import org.forester.phylogeny.data.BranchColor;
import org.forester.phylogeny.data.Confidence;
import org.forester.phylogeny.data.Event;
+import org.forester.phylogeny.data.NodeVisualization;
+import org.forester.phylogeny.data.NodeVisualization.NodeFill;
+import org.forester.phylogeny.data.NodeVisualization.NodeShape;
import org.forester.phylogeny.data.PhylogenyData;
import org.forester.phylogeny.data.PropertiesMap;
import org.forester.phylogeny.data.Property;
private final static NumberFormat FORMATTER_CONFIDENCE;
private final static NumberFormat FORMATTER_BRANCH_LENGTH;
private final static int WIGGLE = 2;
- private int _half_box_size_plus_wiggle;
private final static int LIMIT_FOR_HQ_RENDERING = 1000;
private final static int CONFIDENCE_LEFT_MARGIN = 4;
// TODO "rendering_hints" was static before. Need to make sure everything is OK with it not
final private static double _180_OVER_PI = 180.0 / Math.PI;
private static final float ROUNDED_D = 8;
private int _circ_max_depth;
- private int _circ_num_ext_nodes;
private PhylogenyNode _root;
final private Arc2D _arc = new Arc2D.Double();
final private HashMap<Integer, Double> _urt_nodeid_angle_map = new HashMap<Integer, Double>();
final private HashMap<Integer, Integer> _urt_nodeid_index_map = new HashMap<Integer, Integer>();
+ final private Set<Integer> _collapsed_external_nodeid_set = new HashSet<Integer>();
HashMap<Integer, Short> _nodeid_dist_to_leaf = new HashMap<Integer, Short>();
private AffineTransform _at;
private double _max_distance_to_root = -1;
private boolean _edited = false;
private Popup _node_desc_popup;
private JTextArea _rollover_popup;
- private int _box_size ;
- private int _half_box_size;
+ // private final int _box_size;
+ // private final int _half_box_size;
//private final short _skip_counter = 0;
private final StringBuffer _popup_buffer = new StringBuffer();
final private static Font POPUP_FONT = new Font( Configuration.getDefaultFontFamilyName(),
_configuration = configuration;
_phylogeny = t;
_phy_has_branch_lengths = ForesterUtil.isHasAtLeastOneBranchLengthLargerThanZero( _phylogeny );
- _box_size = tjp.getOptions().getDefaultNodeBoxSize();
- _half_box_size = tjp.getOptions().getDefaultNodeBoxSize() / 2;
-
- _half_box_size_plus_wiggle = _half_box_size + WIGGLE;
init();
// if ( !_phylogeny.isEmpty() ) {
_phylogeny.recalculateNumberOfExternalDescendants( true );
}
}
- final void assignGraphicsForNodeBoxWithColorForParentBranch( final PhylogenyNode node, final Graphics g ) {
+ final Color getGraphicsForNodeBoxWithColorForParentBranch( final PhylogenyNode node ) {
if ( getControlPanel().isColorBranches() && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
- g.setColor( PhylogenyMethods.getBranchColorValue( node ) );
+ return ( PhylogenyMethods.getBranchColorValue( node ) );
}
else {
- g.setColor( getTreeColorSet().getBranchColor() );
+ return ( getTreeColorSet().getBranchColor() );
}
}
if ( !node.isExternal() && !node.isRoot() ) {
final boolean collapse = !node.isCollapse();
Util.collapseSubtree( node, collapse );
+ updateSetOfCollapsedExternalNodes( _phylogeny );
_phylogeny.recalculateNumberOfExternalDescendants( true );
resetNodeIdToDistToLeafMap();
calculateLongestExtNodeInfo();
}
setWaitCursor();
Util.collapseSpeciesSpecificSubtrees( _phylogeny );
+ updateSetOfCollapsedExternalNodes( _phylogeny );
_phylogeny.recalculateNumberOfExternalDescendants( true );
resetNodeIdToDistToLeafMap();
calculateLongestExtNodeInfo();
_rectangle.setFrame( x, y, width, heigth );
g.fill( _rectangle );
}
-
- //TODO FIXME
+
final private void drawRectGradient( final double x,
final double y,
final double width,
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( ( float ) x,
+ ( float ) y,
+ color_1,
+ ( float ) ( x + width ),
+ ( float ) ( y + heigth ),
+ color_2,
+ false ) );
g.fill( _rectangle );
if ( color_border != null ) {
g.setPaint( color_border );
g.draw( _rectangle );
}
}
-
- //TODO FIXME
+
final private void drawOvalGradient( final double x,
final double y,
final double width,
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( ( float ) x,
+ ( float ) y,
+ color_1,
+ ( float ) ( x + width ),
+ ( float ) ( y + heigth ),
+ color_2,
+ false ) );
g.fill( _ellipse );
if ( color_border != null ) {
g.setPaint( color_border );
if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
return null;
}
+ final int half_box_size_plus_wiggle = getOptions().getDefaultNodeShapeSize() / 2 + WIGGLE;
for( final PhylogenyNodeIterator iter = _phylogeny.iteratorPostorder(); iter.hasNext(); ) {
final PhylogenyNode node = iter.next();
if ( ( _phylogeny.isRooted() || !node.isRoot() || ( node.getNumberOfDescendants() > 2 ) )
- && ( ( node.getXcoord() - _half_box_size_plus_wiggle ) <= x )
- && ( ( node.getXcoord() + _half_box_size_plus_wiggle ) >= x )
- && ( ( node.getYcoord() - _half_box_size_plus_wiggle ) <= y )
- && ( ( node.getYcoord() + _half_box_size_plus_wiggle ) >= y ) ) {
+ && ( ( node.getXcoord() - half_box_size_plus_wiggle ) <= x )
+ && ( ( node.getXcoord() + half_box_size_plus_wiggle ) >= x )
+ && ( ( node.getYcoord() - half_box_size_plus_wiggle ) <= y )
+ && ( ( node.getYcoord() + half_box_size_plus_wiggle ) >= y ) ) {
return node;
}
}
final private void paintBranchRectangular( final Graphics2D g,
final float x1,
final float x2,
- float y1,
+ final float y1,
final float y2,
final PhylogenyNode node,
final boolean to_pdf,
g.draw( _cubic_curve );
}
else {
- float x2a = x2;
- float x1a = x1;
- // draw the vertical line
- boolean draw_horizontal = true;
+ final float x2a = x2;
+ final float x1a = x1;
float y2_r = 0;
if ( node.isFirstChildNode() || node.isLastChildNode()
|| ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE )
|| ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) {
- boolean draw_vertical = true;
- final PhylogenyNode parent = node.getParent();
- if ( ( ( getOptions().getDefaultNodeShape() != Options.NodeShape.NONE && !to_pdf && !to_graphics_file ) || ( ( getControlPanel()
- .isEvents() ) && ( parent != null ) && parent.isHasAssignedEvent() ) )
- && ( _phylogeny.isRooted() || !( ( parent != null ) && parent.isRoot() ) )
- && !( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() && !parent
- .isDuplication() ) ) {
- if ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE )
- && ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) {
- if ( Math.abs( y2 - y1 ) <= _half_box_size ) {
- draw_vertical = false;
- }
- else {
- if ( y1 < y2 ) {
- y1 += _half_box_size;
- }
- else {
- if ( !to_pdf ) {
- y1 -= _half_box_size + 1;
- }
- else {
- y1 -= _half_box_size;
- }
- }
- }
- }
- if ( ( x2 - x1 ) <= _half_box_size ) {
- draw_horizontal = false;
- }
- else if ( !draw_vertical ) {
- x1a += _half_box_size;
- }
- if ( ( ( x2 - x1a ) > _half_box_size )
- && !( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() && !node
- .isDuplication() ) ) {
- x2a -= _half_box_size;
- }
+ if ( !to_graphics_file
+ && !to_pdf
+ && ( ( ( y2 < getVisibleRect().getMinY() - 20 ) && ( y1 < getVisibleRect().getMinY() - 20 ) ) || ( ( y2 > getVisibleRect()
+ .getMaxY() + 20 ) && ( y1 > getVisibleRect().getMaxY() + 20 ) ) ) ) {
+ // Do nothing.
}
- if ( draw_vertical ) {
- if ( !to_graphics_file
- && !to_pdf
- && ( ( ( y2 < getVisibleRect().getMinY() - 20 ) && ( y1 < getVisibleRect().getMinY() - 20 ) ) || ( ( y2 > getVisibleRect()
- .getMaxY() + 20 ) && ( y1 > getVisibleRect().getMaxY() + 20 ) ) ) ) {
- // Do nothing.
- }
- else {
- if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
- float x2c = x1 + EURO_D;
- if ( x2c > x2a ) {
- x2c = x2a;
- }
- drawLine( x1, y1, x2c, y2, g );
+ else {
+ if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
+ float x2c = x1 + EURO_D;
+ if ( x2c > x2a ) {
+ x2c = x2a;
}
- else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
- if ( y2 > y1 ) {
- y2_r = y2 - ROUNDED_D;
- if ( y2_r < y1 ) {
- y2_r = y1;
- }
- drawLine( x1, y1, x1, y2_r, g );
- }
- else {
- y2_r = y2 + ROUNDED_D;
- if ( y2_r > y1 ) {
- y2_r = y1;
- }
- drawLine( x1, y1, x1, y2_r, g );
+ drawLine( x1, y1, x2c, y2, g );
+ }
+ else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
+ if ( y2 > y1 ) {
+ y2_r = y2 - ROUNDED_D;
+ if ( y2_r < y1 ) {
+ y2_r = y1;
}
+ drawLine( x1, y1, x1, y2_r, g );
}
else {
- drawLine( x1, y1, x1, y2, g );
+ y2_r = y2 + ROUNDED_D;
+ if ( y2_r > y1 ) {
+ y2_r = y1;
+ }
+ drawLine( x1, y1, x1, y2_r, g );
}
}
+ else {
+ drawLine( x1, y1, x1, y2, g );
+ }
}
}
// draw the horizontal line
return;
}
float x1_r = 0;
- if ( draw_horizontal ) {
- if ( !getControlPanel().isWidthBranches() || ( PhylogenyMethods.getBranchWidthValue( node ) == 1 ) ) {
- if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
- x1_r = x1a + ROUNDED_D;
- if ( x1_r < x2a ) {
- drawLine( x1_r, y2, x2a, y2, g );
- }
+ if ( !getControlPanel().isWidthBranches() || ( PhylogenyMethods.getBranchWidthValue( node ) == 1 ) ) {
+ if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
+ x1_r = x1a + ROUNDED_D;
+ if ( x1_r < x2a ) {
+ drawLine( x1_r, y2, x2a, y2, g );
}
- else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
- final float x1c = x1a + EURO_D;
- if ( x1c < x2a ) {
- drawLine( x1c, y2, x2a, y2, g );
- }
- }
- else {
- drawLine( x1a, y2, x2a, y2, g );
+ }
+ else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
+ final float x1c = x1a + EURO_D;
+ if ( x1c < x2a ) {
+ drawLine( x1c, y2, x2a, y2, g );
}
}
else {
- final double w = PhylogenyMethods.getBranchWidthValue( node );
- if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
- x1_r = x1a + ROUNDED_D;
- if ( x1_r < x2a ) {
- drawRectFilled( x1_r, y2 - ( w / 2 ), x2a - x1_r, w, g );
- }
- }
- else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
- final float x1c = x1a + EURO_D;
- if ( x1c < x2a ) {
- drawRectFilled( x1c, y2 - ( w / 2 ), x2a - x1c, w, g );
- }
+ drawLine( x1a, y2, x2a, y2, g );
+ }
+ }
+ else {
+ final double w = PhylogenyMethods.getBranchWidthValue( node );
+ if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
+ x1_r = x1a + ROUNDED_D;
+ if ( x1_r < x2a ) {
+ drawRectFilled( x1_r, y2 - ( w / 2 ), x2a - x1_r, w, g );
}
- else {
- drawRectFilled( x1a, y2 - ( w / 2 ), x2a - x1a, w, g );
+ }
+ else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
+ final float x1c = x1a + EURO_D;
+ if ( x1c < x2a ) {
+ drawRectFilled( x1c, y2 - ( w / 2 ), x2a - x1c, w, g );
}
}
+ else {
+ drawRectFilled( x1a, y2 - ( w / 2 ), x2a - x1a, w, g );
+ }
}
if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) {
if ( x1_r > x2a ) {
g.draw( _arc );
}
}
- //TODO new *****
if ( node.isExternal() ) {
- //TODO new *****
paintNodeBox( x2, y2, node, g, to_pdf, to_graphics_file, isInFoundNodes( node ) );
}
}
final Graphics2D g,
final boolean to_pdf,
final boolean to_graphics_file ) {
- _circ_num_ext_nodes = phy.getNumberOfExternalNodes();
+ final int circ_num_ext_nodes = phy.getNumberOfExternalNodes() - _collapsed_external_nodeid_set.size();
+ System.out.println( "# collapsed external = " + _collapsed_external_nodeid_set.size() );
_root = phy.getRoot();
_root.setXcoord( center_x );
_root.setYcoord( center_y );
- final boolean radial_labels = getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL;
+ final boolean radial_labels = getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL;
double current_angle = starting_angle;
int i = 0;
for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
final PhylogenyNode n = it.next();
- n.setXcoord( ( float ) ( center_x + ( radius * Math.cos( current_angle ) ) ) );
- n.setYcoord( ( float ) ( center_y + ( radius * Math.sin( current_angle ) ) ) );
- _urt_nodeid_angle_map.put( n.getId(), current_angle );
- _urt_nodeid_index_map.put( n.getId(), i++ );
- current_angle += ( TWO_PI / _circ_num_ext_nodes );
+ if ( !n.isCollapse() ) {
+ n.setXcoord( ( float ) ( center_x + ( radius * Math.cos( current_angle ) ) ) );
+ n.setYcoord( ( float ) ( center_y + ( radius * Math.sin( current_angle ) ) ) );
+ _urt_nodeid_angle_map.put( n.getId(), current_angle );
+ _urt_nodeid_index_map.put( n.getId(), i++ );
+ current_angle += ( TWO_PI / circ_num_ext_nodes );
+ }
+ else {
+ //TODO remove me
+ System.out.println( "is collapse" + n.getName() );
+ }
}
paintCirculars( phy.getRoot(), phy, center_x, center_y, radius, radial_labels, g, to_pdf, to_graphics_file );
paintNodeBox( _root.getXcoord(), _root.getYcoord(), _root, g, to_pdf, to_graphics_file, isInFoundNodes( _root ) );
-
+ }
+
+ private void updateSetOfCollapsedExternalNodes( final Phylogeny phy ) {
+ _collapsed_external_nodeid_set.clear();
+ E: for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
+ final PhylogenyNode ext_node = it.next();
+ PhylogenyNode n = ext_node;
+ while ( !n.isRoot() ) {
+ if ( n.isCollapse() ) {
+ _collapsed_external_nodeid_set.add( ext_node.getId() );
+ continue E;
+ }
+ n = n.getParent();
+ }
+ }
}
final void paintCircularLite( final Phylogeny phy,
final int center_y,
final int radius,
final Graphics2D g ) {
- _circ_num_ext_nodes = phy.getNumberOfExternalNodes();
+ final int circ_num_ext_nodes = phy.getNumberOfExternalNodes();
_root = phy.getRoot();
_root.setXSecondary( center_x );
_root.setYSecondary( center_y );
n.setXSecondary( ( float ) ( center_x + radius * Math.cos( current_angle ) ) );
n.setYSecondary( ( float ) ( center_y + radius * Math.sin( current_angle ) ) );
_urt_nodeid_angle_map.put( n.getId(), current_angle );
- current_angle += ( TWO_PI / _circ_num_ext_nodes );
+ current_angle += ( TWO_PI / circ_num_ext_nodes );
}
paintCircularsLite( phy.getRoot(), phy, center_x, center_y, radius, g );
}
final Graphics2D g,
final boolean to_pdf,
final boolean to_graphics_file ) {
- if ( n.isExternal() ) {
+ if ( n.isExternal() || n.isCollapse() ) { //~~circ collapse
if ( !_urt_nodeid_angle_map.containsKey( n.getId() ) ) {
- System.out.println( "no " + n + ", ERROR!" );//TODO
+ System.out.println( "no " + n + " =====>>>>>>> ERROR!" );//TODO
}
return _urt_nodeid_angle_map.get( n.getId() );
}
final boolean to_graphics_file,
final boolean to_pdf,
final boolean is_in_found_nodes ) {
+ Color c = null;
if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
- g.setColor( Color.BLACK );
+ c = Color.BLACK;
}
else if ( is_in_found_nodes ) {
- g.setColor( getTreeColorSet().getFoundColor() );
+ c = getTreeColorSet().getFoundColor();
}
else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
- g.setColor( getTaxonomyBasedColor( node ) );
+ c = getTaxonomyBasedColor( node );
}
else if ( getOptions().isColorLabelsSameAsParentBranch() && getControlPanel().isColorBranches()
&& ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
- g.setColor( PhylogenyMethods.getBranchColorValue( node ) );
+ c = PhylogenyMethods.getBranchColorValue( node );
}
else {
- g.setColor( getTreeColorSet().getCollapseFillColor() );
+ c = getTreeColorSet().getCollapseFillColor();
}
double d = node.getAllExternalDescendants().size();
if ( d > 1000 ) {
else {
d = ( Math.log10( d ) * _y_distance ) / 2.5;
}
- if ( d < _box_size ) {
- d = _box_size;
+ final int box_size = getOptions().getDefaultNodeShapeSize();
+ if ( d < box_size ) {
+ d = box_size;
}
_polygon.reset();
- _polygon.addPoint( ForesterUtil.roundToInt( node.getXcoord() - _box_size ),
+ _polygon.addPoint( ForesterUtil.roundToInt( node.getXcoord() - box_size ),
ForesterUtil.roundToInt( node.getYcoord() ) );
- _polygon.addPoint( ForesterUtil.roundToInt( node.getXcoord() + _box_size ),
+ _polygon.addPoint( ForesterUtil.roundToInt( node.getXcoord() + box_size ),
ForesterUtil.roundToInt( node.getYcoord() - d ) );
- _polygon.addPoint( ForesterUtil.roundToInt( node.getXcoord() + _box_size ),
+ _polygon.addPoint( ForesterUtil.roundToInt( node.getXcoord() + box_size ),
ForesterUtil.roundToInt( node.getYcoord() + d ) );
- g.fillPolygon( _polygon );
+ if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.SOLID ) {
+ g.setColor( c );
+ g.fillPolygon( _polygon );
+ }
+ else if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.NONE ) {
+ g.setColor( getBackground() );
+ g.fillPolygon( _polygon );
+ g.setColor( c );
+ g.drawPolygon( _polygon );
+ }
+ else if ( getOptions().getDefaultNodeFill() == NodeFill.GRADIENT ) {
+ g.setPaint( new GradientPaint( node.getXcoord() - box_size, node.getYcoord(), getBackground(), ( node
+ .getXcoord() + box_size ), ( float ) ( node.getYcoord() - d ), c, false ) );
+ g.fill( _polygon );
+ g.setPaint( c );
+ g.draw( _polygon );
+ }
paintNodeData( g, node, to_graphics_file, to_pdf, is_in_found_nodes );
}
}
final private void paintFoundNode( final int x, final int y, final Graphics2D g ) {
+ final int box_size = getOptions().getDefaultNodeShapeSize();
+ final int half_box_size = getOptions().getDefaultNodeShapeSize() / 2;
g.setColor( getTreeColorSet().getFoundColor() );
- g.fillRect( x - _half_box_size, y - _half_box_size, _box_size, _box_size );
+ g.fillRect( x - half_box_size, y - half_box_size, box_size, box_size );
}
final private void paintGainedAndLostCharacters( final Graphics2D g,
paintFoundNode( ForesterUtil.roundToInt( x ), ForesterUtil.roundToInt( y ), g );
}
else {
+ Color outline_color = null;
if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
- g.setColor( Color.BLACK );
+ outline_color = Color.BLACK;
}
else if ( getControlPanel().isEvents() && Util.isHasAssignedEvent( node ) ) {
final Event event = node.getNodeData().getEvent();
if ( event.isDuplication() ) {
- g.setColor( getTreeColorSet().getDuplicationBoxColor() );
+ outline_color = getTreeColorSet().getDuplicationBoxColor();
}
else if ( event.isSpeciation() ) {
- g.setColor( getTreeColorSet().getSpecBoxColor() );
+ outline_color = getTreeColorSet().getSpecBoxColor();
}
else if ( event.isSpeciationOrDuplication() ) {
- g.setColor( getTreeColorSet().getDuplicationOrSpeciationColor() );
+ outline_color = getTreeColorSet().getDuplicationOrSpeciationColor();
}
}
+ else if ( getOptions().isTaxonomyColorizeNodeShapes() ) {
+ outline_color = getTaxonomyBasedColor( node );
+ }
else {
- assignGraphicsForNodeBoxWithColorForParentBranch( node, g );
- }
- if ( ( getOptions().getDefaultNodeShape() != Options.NodeShape.NONE && !to_pdf && !to_graphics_file )
- || ( getControlPanel().isEvents() && node.isHasAssignedEvent() ) ) {
- if ( to_pdf || to_graphics_file ) {
- if ( node.isDuplication() || !getOptions().isPrintBlackAndWhite() ) {
- //TODO FIXME
- //drawOvalFilled( x - _half_box_size, y - _half_box_size, _box_size, _box_size, g );
- drawOvalGradient( x - _half_box_size, y - _half_box_size, _box_size, _box_size, g
- ,Color.BLACK,
- g.getColor(), g.getColor());
+ outline_color = getGraphicsForNodeBoxWithColorForParentBranch( node );
+ if ( to_pdf && ( outline_color == getTreeColorSet().getBranchColor() ) ) {
+ outline_color = getTreeColorSet().getBranchColorForPdf();
+ }
+ }
+ final int box_size = getOptions().getDefaultNodeShapeSize();
+ final int half_box_size = box_size / 2;
+ if ( getOptions().isShowDefaultNodeShapes() || ( getControlPanel().isEvents() && node.isHasAssignedEvent() ) ) {
+ if ( getOptions().getDefaultNodeShape() == NodeShape.CIRCLE ) {
+ if ( getOptions().getDefaultNodeFill() == 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 ) {
+ Color background = getBackground();
+ if ( to_pdf ) {
+ background = Color.WHITE;
+ }
+ drawOvalGradient( x - half_box_size,
+ y - half_box_size,
+ box_size,
+ box_size,
+ g,
+ background,
+ background,
+ outline_color );
+ }
+ else if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.SOLID ) {
+ g.setColor( outline_color );
+ drawOvalFilled( x - half_box_size, y - half_box_size, box_size, box_size, g );
}
}
- else {
- //TODO FIXME
- //drawRectFilled( x - HALF_BOX_SIZE, y - HALF_BOX_SIZE, BOX_SIZE, BOX_SIZE, g );
- drawOvalGradient( x - _half_box_size, y - _half_box_size, _box_size, _box_size, g
- ,Color.BLACK,
- g.getColor(), g.getColor());
+ else if ( getOptions().getDefaultNodeShape() == NodeVisualization.NodeShape.RECTANGLE ) {
+ if ( getOptions().getDefaultNodeFill() == NodeVisualization.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() == NodeVisualization.NodeFill.NONE ) {
+ Color background = getBackground();
+ if ( to_pdf ) {
+ background = Color.WHITE;
+ }
+ drawRectGradient( x - half_box_size,
+ y - half_box_size,
+ box_size,
+ box_size,
+ g,
+ background,
+ background,
+ outline_color );
+ }
+ else if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.SOLID ) {
+ g.setColor( outline_color );
+ drawRectFilled( x - half_box_size, y - half_box_size, box_size, box_size, g );
+ }
}
}
}
return;
}
int x = 0;
+ final int half_box_size = getOptions().getDefaultNodeShapeSize() / 2;
if ( getControlPanel().isShowTaxonomyImages()
&& ( getImageMap() != null )
&& !getImageMap().isEmpty()
&& node.getNodeData().isHasTaxonomy()
&& ( ( node.getNodeData().getTaxonomy().getUris() != null ) && !node.getNodeData().getTaxonomy()
.getUris().isEmpty() ) ) {
- x += drawTaxonomyImage( node.getXcoord() + 2 + _half_box_size, node.getYcoord(), node, g );
+ x += drawTaxonomyImage( node.getXcoord() + 2 + half_box_size, node.getYcoord(), node, g );
}
if ( ( getControlPanel().isShowTaxonomyCode() || getControlPanel().isShowTaxonomyScientificNames() || getControlPanel()
.isShowTaxonomyCommonNames() ) && node.getNodeData().isHasTaxonomy() ) {
if ( !node.isExternal() && ( node.getNumberOfDescendants() == 1 ) ) {
down_shift_factor = 1;
}
- final double pos_x = node.getXcoord() + x + 2 + _half_box_size;
+ 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 ______________
&& seqRelation.getType().equals( getControlPanel().getSequenceRelationTypeBox()
.getSelectedItem() );
if ( fGotRelationWithQuery ) { // we will underline the text to show that this sequence is ortholog to the query
- final double linePosX = node.getXcoord() + 2 + _half_box_size;
+ final double linePosX = node.getXcoord() + 2 + half_box_size;
final String sConfidence = ( !getControlPanel().isShowSequenceRelationConfidence() || ( seqRelation
.getConfidence() == null ) ) ? null : " (" + seqRelation.getConfidence().getValue()
+ ")";
g.setColor( calculateColorForAnnotation( ann ) );
}
final String ann_str = ann.asSimpleText().toString();
- TreePanel.drawString( ann_str, node.getXcoord() + x + 3 + _half_box_size, node.getYcoord()
+ TreePanel.drawString( ann_str, node.getXcoord() + x + 3 + half_box_size, node.getYcoord()
+ ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g );
_sb.setLength( 0 );
_sb.append( ann_str );
}
if ( getControlPanel().isShowBinaryCharacters() ) {
TreePanel.drawString( node.getNodeData().getBinaryCharacters().getPresentCharactersAsStringBuffer()
- .toString(), node.getXcoord() + x + 1 + _half_box_size, node.getYcoord()
+ .toString(), node.getXcoord() + x + 1 + half_box_size, node.getYcoord()
+ ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g );
paintGainedAndLostCharacters( g, node, node.getNodeData().getBinaryCharacters()
.getGainedCharactersAsStringBuffer().toString(), node.getNodeData().getBinaryCharacters()
}
final double mean = ForesterUtil.round( sum / count, 1 );
TreePanel.drawString( " " + node.getNodeData().getBinaryCharacters().getPresentCount() + " ["
- + mean + "]", node.getXcoord() + x + 4 + _half_box_size, node.getYcoord()
+ + mean + "]", node.getXcoord() + x + 4 + half_box_size, node.getYcoord()
+ ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g );
}
else {
TreePanel.drawString( " " + node.getNodeData().getBinaryCharacters().getPresentCount(),
- node.getXcoord() + x + 4 + _half_box_size,
+ node.getXcoord() + x + 4 + half_box_size,
node.getYcoord()
+ ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ),
g );
child_node.setYcoord( y2 );
y2 += _y_distance * child_node.getNumberOfExternalNodes();
}
- //TODO new *****
- paintNodeBox( node.getXcoord(), node.getYcoord(), node, g, to_pdf, to_graphics_file, isInFoundNodes( node ) );
- //TODO new *****
+ paintNodeBox( node.getXcoord(), node.getYcoord(), node, g, to_pdf, to_graphics_file, isInFoundNodes( node ) );
}
if ( dynamically_hide
&& !is_in_found_nodes
else {
g.setColor( getTreeColorSet().getTaxonomyColor() );
}
- final double start_x = node.getXcoord() + 3 + _half_box_size + x_shift;
+ 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 );
final float new_y = ( float ) ( y + Math.sin( mid_angle ) * length );
desc.setXcoord( new_x );
desc.setYcoord( new_y );
-
paintUnrooted( desc, current_angle, current_angle + arc_size, radial_labels, g, to_pdf, to_graphics_file );
current_angle += arc_size;
assignGraphicsForBranchWithColorForParentBranch( desc, false, g, to_pdf, to_graphics_file );
drawLine( x, y, new_x, new_y, g );
-
paintNodeBox( new_x, new_y, desc, g, to_pdf, to_graphics_file, isInFoundNodes( desc ) );
-
}
if ( n.isRoot() ) {
paintNodeBox( n.getXcoord(), n.getYcoord(), n, g, to_pdf, to_graphics_file, isInFoundNodes( n ) );
}
final private static Phylogeny subTree( final PhylogenyNode new_root, final Phylogeny source_phy ) {
-
final Phylogeny new_phy = new Phylogeny();
new_phy.setRooted( true );
new_phy.setName( source_phy.getName() );
git://source.jalview.org / jalview.git / blobdiff