );
}
- _color_chooser.setPreviewPanel( new JPanel() );
- SubtreeColorizationActionListener al;
- if ( ( getFoundNodes0() != null ) || ( getFoundNodes1() != null ) ) {
- final List<PhylogenyNode> additional_nodes = getFoundNodesAsListOfPhylogenyNodes();
- al = new SubtreeColorizationActionListener( _color_chooser, node, additional_nodes );
+ if ( node != null ) {
+ for( final PreorderTreeIterator it = new PreorderTreeIterator( node ); it.hasNext(); ) {
+ it.next().getBranchData().setBranchColor( new BranchColor( c ) );
+ }
}
- else {
- al = new SubtreeColorizationActionListener( _color_chooser, node );
+ if ( additional_nodes != null ) {
+ for( final PhylogenyNode an : additional_nodes ) {
+ // n.getBranchData().setBranchColor( new BranchColor( c ) );
+ for( final PreorderTreeIterator it = new PreorderTreeIterator( an ); it.hasNext(); ) {
+ it.next().getBranchData().setBranchColor( new BranchColor( c ) );
+ }
+ }
}
- final JDialog dialog = JColorChooser
- .createDialog( this, "Subtree colorization", true, _color_chooser, al, null );
- dialog.setVisible( true );
+ repaint();
}
private void colorNodeFont( final PhylogenyNode node ) {
dialog.setVisible( true );
}
- private void changeNodeFont( final PhylogenyNode node ) {
- final FontChooser fc = new FontChooser();
- Font f = null;
- if ( ( node.getNodeData().getNodeVisualData() != null ) && !node.getNodeData().getNodeVisualData().isEmpty() ) {
- f = node.getNodeData().getNodeVisualData().getFont();
+ final private void colorSubtree( final PhylogenyNode node ) {
+ if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
+ JOptionPane.showMessageDialog( this,
+ "Cannot colorize subtree in unrooted display type",
+ "Attempt to colorize subtree in unrooted display",
+ JOptionPane.WARNING_MESSAGE );
+ return;
}
- if ( f != null ) {
- fc.setFont( f );
+ _color_chooser.setPreviewPanel( new JPanel() );
+ SubtreeColorizationActionListener al;
+ if ( ( getFoundNodes0() != null ) || ( getFoundNodes1() != null ) ) {
+ final List<PhylogenyNode> additional_nodes = getFoundNodesAsListOfPhylogenyNodes();
+ al = new SubtreeColorizationActionListener( _color_chooser, node, additional_nodes );
}
else {
- fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );
- }
- fc.showDialog( this, "Select Font" );
- if ( ( fc.getFont() != null ) && !ForesterUtil.isEmpty( fc.getFont().getFamily().trim() ) ) {
- List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
- if ( ( getFoundNodes0() != null ) || ( getFoundNodes1() != null ) ) {
- nodes = getFoundNodesAsListOfPhylogenyNodes();
- }
- 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 ( _control_panel.getUseVisualStylesCb() != null ) {
- getControlPanel().getUseVisualStylesCb().setSelected( true );
- }
+ al = new SubtreeColorizationActionListener( _color_chooser, node );
}
- repaint();
+ final JDialog dialog = JColorChooser
+ .createDialog( this, "Subtree colorization", true, _color_chooser, al, null );
+ dialog.setVisible( true );
}
final private void copySubtree( final PhylogenyNode node ) {
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 );
return getMainPanel().getCutOrCopiedTree();
}
+ private FontMetrics getFontMetricsForLargeDefaultFont() {
+ return getTreeFontSet().getFontMetricsLarge();
+ }
+
private List<PhylogenyNode> getFoundNodesAsListOfPhylogenyNodes() {
final List<PhylogenyNode> additional_nodes = new ArrayList<PhylogenyNode>();
if ( getFoundNodes0() != null ) {
}
}
+ 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:
if ( !node.isRoot() ) {
if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), node.getParent()
- .getXcoord() + EURO_D, node.getYcoord() - getTreeFontSet()._small_max_descent, g );
+ .getXcoord() + EURO_D, node.getYcoord() - getTreeFontSet().getSmallMaxDescent(), g );
}
else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), node.getParent()
- .getXcoord() + ROUNDED_D, node.getYcoord() - getTreeFontSet()._small_max_descent, g );
+ .getXcoord() + ROUNDED_D, node.getYcoord() - getTreeFontSet().getSmallMaxDescent(), g );
}
else {
TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), node.getParent()
- .getXcoord() + 3, node.getYcoord() - getTreeFontSet()._small_max_descent, g );
+ .getXcoord() + 3, node.getYcoord() - getTreeFontSet().getSmallMaxDescent(), g );
}
}
else {
TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), 3, node.getYcoord()
- - getTreeFontSet()._small_max_descent, g );
+ - getTreeFontSet().getSmallMaxDescent(), g );
}
}
else if ( is_in_found_nodes ) {
c = getColorForFoundNode( node );
}
+ else if ( getControlPanel().isColorAccordingToSequence() ) {
+ c = getSequenceBasedColor( node );
+ }
else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
c = getTaxonomyBasedColor( node );
}
}
}
if ( sb.length() > 0 ) {
- final double parent_x = node.getParent().getXcoord();
- double x = node.getXcoord();
+ final float parent_x = node.getParent().getXcoord();
+ float x = node.getXcoord();
g.setFont( getTreeFontSet().getSmallFont() );
if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
x += EURO_D;
g.setColor( getTreeColorSet().getConfidenceColor() );
}
final String conf_str = sb.toString();
- TreePanel
- .drawString( conf_str,
- parent_x
- + ( ( x - parent_x - getTreeFontSet()._fm_small.stringWidth( conf_str ) ) / 2 ),
- ( node.getYcoord() + getTreeFontSet()._small_max_ascent ) - 1,
- g );
+ TreePanel.drawString( conf_str,
+ parent_x
+ + ( ( x - parent_x - getTreeFontSet().getFontMetricsSmall()
+ .stringWidth( conf_str ) ) / 2 ),
+ ( node.getYcoord() + getTreeFontSet().getSmallMaxAscent() ) - 1,
+ g );
}
}
final String gained,
final String lost ) {
if ( node.getParent() != null ) {
- final double parent_x = node.getParent().getXcoord();
- final double x = node.getXcoord();
+ final float parent_x = node.getParent().getXcoord();
+ final float x = node.getXcoord();
g.setFont( getTreeFontSet().getLargeFont() );
g.setColor( getTreeColorSet().getGainedCharactersColor() );
if ( Constants.SPECIAL_CUSTOM ) {
}
TreePanel
.drawString( gained,
- parent_x + ( ( x - parent_x - getTreeFontSet()._fm_large.stringWidth( gained ) ) / 2 ),
- ( node.getYcoord() - getTreeFontSet()._fm_large.getMaxDescent() ),
+ parent_x
+ + ( ( x - parent_x - getFontMetricsForLargeDefaultFont().stringWidth( gained ) ) / 2 ),
+ ( node.getYcoord() - getFontMetricsForLargeDefaultFont().getMaxDescent() ),
g );
g.setColor( getTreeColorSet().getLostCharactersColor() );
- TreePanel.drawString( lost,
- parent_x + ( ( x - parent_x - getTreeFontSet()._fm_large.stringWidth( lost ) ) / 2 ),
- ( node.getYcoord() + getTreeFontSet()._fm_large.getMaxAscent() ),
- g );
+ TreePanel
+ .drawString( lost,
+ parent_x
+ + ( ( x - parent_x - getFontMetricsForLargeDefaultFont().stringWidth( lost ) ) / 2 ),
+ ( node.getYcoord() + getFontMetricsForLargeDefaultFont().getMaxAscent() ),
+ g );
}
}
* @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 );
}
}
}
}
- final private void paintNodeData( final Graphics2D g,
- final PhylogenyNode node,
- final boolean to_graphics_file,
- final boolean to_pdf,
- final boolean is_in_found_nodes ) {
+ final private int paintNodeData( final Graphics2D g,
+ final PhylogenyNode node,
+ final boolean to_graphics_file,
+ final boolean to_pdf,
+ final boolean is_in_found_nodes ) {
if ( isNodeDataInvisible( node ) && !to_graphics_file && !to_pdf ) {
- return;
+ return 0;
}
if ( getOptions().isShowBranchLengthValues()
&& ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR )
paintBranchLength( g, node, to_pdf, to_graphics_file );
}
if ( !getControlPanel().isShowInternalData() && !node.isExternal() && !node.isCollapse() ) {
- return;
+ return 0;
}
_sb.setLength( 0 );
int x = 0;
.isShowTaxonomyCommonNames() ) && node.getNodeData().isHasTaxonomy() ) {
x += paintTaxonomy( g, node, is_in_found_nodes, to_pdf, to_graphics_file, x );
}
- if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
- g.setColor( Color.BLACK );
- }
- 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 ) );
- }
- else if ( getControlPanel().isColorAccordingToAnnotation()
- && ( node.getNodeData().isHasSequence() && ( node.getNodeData().getSequence().getAnnotations() != null ) && ( !node
- .getNodeData().getSequence().getAnnotations().isEmpty() ) ) ) {
- g.setColor( calculateColorForAnnotation( node.getNodeData().getSequence().getAnnotations() ) );
- }
- else if ( getOptions().isColorLabelsSameAsParentBranch() && getControlPanel().isUseVisualStyles()
- && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
- g.setColor( PhylogenyMethods.getBranchColorValue( node ) );
- }
- else if ( to_pdf ) {
- g.setColor( Color.BLACK );
- }
- else {
- g.setColor( getTreeColorSet().getSequenceColor() );
- }
+ setColor( g, node, to_graphics_file, to_pdf, is_in_found_nodes, getTreeColorSet().getSequenceColor() );
if ( node.isCollapse() && ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) ) {
if ( _sb.length() > 0 ) {
_sb.setLength( 0 );
- _sb.append( "(" );
+ _sb.append( " (" );
_sb.append( node.getAllExternalDescendants().size() );
_sb.append( ")" );
}
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 ) ) {
+ down_shift_factor = 1;
}
- if ( getControlPanel().isUseVisualStyles() && ( node.getNodeData().getNodeVisualData() != null ) ) {
- final Font f = node.getNodeData().getNodeVisualData().getFont();
- g.setFont( f != null ? f : getTreeFontSet().getLargeFont() );
+ final float pos_x = node.getXcoord() + x + 2 + half_box_size;
+ float pos_y;
+ if ( !using_visual_font ) {
+ pos_y = ( node.getYcoord() + ( getFontMetricsForLargeDefaultFont().getAscent() / down_shift_factor ) );
}
else {
- g.setFont( getTreeFontSet().getLargeFont() );
- }
- if ( is_in_found_nodes ) {
- g.setFont( getTreeFontSet().getLargeFont().deriveFont( Font.BOLD ) );
+ pos_y = ( node.getYcoord() + ( getFontMetrics( g.getFont() ).getAscent() / down_shift_factor ) );
}
- double down_shift_factor = 3.0;
- if ( !node.isExternal() && ( node.getNumberOfDescendants() == 1 ) ) {
- down_shift_factor = 1;
- }
- final double pos_x = node.getXcoord() + x + 2 + half_box_size;
- final double pos_y = ( node.getYcoord() + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ) );
final String sb_str = _sb.toString();
// GUILHEM_BEG ______________
if ( _control_panel.isShowSequenceRelations() && node.getNodeData().isHasSequence()
.getConfidence() == null ) ) ? null : " (" + seqRelation.getConfidence().getValue()
+ ")";
if ( sConfidence != null ) {
- double confidenceX = pos_x;
+ float confidenceX = pos_x;
if ( sb_str.length() > 0 ) {
confidenceX += new TextLayout( sb_str, g.getFont(), _frc ).getBounds().getWidth()
+ CONFIDENCE_LEFT_MARGIN;
TreePanel.drawString( sb_str, pos_x, pos_y, g );
}
// GUILHEM_END _____________
- // COMMENTED_OUT_BY_GUILHEM_BEG _______________
- // TODO FIXME need to check this one!
- //if ( _sb.length() > 0 ) {
- // TreePanel.drawString( _sb.toString(), node.getXcoord() + x + 2 + TreePanel.HALF_BOX_SIZE, node.getYcoord()
- // + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g );
- //}
- // COMMENTED_OUT_BY_GUILHEM_END ________________
+ if ( _sb.length() > 0 ) {
+ if ( !using_visual_font && !is_in_found_nodes ) {
+ x += getFontMetricsForLargeDefaultFont().stringWidth( _sb.toString() ) + 5;
+ }
+ else {
+ x += getFontMetrics( g.getFont() ).stringWidth( _sb.toString() ) + 5;
+ }
+ }
if ( getControlPanel().isShowAnnotation() && node.getNodeData().isHasSequence()
&& ( node.getNodeData().getSequence().getAnnotations() != null )
&& ( !node.getNodeData().getSequence().getAnnotations().isEmpty() ) ) {
- if ( _sb.length() > 0 ) {
- x += getTreeFontSet()._fm_large.stringWidth( _sb.toString() ) + 5;
- }
final SortedSet<Annotation> ann = node.getNodeData().getSequence().getAnnotations();
if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
g.setColor( Color.BLACK );
}
final String ann_str = TreePanelUtil.createAnnotationString( ann, getOptions().isShowAnnotationRefSource() );
TreePanel.drawString( ann_str, node.getXcoord() + x + 3 + half_box_size, node.getYcoord()
- + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g );
+ + ( getFontMetricsForLargeDefaultFont().getAscent() / down_shift_factor ), g );
_sb.setLength( 0 );
_sb.append( ann_str );
+ if ( _sb.length() > 0 ) {
+ if ( !using_visual_font && !is_in_found_nodes ) {
+ x += getFontMetricsForLargeDefaultFont().stringWidth( _sb.toString() ) + 5;
+ }
+ else {
+ x += getFontMetrics( g.getFont() ).stringWidth( _sb.toString() ) + 5;
+ }
+ }
}
if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR )
|| ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE )
|| ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) {
if ( ( getControlPanel().isShowBinaryCharacters() || getControlPanel().isShowBinaryCharacterCounts() )
&& node.getNodeData().isHasBinaryCharacters() ) {
- if ( _sb.length() > 0 ) {
- x += getTreeFontSet()._fm_large.stringWidth( _sb.toString() ) + 5;
- }
if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
g.setColor( Color.BLACK );
}
if ( getControlPanel().isShowBinaryCharacters() ) {
TreePanel.drawString( node.getNodeData().getBinaryCharacters().getPresentCharactersAsStringBuffer()
.toString(), node.getXcoord() + x + 1 + half_box_size, node.getYcoord()
- + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g );
+ + ( getFontMetricsForLargeDefaultFont().getAscent() / down_shift_factor ), g );
paintGainedAndLostCharacters( g, node, node.getNodeData().getBinaryCharacters()
.getGainedCharactersAsStringBuffer().toString(), node.getNodeData().getBinaryCharacters()
.getLostCharactersAsStringBuffer().toString() );
}
else {
- TreePanel.drawString( " " + node.getNodeData().getBinaryCharacters().getPresentCount(),
- node.getXcoord() + x + 4 + half_box_size,
- node.getYcoord()
- + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ),
- g );
+ TreePanel
+ .drawString( " " + node.getNodeData().getBinaryCharacters().getPresentCount(),
+ node.getXcoord() + x + 4 + half_box_size,
+ node.getYcoord()
+ + ( getFontMetricsForLargeDefaultFont().getAscent() / down_shift_factor ),
+ g );
paintGainedAndLostCharacters( g, node, "+"
+ node.getNodeData().getBinaryCharacters().getGainedCount(), "-"
+ node.getNodeData().getBinaryCharacters().getLostCount() );
}
}
}
+ return x;
}
final private void paintNodeDataUnrootedCirc( final Graphics2D g,
if ( isNodeDataInvisibleUnrootedCirc( node ) && !to_graphics_file && !to_pdf ) {
return;
}
- if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
- g.setColor( Color.BLACK );
- }
- else if ( is_in_found_nodes ) {
- g.setColor( getColorForFoundNode( node ) );
- }
- else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
- g.setColor( getTaxonomyBasedColor( node ) );
- }
- else if ( getControlPanel().isColorAccordingToAnnotation()
- && ( node.getNodeData().isHasSequence() && ( node.getNodeData().getSequence().getAnnotations() != null ) && ( !node
- .getNodeData().getSequence().getAnnotations().isEmpty() ) ) ) {
- g.setColor( calculateColorForAnnotation( node.getNodeData().getSequence().getAnnotations() ) );
- }
- else {
- g.setColor( getTreeColorSet().getSequenceColor() );
- }
_sb.setLength( 0 );
_sb.append( " " );
if ( node.getNodeData().isHasTaxonomy()
_sb.append( node.getNodeData().getSequence().getName() );
}
}
- g.setFont( getTreeFontSet().getLargeFont() );
- if ( is_in_found_nodes ) {
- g.setFont( getTreeFontSet().getLargeFont().deriveFont( Font.BOLD ) );
- }
+ //g.setFont( getTreeFontSet().getLargeFont() );
+ //if ( is_in_found_nodes ) {
+ // g.setFont( getTreeFontSet().getLargeFont().deriveFont( Font.BOLD ) );
+ // }
if ( _sb.length() > 1 ) {
+ setColor( g, node, to_graphics_file, to_pdf, is_in_found_nodes, getTreeColorSet().getSequenceColor() );
+ final boolean using_visual_font = setFont( g, node, is_in_found_nodes );
final String sb_str = _sb.toString();
double m = 0;
if ( _graphics_type == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) {
_at = g.getTransform();
boolean need_to_reset = false;
final float x_coord = node.getXcoord();
- final float y_coord = node.getYcoord() + ( getTreeFontSet()._fm_large.getAscent() / 3.0f );
+ float y_coord;
+ if ( !using_visual_font ) {
+ y_coord = node.getYcoord() + ( getFontMetricsForLargeDefaultFont().getAscent() / 3.0f );
+ }
+ else {
+ y_coord = node.getYcoord() + ( getFontMetrics( g.getFont() ).getAscent() / 3.0f );
+ }
if ( radial_labels ) {
need_to_reset = true;
boolean left = false;
}
g.rotate( m, x_coord, node.getYcoord() );
if ( left ) {
- g.translate( -( getTreeFontSet()._fm_large.getStringBounds( sb_str, g ).getWidth() ), 0 );
+ if ( !using_visual_font ) {
+ g.translate( -( getFontMetricsForLargeDefaultFont().getStringBounds( sb_str, g ).getWidth() ),
+ 0 );
+ }
+ else {
+ g.translate( -( getFontMetrics( g.getFont() ).getStringBounds( sb_str, g ).getWidth() ), 0 );
+ }
}
}
else {
if ( ( m > HALF_PI ) && ( m < ONEHALF_PI ) ) {
need_to_reset = true;
- g.translate( -getTreeFontSet()._fm_large.getStringBounds( sb_str, g ).getWidth(), 0 );
+ if ( !using_visual_font ) {
+ g.translate( -getFontMetricsForLargeDefaultFont().getStringBounds( sb_str, g ).getWidth(), 0 );
+ }
+ else {
+ g.translate( -getFontMetrics( g.getFont() ).getStringBounds( sb_str, g ).getWidth(), 0 );
+ }
}
}
TreePanel.drawString( sb_str, x_coord, y_coord, g );
if ( dynamically_hide
&& !is_in_found_nodes
&& ( ( node.isExternal() && ( ( _external_node_index % dynamic_hiding_factor ) != 1 ) ) || ( !node
- .isExternal() && ( ( new_x_min < 20 ) || ( ( _y_distance * node.getNumberOfExternalNodes() ) < getTreeFontSet()._fm_large
+ .isExternal() && ( ( new_x_min < 20 ) || ( ( _y_distance * node.getNumberOfExternalNodes() ) < getFontMetricsForLargeDefaultFont()
.getHeight() ) ) ) ) ) {
return;
}
- paintNodeData( g, node, to_graphics_file, to_pdf, is_in_found_nodes );
- paintNodeWithRenderableData( g, node, to_graphics_file, to_pdf );
+ final int x = paintNodeData( g, node, to_graphics_file, to_pdf, is_in_found_nodes );
+ paintNodeWithRenderableData( x, g, node, to_graphics_file, to_pdf );
}
- final private void paintNodeWithRenderableData( final Graphics2D g,
+ final private void paintNodeWithRenderableData( final int x,
+ final Graphics2D g,
final PhylogenyNode node,
final boolean to_graphics_file,
final boolean to_pdf ) {
}
if ( rds != null ) {
rds.setRenderingHeight( 6 );
- int x = 0;
- if ( node.getNodeData().isHasTaxonomy() ) {
- if ( getControlPanel().isShowTaxonomyCode()
- && ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getTaxonomyCode() ) ) ) {
- x += getTreeFontSet()._fm_large_italic.stringWidth( node.getNodeData().getTaxonomy()
- .getTaxonomyCode()
- + " " );
- }
- if ( getControlPanel().isShowTaxonomyScientificNames()
- && ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getScientificName() ) ) ) {
- x += getTreeFontSet()._fm_large_italic.stringWidth( node.getNodeData().getTaxonomy()
- .getScientificName()
- + " " );
- }
- if ( getControlPanel().isShowTaxonomyCommonNames()
- && ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getCommonName() ) ) ) {
- x += getTreeFontSet()._fm_large_italic.stringWidth( node.getNodeData().getTaxonomy()
- .getCommonName()
- + " " );
- }
- }
- if ( node.getNodeData().isHasSequence() ) {
- if ( getControlPanel().isShowSeqNames()
- && ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getName() ) ) ) {
- x += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getName()
- + " " );
- }
- if ( getControlPanel().isShowSeqSymbols()
- && ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getSymbol() ) ) ) {
- x += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getSymbol()
- + " " );
- }
- if ( getControlPanel().isShowGeneNames()
- && ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getGeneName() ) ) ) {
- x += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getGeneName()
- + " " );
- }
- if ( getControlPanel().isShowSequenceAcc()
- && ( node.getNodeData().getSequence().getAccession() != null ) ) {
- x += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence()
- .getAccession().toString()
- + " " );
- }
- if ( getControlPanel().isShowAnnotation()
- && ( node.getNodeData().getSequence().getAnnotations() != null )
- && ( !node.getNodeData().getSequence().getAnnotations().isEmpty() ) ) {
- x += getTreeFontSet()._fm_large.stringWidth( TreePanelUtil.createAnnotationString( node
- .getNodeData().getSequence().getAnnotations(), getOptions()
- .isShowAnnotationRefSource() )
- + " " );
- }
- }
- if ( getControlPanel().isShowNodeNames() && !ForesterUtil.isEmpty( node.getName() ) ) {
- x += getTreeFontSet()._fm_large.stringWidth( node.getName() + " " );
- }
rds.render( node.getXcoord() + x, node.getYcoord() - 3, g, this, to_pdf );
}
}
getStatisticsForExpressionValues(),
getConfiguration() );
if ( rv != null ) {
- int x = 0;
+ int xx = 0;
PhylogenyNode my_node = node;
if ( !getControlPanel().isDrawPhylogram() ) {
my_node = getPhylogeny().getFirstExternalNode();
}
if ( getControlPanel().isShowTaxonomyCode() && ( PhylogenyMethods.getSpecies( my_node ).length() > 0 ) ) {
- x += getTreeFontSet()._fm_large_italic.stringWidth( PhylogenyMethods.getSpecies( my_node ) + " " );
+ xx += getFontMetricsForLargeDefaultFont()
+ .stringWidth( PhylogenyMethods.getSpecies( my_node ) + " " );
}
if ( getControlPanel().isShowNodeNames() && ( my_node.getName().length() > 0 ) ) {
- x += getTreeFontSet()._fm_large.stringWidth( my_node.getName() + " " );
+ xx += getFontMetricsForLargeDefaultFont().stringWidth( my_node.getName() + " " );
}
- rv.render( my_node.getXcoord() + x, node.getYcoord() - 5, g, this, to_pdf );
+ rv.render( my_node.getXcoord() + xx, node.getYcoord() - 5, g, this, to_pdf );
}
}
//////////////
final boolean is_in_found_nodes,
final boolean to_pdf,
final boolean to_graphics_file,
- final double x_shift ) {
+ final float x_shift ) {
final Taxonomy taxonomy = node.getNodeData().getTaxonomy();
- g.setFont( getTreeFontSet().getLargeItalicFont() );
- if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
- g.setColor( Color.BLACK );
- }
- else if ( is_in_found_nodes ) {
- g.setFont( getTreeFontSet().getLargeItalicFont().deriveFont( TreeFontSet.BOLD_AND_ITALIC ) );
- g.setColor( getColorForFoundNode( node ) );
- }
- else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
- g.setColor( getTaxonomyBasedColor( node ) );
- }
- else if ( getOptions().isColorLabelsSameAsParentBranch() && getControlPanel().isUseVisualStyles()
- && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
- g.setColor( PhylogenyMethods.getBranchColorValue( node ) );
- }
- else if ( to_pdf ) {
- g.setColor( Color.BLACK );
+ final boolean using_visual_font = setFont( g, node, is_in_found_nodes );
+ setColor( g, node, to_graphics_file, to_pdf, is_in_found_nodes, getTreeColorSet().getTaxonomyColor() );
+ final float start_x = node.getXcoord() + 3 + ( getOptions().getDefaultNodeShapeSize() / 2 ) + x_shift;
+ float start_y;
+ if ( !using_visual_font ) {
+ start_y = node.getYcoord()
+ + ( getFontMetricsForLargeDefaultFont().getAscent() / ( node.getNumberOfDescendants() == 1 ? 1
+ : 3.0f ) );
}
else {
- g.setColor( getTreeColorSet().getTaxonomyColor() );
+ start_y = node.getYcoord()
+ + ( getFontMetrics( g.getFont() ).getAscent() / ( node.getNumberOfDescendants() == 1 ? 1 : 3.0f ) );
}
- final double start_x = node.getXcoord() + 3 + ( getOptions().getDefaultNodeShapeSize() / 2 ) + x_shift;
- final double start_y = node.getYcoord()
- + ( getTreeFontSet()._fm_large.getAscent() / ( node.getNumberOfDescendants() == 1 ? 1 : 3.0 ) );
_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 )
}
/* GUILHEM_END */
TreePanel.drawString( label, start_x, start_y, g );
- if ( is_in_found_nodes ) {
- return getTreeFontSet()._fm_large_italic_bold.stringWidth( label );
- }
- else {
- return getTreeFontSet()._fm_large_italic.stringWidth( label );
+ if ( !using_visual_font && !is_in_found_nodes ) {
+ return getFontMetricsForLargeDefaultFont().stringWidth( label );
}
+ return getFontMetrics( g.getFont() ).stringWidth( label );
}
final private void paintUnrooted( final PhylogenyNode n,
return sb;
}
+ private void setColor( final Graphics2D g,
+ final PhylogenyNode node,
+ final boolean to_graphics_file,
+ final boolean to_pdf,
+ final boolean is_in_found_nodes,
+ final Color default_color ) {
+ if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
+ g.setColor( Color.BLACK );
+ }
+ 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().isColorAccordingToSequence() ) {
+ g.setColor( getSequenceBasedColor( node ) );
+ }
+ else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
+ g.setColor( getTaxonomyBasedColor( node ) );
+ }
+ else if ( getControlPanel().isColorAccordingToAnnotation()
+ && ( node.getNodeData().isHasSequence() && ( node.getNodeData().getSequence().getAnnotations() != null ) && ( !node
+ .getNodeData().getSequence().getAnnotations().isEmpty() ) ) ) {
+ g.setColor( calculateColorForAnnotation( node.getNodeData().getSequence().getAnnotations() ) );
+ }
+ else if ( getOptions().isColorLabelsSameAsParentBranch() && getControlPanel().isUseVisualStyles()
+ && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
+ g.setColor( PhylogenyMethods.getBranchColorValue( node ) );
+ }
+ else if ( to_pdf ) {
+ g.setColor( Color.BLACK );
+ }
+ else {
+ g.setColor( default_color );
+ }
+ }
+
final private void setCopiedAndPastedNodes( final Set<Long> nodeIds ) {
getMainPanel().setCopiedAndPastedNodes( nodeIds );
}
getMainPanel().setCutOrCopiedTree( cut_or_copied_tree );
}
+ private boolean setFont( final Graphics2D g, final PhylogenyNode node, final boolean is_in_found_nodes ) {
+ Font visual_font = null;
+ if ( getControlPanel().isUseVisualStyles() && ( node.getNodeData().getNodeVisualData() != null ) ) {
+ visual_font = node.getNodeData().getNodeVisualData().getFont();
+ g.setFont( visual_font != null ? visual_font : getTreeFontSet().getLargeFont() );
+ }
+ else {
+ g.setFont( getTreeFontSet().getLargeFont() );
+ }
+ if ( is_in_found_nodes ) {
+ g.setFont( g.getFont().deriveFont( Font.BOLD ) );
+ }
+ return visual_font != null;
+ }
+
final private void setInOv( final boolean in_ov ) {
_in_ov = in_ov;
}
else if ( isInFoundNodes0( node ) && isInFoundNodes1( node ) ) {
_rollover_popup.setForeground( getTreeColorSet().getFoundColor0and1() );
}
- else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
- _rollover_popup.setForeground( getTaxonomyBasedColor( node ) );
- }
else {
_rollover_popup.setForeground( getTreeColorSet().getSequenceColor() );
}
}
}
- final private static void drawString( final String str, final double x, final double y, final Graphics2D g ) {
- g.drawString( str, ( int ) ( x + 0.5 ), ( int ) ( y + 0.5 ) );
+ private final static void colorizeNodesHelper( final Color c, final PhylogenyNode node ) {
+ if ( node.getNodeData().getNodeVisualData() == null ) {
+ node.getNodeData().setNodeVisualData( new NodeVisualData() );
+ }
+ node.getNodeData().getNodeVisualData().setFontColor( new Color( c.getRed(), c.getGreen(), c.getBlue() ) );
+ }
+
+ final private static void drawString( final String str, final float x, final float y, final Graphics2D g ) {
+ g.drawString( str, x, y );
}
final private static boolean plusPressed( final int key_code ) {
|| ( key_code == KeyEvent.VK_EQUALS ) || ( key_code == KeyEvent.VK_SEMICOLON ) || ( key_code == KeyEvent.VK_1 ) );
}
- final private class SubtreeColorizationActionListener implements ActionListener {
+ final private class NodeColorizationActionListener implements ActionListener {
List<PhylogenyNode> _additional_nodes = null;
JColorChooser _chooser = null;
PhylogenyNode _node = null;
- SubtreeColorizationActionListener( final JColorChooser chooser, final PhylogenyNode node ) {
+ NodeColorizationActionListener( final JColorChooser chooser, final PhylogenyNode node ) {
_chooser = chooser;
_node = node;
}
- SubtreeColorizationActionListener( final JColorChooser chooser,
- final PhylogenyNode node,
- final List<PhylogenyNode> additional_nodes ) {
+ NodeColorizationActionListener( final JColorChooser chooser,
+ final PhylogenyNode node,
+ final List<PhylogenyNode> additional_nodes ) {
_chooser = chooser;
_node = node;
_additional_nodes = additional_nodes;
public void actionPerformed( final ActionEvent e ) {
final Color c = _chooser.getColor();
if ( c != null ) {
- colorizeSubtree( c, _node, _additional_nodes );
+ colorizeNodes( c, _node, _additional_nodes );
}
}
}
- final private class NodeColorizationActionListener implements ActionListener {
+ final private class SubtreeColorizationActionListener implements ActionListener {
List<PhylogenyNode> _additional_nodes = null;
JColorChooser _chooser = null;
PhylogenyNode _node = null;
- NodeColorizationActionListener( final JColorChooser chooser, final PhylogenyNode node ) {
+ SubtreeColorizationActionListener( final JColorChooser chooser, final PhylogenyNode node ) {
_chooser = chooser;
_node = node;
}
- NodeColorizationActionListener( final JColorChooser chooser,
- final PhylogenyNode node,
- final List<PhylogenyNode> additional_nodes ) {
+ SubtreeColorizationActionListener( final JColorChooser chooser,
+ final PhylogenyNode node,
+ final List<PhylogenyNode> additional_nodes ) {
_chooser = chooser;
_node = node;
_additional_nodes = additional_nodes;
public void actionPerformed( final ActionEvent e ) {
final Color c = _chooser.getColor();
if ( c != null ) {
- colorizeNodes( c, _node, _additional_nodes );
+ colorizeSubtree( c, _node, _additional_nodes );
}
}
}
git://source.jalview.org / jalview.git / blobdiff