From 75868964110d90c488348f014861f48bb6ae954d Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Wed, 22 Jan 2014 04:27:30 +0000 Subject: [PATCH] inprogress --- .../org/forester/archaeopteryx/ArchaeopteryxE.java | 9 -- .../org/forester/archaeopteryx/Configuration.java | 12 -- .../src/org/forester/archaeopteryx/MainFrame.java | 6 - .../forester/archaeopteryx/MainFrameApplet.java | 3 - .../archaeopteryx/MainFrameApplication.java | 3 - .../src/org/forester/archaeopteryx/Options.java | 11 -- .../src/org/forester/archaeopteryx/TreePanel.java | 160 +++++++++----------- 7 files changed, 68 insertions(+), 136 deletions(-) diff --git a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java index 72bb43f..36767b6 100644 --- a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java +++ b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java @@ -125,7 +125,6 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { private JMenuItem _cycle_node_shape_mi; private JMenuItem _cycle_node_fill_mi; private JMenuItem _choose_node_size_mi; - private JCheckBoxMenuItem _taxonomy_colorize_node_shapes_cbmi; private JCheckBoxMenuItem _show_confidence_stddev_cbmi; private final LinkedList _textframes = new LinkedList(); private JMenu _analysis_menu; @@ -300,9 +299,6 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { else if ( o == _show_default_node_shapes_external_cbmi ) { updateOptions( getOptions() ); } - else if ( o == _taxonomy_colorize_node_shapes_cbmi ) { - updateOptions( getOptions() ); - } else if ( o == _about_item ) { MainFrame.about(); } @@ -724,8 +720,6 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { _options_jmenu .add( _color_by_taxonomic_group_cbmi = new JCheckBoxMenuItem( MainFrame.COLOR_BY_TAXONOMIC_GROUP ) ); _options_jmenu - .add( _taxonomy_colorize_node_shapes_cbmi = new JCheckBoxMenuItem( MainFrame.TAXONOMY_COLORIZE_NODE_SHAPES_LABEL ) ); - _options_jmenu .add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( MainFrame.COLOR_LABELS_LABEL ) ); _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP ); _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( MainFrame.ABBREV_SN_LABEL ) ); @@ -765,7 +759,6 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { .isShowDefaultNodeShapesExternal() ); customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions() .isShowDefaultNodeShapesInternal() ); - customizeCheckBoxMenuItem( _taxonomy_colorize_node_shapes_cbmi, getOptions().isTaxonomyColorizeNodeShapes() ); customizeJMenuItem( _cycle_node_shape_mi ); customizeJMenuItem( _cycle_node_fill_mi ); customizeJMenuItem( _choose_node_size_mi ); @@ -1305,8 +1298,6 @@ public class ArchaeopteryxE extends JApplet implements ActionListener { && _show_default_node_shapes_internal_cbmi.isSelected() ); options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null ) && _show_default_node_shapes_external_cbmi.isSelected() ); - options.setTaxonomyColorizeNodeShapes( ( _taxonomy_colorize_node_shapes_cbmi != null ) - && _taxonomy_colorize_node_shapes_cbmi.isSelected() ); if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) { options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP ); } diff --git a/forester/java/src/org/forester/archaeopteryx/Configuration.java b/forester/java/src/org/forester/archaeopteryx/Configuration.java index ab9802c..37f3b2d 100644 --- a/forester/java/src/org/forester/archaeopteryx/Configuration.java +++ b/forester/java/src/org/forester/archaeopteryx/Configuration.java @@ -218,7 +218,6 @@ public final class Configuration { private boolean _show_domain_labels = true; private boolean _show_overview = true; private boolean _show_scale = false; - private boolean _taxonomy_colorize_node_shapes = false; private TAXONOMY_EXTRACTION _taxonomy_extraction = TAXONOMY_EXTRACTION.NO; private UI _ui = UI.UNKNOWN; private boolean _use_tabbed_display = false; @@ -395,10 +394,6 @@ public final class Configuration { return _show_domain_labels; } - public boolean isTaxonomyColorizeNodeShapes() { - return _taxonomy_colorize_node_shapes; - } - public void putDisplayColors( final String key, final Color color ) { getDisplayColors().put( key, color ); } @@ -563,10 +558,6 @@ public final class Configuration { display_options[ color_according_to_species ][ 2 ] = b ? "yes" : "no"; } - public void setTaxonomyColorizeNodeShapes( final boolean taxonomy_colorize_node_shapes ) { - _taxonomy_colorize_node_shapes = taxonomy_colorize_node_shapes; - } - public void setUseBranchesWidths( final boolean b ) { display_options[ width_branches ][ 2 ] = b ? "yes" : "no"; } @@ -1427,9 +1418,6 @@ public final class Configuration { + "] for [default_node_shape]" ); } } - else if ( key.equals( "taxonomy_colorize_node_shapes" ) ) { - setTaxonomyColorizeNodeShapes( parseBoolean( ( String ) st.nextElement() ) ); - } else if ( key.equals( "midpoint_reroot" ) ) { setMidpointReroot( parseBoolean( ( String ) st.nextElement() ) ); } diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrame.java b/forester/java/src/org/forester/archaeopteryx/MainFrame.java index ee537d0..fc6bb32 100644 --- a/forester/java/src/org/forester/archaeopteryx/MainFrame.java +++ b/forester/java/src/org/forester/archaeopteryx/MainFrame.java @@ -192,7 +192,6 @@ public abstract class MainFrame extends JFrame implements ActionListener { JMenuItem _cycle_node_shape_mi; JMenuItem _cycle_node_fill_mi; JMenuItem _choose_node_size_mi; - JCheckBoxMenuItem _taxonomy_colorize_node_shapes_cbmi; JCheckBoxMenuItem _show_confidence_stddev_cbmi; // _ print JCheckBoxMenuItem _graphics_export_visible_only_cbmi; @@ -407,9 +406,6 @@ public abstract class MainFrame extends JFrame implements ActionListener { else if ( o == _show_default_node_shapes_external_cbmi ) { updateOptions( getOptions() ); } - else if ( o == _taxonomy_colorize_node_shapes_cbmi ) { - updateOptions( getOptions() ); - } else if ( o == _non_lined_up_cladograms_rbmi ) { updateOptions( getOptions() ); showWhole(); @@ -1283,8 +1279,6 @@ public abstract class MainFrame extends JFrame implements ActionListener { && _show_default_node_shapes_internal_cbmi.isSelected() ); options.setShowDefaultNodeShapesExternal( ( _show_default_node_shapes_external_cbmi != null ) && _show_default_node_shapes_external_cbmi.isSelected() ); - options.setTaxonomyColorizeNodeShapes( ( _taxonomy_colorize_node_shapes_cbmi != null ) - && _taxonomy_colorize_node_shapes_cbmi.isSelected() ); if ( ( _non_lined_up_cladograms_rbmi != null ) && ( _non_lined_up_cladograms_rbmi.isSelected() ) ) { options.setCladogramType( CLADOGRAM_TYPE.NON_LINED_UP ); } diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java index a5cd07d..1fd72c4 100644 --- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java +++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplet.java @@ -225,8 +225,6 @@ public final class MainFrameApplet extends MainFrame { _options_jmenu .add( _color_by_taxonomic_group_cbmi = new JCheckBoxMenuItem( MainFrame.COLOR_BY_TAXONOMIC_GROUP ) ); _options_jmenu - .add( _taxonomy_colorize_node_shapes_cbmi = new JCheckBoxMenuItem( MainFrame.TAXONOMY_COLORIZE_NODE_SHAPES_LABEL ) ); - _options_jmenu .add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( MainFrame.COLOR_LABELS_LABEL ) ); _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP ); _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( MainFrame.ABBREV_SN_LABEL ) ); @@ -257,7 +255,6 @@ public final class MainFrameApplet extends MainFrame { .isShowDefaultNodeShapesInternal() ); customizeCheckBoxMenuItem( _show_default_node_shapes_external_cbmi, getOptions() .isShowDefaultNodeShapesExternal() ); - customizeCheckBoxMenuItem( _taxonomy_colorize_node_shapes_cbmi, getOptions().isTaxonomyColorizeNodeShapes() ); customizeJMenuItem( _cycle_node_shape_mi ); customizeJMenuItem( _cycle_node_fill_mi ); customizeJMenuItem( _choose_node_size_mi ); diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java index c146900..218160f 100644 --- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java +++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java @@ -899,8 +899,6 @@ public final class MainFrameApplication extends MainFrame { _options_jmenu.add( _show_annotation_ref_source = new JCheckBoxMenuItem( SHOW_ANN_REF_SOURCE_LABEL ) ); _options_jmenu.add( _show_confidence_stddev_cbmi = new JCheckBoxMenuItem( SHOW_CONF_STDDEV_LABEL ) ); _options_jmenu.add( _color_by_taxonomic_group_cbmi = new JCheckBoxMenuItem( COLOR_BY_TAXONOMIC_GROUP ) ); - _options_jmenu - .add( _taxonomy_colorize_node_shapes_cbmi = new JCheckBoxMenuItem( MainFrame.TAXONOMY_COLORIZE_NODE_SHAPES_LABEL ) ); _options_jmenu.add( _color_labels_same_as_parent_branch = new JCheckBoxMenuItem( COLOR_LABELS_LABEL ) ); _color_labels_same_as_parent_branch.setToolTipText( MainFrame.COLOR_LABELS_TIP ); _options_jmenu.add( _abbreviate_scientific_names = new JCheckBoxMenuItem( ABBREV_SN_LABEL ) ); @@ -976,7 +974,6 @@ public final class MainFrameApplication extends MainFrame { .isShowDefaultNodeShapesExternal() ); customizeCheckBoxMenuItem( _show_default_node_shapes_internal_cbmi, getOptions() .isShowDefaultNodeShapesInternal() ); - customizeCheckBoxMenuItem( _taxonomy_colorize_node_shapes_cbmi, getOptions().isTaxonomyColorizeNodeShapes() ); customizeJMenuItem( _cycle_node_shape_mi ); customizeJMenuItem( _cycle_node_fill_mi ); customizeJMenuItem( _choose_node_size_mi ); diff --git a/forester/java/src/org/forester/archaeopteryx/Options.java b/forester/java/src/org/forester/archaeopteryx/Options.java index 4f92653..a4c15b3 100644 --- a/forester/java/src/org/forester/archaeopteryx/Options.java +++ b/forester/java/src/org/forester/archaeopteryx/Options.java @@ -79,7 +79,6 @@ final public class Options { private NodeVisualization.NodeShape _default_node_shape; private NodeVisualization.NodeFill _default_node_fill; private short _default_node_shape_size; - private boolean _taxonomy_colorize_node_shapes; private boolean _show_default_node_shapes_internal; private boolean _show_default_node_shapes_external; private boolean _show_confidence_stddev; @@ -282,10 +281,6 @@ final public class Options { return _show_scale; } - boolean isTaxonomyColorizeNodeShapes() { - return _taxonomy_colorize_node_shapes; - } - final void setAbbreviateScientificTaxonNames( final boolean abbreviate_scientific_names ) { _abbreviate_scientific_names = abbreviate_scientific_names; } @@ -428,10 +423,6 @@ final public class Options { _show_scale = show_scale; } - void setTaxonomyColorizeNodeShapes( final boolean taxonomy_colorize_node_shapes ) { - _taxonomy_colorize_node_shapes = taxonomy_colorize_node_shapes; - } - final void setTaxonomyExtraction( final TAXONOMY_EXTRACTION taxonomy_extraction ) { _taxonomy_extraction = taxonomy_extraction; } @@ -440,7 +431,6 @@ final public class Options { _default_node_shape = NodeShape.CIRCLE; _default_node_fill = NodeFill.GRADIENT; _default_node_shape_size = Constants.DEFAULT_NODE_SHAPE_SIZE_DEFAULT; - _taxonomy_colorize_node_shapes = false; _show_branch_length_values = false; _internal_number_are_confidence_for_nh_parsing = false; _show_scale = false; @@ -553,7 +543,6 @@ final public class Options { if ( configuration.getDefaultNodeShapeSize() >= 0 ) { instance.setDefaultNodeShapeSize( configuration.getDefaultNodeShapeSize() ); } - instance.setTaxonomyColorizeNodeShapes( configuration.isTaxonomyColorizeNodeShapes() ); instance.setShowDefaultNodeShapesInternal( configuration.isShowDefaultNodeShapesInternal() ); instance.setShowDefaultNodeShapesExternal( configuration.isShowDefaultNodeShapesExternal() ); if ( configuration.getExtDescNodeDataToReturn() != null ) { diff --git a/forester/java/src/org/forester/archaeopteryx/TreePanel.java b/forester/java/src/org/forester/archaeopteryx/TreePanel.java index 7301784..e5510da 100644 --- a/forester/java/src/org/forester/archaeopteryx/TreePanel.java +++ b/forester/java/src/org/forester/archaeopteryx/TreePanel.java @@ -168,6 +168,8 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee 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 _nodeid_dist_to_leaf = new HashMap(); final private Arc2D _arc = new Arc2D.Double(); private AffineTransform _at; @@ -1461,17 +1463,10 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee root_x + ( Math.cos( angle ) * parent_radius ), root_y + ( Math.sin( angle ) * parent_radius ), g ); - if ( ( isInFoundNodes0( c ) && !isInFoundNodes1( c ) ) || isInCurrentExternalNodes( c ) ) { - g.setColor( getTreeColorSet().getFoundColor0() ); - drawRectFilled( c.getXSecondary() - 1, c.getYSecondary() - 1, 3, 3, g ); - } - else if ( ( isInFoundNodes1( c ) && !isInFoundNodes0( c ) ) ) { - g.setColor( getTreeColorSet().getFoundColor1() ); - drawRectFilled( c.getXSecondary() - 1, c.getYSecondary() - 1, 3, 3, g ); - } - else if ( isInFoundNodes0( c ) && isInFoundNodes1( c ) ) { - g.setColor( getTreeColorSet().getFoundColor0and1() ); - drawRectFilled( c.getXSecondary() - 1, c.getYSecondary() - 1, 3, 3, g ); + if ( isInFoundNodes( c ) || isInCurrentExternalNodes( c ) ) { + g.setColor( getColorForFoundNode( c ) ); + drawRectFilled( c.getXSecondary() - OVERVIEW_FOUND_NODE_BOX_SIZE_HALF, c.getYSecondary() + - OVERVIEW_FOUND_NODE_BOX_SIZE_HALF, OVERVIEW_FOUND_NODE_BOX_SIZE, OVERVIEW_FOUND_NODE_BOX_SIZE, g ); } } @@ -3897,17 +3892,6 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } } - final private void paintFoundNode( final PhylogenyNode n, final double x, final double y, final Graphics2D g ) { - final int box_size = getOptions().getDefaultNodeShapeSize(); - final double half_box_size = getOptions().getDefaultNodeShapeSize() / 2.0; - g.setColor( getColorForFoundNode( n ) ); - //g.fillRect( x - half_box_size, y - half_box_size, box_size, box_size ); - //TODO check me - //FIXME - _rectangle.setRect( x - half_box_size, y - half_box_size, box_size, box_size ); - g.fill( _rectangle ); - } - final private void paintGainedAndLostCharacters( final Graphics2D g, final PhylogenyNode node, final String gained, @@ -3957,14 +3941,22 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee drawOval( x - 9, y - 8, 17, 17, g ); drawOval( x - 9, y - 9, 18, 18, g ); } - if ( isInFoundNodes( node ) || isInCurrentExternalNodes( node ) ) { - paintFoundNode( node, x, y, g ); - } - else { + if ( ( isInFoundNodes( node ) || isInCurrentExternalNodes( node ) ) + || ( getOptions().isShowDefaultNodeShapesExternal() && node.isExternal() ) + || ( getOptions().isShowDefaultNodeShapesInternal() && node.isInternal() ) + || ( 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; 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 ( getControlPanel().isEvents() && TreePanelUtil.isHasAssignedEvent( node ) ) { final Event event = node.getNodeData().getEvent(); if ( event.isDuplication() ) { @@ -3977,79 +3969,58 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee outline_color = getTreeColorSet().getDuplicationOrSpeciationColor(); } } - else if ( getOptions().isTaxonomyColorizeNodeShapes() ) { - outline_color = getTaxonomyBasedColor( node ); - } else { 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().isShowDefaultNodeShapesExternal() && node.isExternal() ) - || ( getOptions().isShowDefaultNodeShapesInternal() && node.isInternal() ) - || ( 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 ); - } + 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().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() == NodeFill.NONE ) { + Color background = getBackground(); + if ( to_pdf ) { + background = Color.WHITE; } - 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 ); + 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 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 ); } } } @@ -4443,7 +4414,8 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } if ( isInFoundNodes( node ) || isInCurrentExternalNodes( node ) ) { g.setColor( getColorForFoundNode( node ) ); - drawRectFilled( node.getXSecondary() - 1, node.getYSecondary() - 1, 3, 3, g ); + drawRectFilled( node.getXSecondary() - OVERVIEW_FOUND_NODE_BOX_SIZE_HALF, node.getYSecondary() + - OVERVIEW_FOUND_NODE_BOX_SIZE_HALF, OVERVIEW_FOUND_NODE_BOX_SIZE, OVERVIEW_FOUND_NODE_BOX_SIZE, g ); } float new_x = 0; if ( !node.isExternal() && !node.isCollapse() ) { @@ -5016,7 +4988,11 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee desc.setYSecondary( new_y ); if ( isInFoundNodes( desc ) || isInCurrentExternalNodes( desc ) ) { g.setColor( getColorForFoundNode( desc ) ); - drawRectFilled( desc.getXSecondary() - 1, desc.getYSecondary() - 1, 3, 3, g ); + drawRectFilled( desc.getXSecondary() - OVERVIEW_FOUND_NODE_BOX_SIZE_HALF, + desc.getYSecondary() - OVERVIEW_FOUND_NODE_BOX_SIZE_HALF, + OVERVIEW_FOUND_NODE_BOX_SIZE, + OVERVIEW_FOUND_NODE_BOX_SIZE, + g ); g.setColor( getTreeColorSet().getOvColor() ); } paintUnrootedLite( desc, current_angle, current_angle + arc_size, g, urt_ov_factor ); -- 1.7.10.2