import org.forester.phylogeny.data.Confidence;
import org.forester.phylogeny.data.Event;
import org.forester.phylogeny.data.NodeData.NODE_DATA;
-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.NodeVisualData;
+import org.forester.phylogeny.data.NodeVisualData.FontType;
+import org.forester.phylogeny.data.NodeVisualData.NodeFill;
+import org.forester.phylogeny.data.NodeVisualData.NodeShape;
import org.forester.phylogeny.data.PhylogenyDataUtil;
import org.forester.phylogeny.data.PropertiesMap;
import org.forester.phylogeny.data.Property;
public final class TreePanel extends JPanel implements ActionListener, MouseWheelListener, Printable {
- private static final BasicStroke STROKE_2 = new BasicStroke( 2f );
- private static final BasicStroke STROKE_1 = new BasicStroke( 1f );
- private static final BasicStroke STROKE_075 = new BasicStroke( 0.75f );
- private static final BasicStroke STROKE_05 = new BasicStroke( 0.5f );
- private static final BasicStroke STROKE_025 = new BasicStroke( 0.25f );
- private static final BasicStroke STROKE_01 = new BasicStroke( 0.1f );
- private static final BasicStroke STROKE_005 = new BasicStroke( 0.05f );
- private static final float PI = ( float ) ( Math.PI );
- private static final double TWO_PI = 2 * Math.PI;
- private static final float ONEHALF_PI = ( float ) ( 1.5 * Math.PI );
- private static final float HALF_PI = ( float ) ( Math.PI / 2.0 );
- private static final float ANGLE_ROTATION_UNIT = ( float ) ( Math.PI / 32 );
- private static final short OV_BORDER = 10;
- final static Cursor CUT_CURSOR = Cursor.getPredefinedCursor( Cursor.CROSSHAIR_CURSOR );
- final static Cursor MOVE_CURSOR = Cursor.getPredefinedCursor( Cursor.MOVE_CURSOR );
final static Cursor ARROW_CURSOR = Cursor.getPredefinedCursor( Cursor.DEFAULT_CURSOR );
+ final static Cursor CUT_CURSOR = Cursor.getPredefinedCursor( Cursor.CROSSHAIR_CURSOR );
final static Cursor HAND_CURSOR = Cursor.getPredefinedCursor( Cursor.HAND_CURSOR );
+ final static Cursor MOVE_CURSOR = Cursor.getPredefinedCursor( Cursor.MOVE_CURSOR );
final static Cursor WAIT_CURSOR = Cursor.getPredefinedCursor( Cursor.WAIT_CURSOR );
- private final static long serialVersionUID = -978349745916505029L;
+ final private static double _180_OVER_PI = 180.0 / Math.PI;
+ private static final float ANGLE_ROTATION_UNIT = ( float ) ( Math.PI / 32 );
+ private final static int CONFIDENCE_LEFT_MARGIN = 4;
private final static int EURO_D = 10;
- private final static String NODE_POPMENU_NODE_CLIENT_PROPERTY = "node";
- private final static int MIN_ROOT_LENGTH = 3;
- private final static int MAX_SUBTREES = 100;
+ private final static NumberFormat FORMATTER_BRANCH_LENGTH;
+ private final static NumberFormat FORMATTER_CONFIDENCE;
+ private static final float HALF_PI = ( float ) ( Math.PI / 2.0 );
+ private final static int LIMIT_FOR_HQ_RENDERING = 2000;
private final static int MAX_NODE_FRAMES = 10;
+ private final static int MAX_SUBTREES = 100;
+ private final static int MIN_ROOT_LENGTH = 3;
private final static int MOVE = 20;
- private final static NumberFormat FORMATTER_CONFIDENCE;
- private final static NumberFormat FORMATTER_BRANCH_LENGTH;
+ 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 static final float PI = ( float ) ( Math.PI );
+ final private static Font POPUP_FONT = new Font( Configuration.getDefaultFontFamilyName(),
+ Font.PLAIN,
+ 12 );
+ private static final float ROUNDED_D = 8;
+ private final static long serialVersionUID = -978349745916505029L;
+ private static final BasicStroke STROKE_005 = new BasicStroke( 0.05f );
+ private static final BasicStroke STROKE_01 = new BasicStroke( 0.1f );
+ private static final BasicStroke STROKE_025 = new BasicStroke( 0.25f );
+ private static final BasicStroke STROKE_05 = new BasicStroke( 0.5f );
+ private static final BasicStroke STROKE_075 = new BasicStroke( 0.75f );
+ private static final BasicStroke STROKE_1 = new BasicStroke( 1f );
+ 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 int LIMIT_FOR_HQ_RENDERING = 2000;
- private final static int CONFIDENCE_LEFT_MARGIN = 4;
- private final RenderingHints _rendering_hints = new RenderingHints( RenderingHints.KEY_RENDERING,
- RenderingHints.VALUE_RENDER_DEFAULT );
- private File _treefile = null;
+ 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;
+ private int _circ_max_depth;
+ final private Set<Long> _collapsed_external_nodeid_set = new HashSet<Long>();
+ private JColorChooser _color_chooser = null;
private Configuration _configuration = null;
- private final NodeFrame[] _node_frames = new NodeFrame[ TreePanel.MAX_NODE_FRAMES ];
- private int _node_frame_index = 0;
- private Phylogeny _phylogeny = null;
- private final Phylogeny[] _sub_phylogenies = new Phylogeny[ TreePanel.MAX_SUBTREES ];
- private final PhylogenyNode[] _sub_phylogenies_temp_roots = new PhylogenyNode[ TreePanel.MAX_SUBTREES ];
- private int _subtree_index = 0;
- private MainPanel _main_panel = null;
- private Set<Long> _found_nodes = null;
- private PhylogenyNode _highlight_node = null;
- private JPopupMenu _node_popup_menu = null;
- private JMenuItem _node_popup_menu_items[] = null;
- private int _longest_ext_node_info = 0;
- private float _x_correction_factor = 0.0f;
- private float _ov_x_correction_factor = 0.0f;
- private float _x_distance = 0.0f;
- private float _y_distance = 0.0f;
- private PHYLOGENY_GRAPHICS_TYPE _graphics_type = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR;
- private double _domain_structure_width = Constants.DOMAIN_STRUCTURE_DEFAULT_WIDTH;
+ private ControlPanel _control_panel = null;
+ private final CubicCurve2D _cubic_curve = new CubicCurve2D.Float();
+ private Set<Long> _current_external_nodes = null;
+ private StringBuilder _current_external_nodes_data_buffer = new StringBuilder();
+ private int _current_external_nodes_data_buffer_change_counter = 0;
private int _domain_structure_e_value_thr_exp = Constants.DOMAIN_STRUCTURE_E_VALUE_THR_DEFAULT_EXP;
+ private double _domain_structure_width = Constants.DOMAIN_STRUCTURE_DEFAULT_WIDTH;
+ private int _dynamic_hiding_factor = 0;
+ private boolean _edited = false;
+ private final Ellipse2D _ellipse = new Ellipse2D.Float();
+ private int _external_node_index = 0;
+ private Set<Long> _found_nodes_0 = null;
+ private Set<Long> _found_nodes_1 = null;
+ private final FontRenderContext _frc = new FontRenderContext( null,
+ false,
+ false );
+ private PHYLOGENY_GRAPHICS_TYPE _graphics_type = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR;
+ private PhylogenyNode _highlight_node = null;
+ private boolean _in_ov = false;
+ private boolean _in_ov_rect = false;
private float _last_drag_point_x = 0;
private float _last_drag_point_y = 0;
- private ControlPanel _control_panel = null;
- private int _external_node_index = 0;
- private final Path2D.Float _polygon = new Path2D.Float();
- private final StringBuilder _sb = new StringBuilder();
- private JColorChooser _color_chooser = null;
- private double _scale_distance = 0.0;
- private String _scale_label = null;
- private final CubicCurve2D _cubic_curve = new CubicCurve2D.Float();
- private final QuadCurve2D _quad_curve = new QuadCurve2D.Float();
private final Line2D _line = new Line2D.Float();
- private final Ellipse2D _ellipse = new Ellipse2D.Float();
- private final Rectangle2D _rectangle = new Rectangle2D.Float();
+ private int _longest_ext_node_info = 0;
+ private MainPanel _main_panel = null;
+ private double _max_distance_to_root = -1;
+ private Popup _node_desc_popup;
+ private int _node_frame_index = 0;
+ private final NodeFrame[] _node_frames = new NodeFrame[ TreePanel.MAX_NODE_FRAMES ];
+ private JPopupMenu _node_popup_menu = null;
+ private JMenuItem _node_popup_menu_items[] = null;
+ private PhylogenyNode[] _nodes_in_preorder = null;
private Options _options = null;
- private float _ov_max_width = 0;
private float _ov_max_height = 0;
+ private float _ov_max_width = 0;
+ private boolean _ov_on = false;
+ private final Rectangle2D _ov_rectangle = new Rectangle2D.Float();
+ private final Rectangle _ov_virtual_rectangle = new Rectangle();
+ private float _ov_x_correction_factor = 0.0f;
+ private float _ov_x_distance = 0;
private int _ov_x_position = 0;
+ private float _ov_y_distance = 0;
private int _ov_y_position = 0;
private int _ov_y_start = 0;
- private float _ov_y_distance = 0;
- private float _ov_x_distance = 0;
- private boolean _ov_on = false;
- private double _urt_starting_angle = ( float ) ( Math.PI / 2 );
- private float _urt_factor = 1;
- private float _urt_factor_ov = 1;
private final boolean _phy_has_branch_lengths;
- private final Rectangle2D _ov_rectangle = new Rectangle2D.Float();
- private boolean _in_ov_rect = false;
- private boolean _in_ov = false;
- private final Rectangle _ov_virtual_rectangle = new Rectangle();
- final private static double _180_OVER_PI = 180.0 / Math.PI;
- private static final float ROUNDED_D = 8;
- private int _circ_max_depth;
- private PhylogenyNode _root;
- final private Arc2D _arc = new Arc2D.Double();
- final private HashMap<Long, Double> _urt_nodeid_angle_map = new HashMap<Long, Double>();
- final private HashMap<Long, Integer> _urt_nodeid_index_map = new HashMap<Long, Integer>();
- final private Set<Long> _collapsed_external_nodeid_set = new HashSet<Long>();
- HashMap<Long, Short> _nodeid_dist_to_leaf = new HashMap<Long, Short>();
- private AffineTransform _at;
- private double _max_distance_to_root = -1;
- private int _dynamic_hiding_factor = 0;
- private boolean _edited = false;
- private Popup _node_desc_popup;
- private JTextArea _rollover_popup;
+ private Phylogeny _phylogeny = null;
+ private final Path2D.Float _polygon = new Path2D.Float();
private final StringBuffer _popup_buffer = new StringBuffer();
- final private static Font POPUP_FONT = new Font( Configuration.getDefaultFontFamilyName(),
- Font.PLAIN,
- 12 );
+ private final QuadCurve2D _quad_curve = new QuadCurve2D.Float();
private Sequence _query_sequence = null;
- private final FontRenderContext _frc = new FontRenderContext( null,
- false,
- false );
+ private final Rectangle2D _rectangle = new Rectangle2D.Float();
+ private final RenderingHints _rendering_hints = new RenderingHints( RenderingHints.KEY_RENDERING,
+ RenderingHints.VALUE_RENDER_DEFAULT );
+ private JTextArea _rollover_popup;
+ private PhylogenyNode _root;
+ private final StringBuilder _sb = new StringBuilder();
+ private double _scale_distance = 0.0;
+ private String _scale_label = null;
// expression values menu:
private DescriptiveStatistics _statistics_for_vector_data;
- private PhylogenyNode[] _nodes_in_preorder = null;
- private StringBuilder _current_external_nodes_data_buffer = new StringBuilder();
- private int _current_external_nodes_data_buffer_change_counter = 0;
- private Set<Long> _current_external_nodes = null;
+ private final Phylogeny[] _sub_phylogenies = new Phylogeny[ TreePanel.MAX_SUBTREES ];
+ private final PhylogenyNode[] _sub_phylogenies_temp_roots = new PhylogenyNode[ TreePanel.MAX_SUBTREES ];
+ private int _subtree_index = 0;
+ private File _treefile = null;
+ private float _urt_factor = 1;
+ private float _urt_factor_ov = 1;
+ final private HashMap<Long, Double> _urt_nodeid_angle_map = new HashMap<Long, Double>();
+ final private HashMap<Long, Integer> _urt_nodeid_index_map = new HashMap<Long, Integer>();
+ private double _urt_starting_angle = ( float ) ( Math.PI / 2 );
+ private float _x_correction_factor = 0.0f;
+ private float _x_distance = 0.0f;
+ private float _y_distance = 0.0f;
// private Image offscreenImage;
// private Graphics offscreenGraphics;
// private Dimension offscreenDimension;
}
final Color calculateTaxonomyBasedColor( final Taxonomy tax ) {
- if ( getOptions().isColorByTaxonomicGroup() && !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
- boolean ex = false;
- String group = null;
- try {
- group = TaxonomyUtil.getTaxGroupByTaxCode( tax.getTaxonomyCode() );
- }
- catch ( final Exception e ) {
- ex = true;
- }
- if ( !ex && !ForesterUtil.isEmpty( group ) ) {
- final Color c = ForesterUtil.obtainColorDependingOnTaxonomyGroup( group );
- if ( c != null ) {
- return c;
+ if ( getOptions().isColorByTaxonomicGroup() ) {
+ if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
+ boolean ex = false;
+ String group = null;
+ try {
+ group = TaxonomyUtil.getTaxGroupByTaxCode( tax.getTaxonomyCode() );
+ }
+ catch ( final Exception e ) {
+ ex = true;
+ }
+ if ( !ex && !ForesterUtil.isEmpty( group ) ) {
+ final Color c = ForesterUtil.obtainColorDependingOnTaxonomyGroup( group );
+ if ( c != null ) {
+ return c;
+ }
}
}
return getTreeColorSet().getTaxonomyColor();
return _domain_structure_e_value_thr_exp;
}
- final Set<Long> getFoundNodes() {
- return _found_nodes;
+ final Set<Long> getFoundNodes0() {
+ return _found_nodes_0;
+ }
+
+ final Set<Long> getFoundNodes1() {
+ return _found_nodes_1;
}
final Color getGraphicsForNodeBoxWithColorForParentBranch( final PhylogenyNode node ) {
// Check if shift key is down
if ( ( e.getModifiers() & InputEvent.SHIFT_MASK ) != 0 ) {
// Yes, so add to _found_nodes
- if ( getFoundNodes() == null ) {
- setFoundNodes( new HashSet<Long>() );
+ if ( getFoundNodes0() == null ) {
+ setFoundNodes0( new HashSet<Long>() );
}
- getFoundNodes().add( node.getId() );
+ getFoundNodes0().add( node.getId() );
// Check if control key is down
}
else if ( ( e.getModifiers() & InputEvent.CTRL_MASK ) != 0 ) {
root_x + ( Math.cos( angle ) * parent_radius ),
root_y + ( Math.sin( angle ) * parent_radius ),
g );
- paintNodeBox( c.getXcoord(), c.getYcoord(), c, g, to_pdf, to_graphics_file, isInFoundNodes( c )
- || isInCurrentExternalNodes( c ) );
+ paintNodeBox( c.getXcoord(), c.getYcoord(), c, g, to_pdf, to_graphics_file );
if ( c.isExternal() ) {
- final boolean is_in_found_nodes = isInFoundNodes( c ) || isInCurrentExternalNodes( c );
+ final boolean is_in_found_nodes = isInFoundNodes0( c ) || isInFoundNodes1( c )
+ || isInCurrentExternalNodes( c );
if ( ( _dynamic_hiding_factor > 1 ) && !is_in_found_nodes
&& ( ( _urt_nodeid_index_map.get( c.getId() ) % _dynamic_hiding_factor ) != 1 ) ) {
return;
root_y + ( Math.sin( angle ) * parent_radius ),
g );
if ( isInFoundNodes( c ) || isInCurrentExternalNodes( c ) ) {
- g.setColor( getTreeColorSet().getFoundColor() );
- drawRectFilled( c.getXSecondary() - 1, c.getYSecondary() - 1, 3, 3, g );
+ 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 );
}
}
}
}
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 ) );
+ paintNodeBox( _root.getXcoord(), _root.getYcoord(), _root, g, to_pdf, to_graphics_file );
}
final void paintCircularLite( final Phylogeny phy,
}
final void selectNode( final PhylogenyNode node ) {
- if ( ( getFoundNodes() != null ) && getFoundNodes().contains( node.getId() ) ) {
- getFoundNodes().remove( node.getId() );
- getControlPanel().setSearchFoundCountsOnLabel( getFoundNodes().size() );
- if ( getFoundNodes().size() < 1 ) {
- getControlPanel().searchReset();
+ if ( ( getFoundNodes0() != null ) && getFoundNodes0().contains( node.getId() ) ) {
+ getFoundNodes0().remove( node.getId() );
+ getControlPanel().setSearchFoundCountsOnLabel0( getFoundNodes0().size() );
+ if ( getFoundNodes0().size() < 1 ) {
+ getControlPanel().searchReset0();
}
}
else {
- getControlPanel().getSearchFoundCountsLabel().setVisible( true );
- getControlPanel().getSearchResetButton().setEnabled( true );
- getControlPanel().getSearchResetButton().setVisible( true );
- if ( getFoundNodes() == null ) {
- setFoundNodes( new HashSet<Long>() );
+ getControlPanel().getSearchFoundCountsLabel0().setVisible( true );
+ getControlPanel().getSearchResetButton0().setEnabled( true );
+ getControlPanel().getSearchResetButton0().setVisible( true );
+ if ( getFoundNodes0() == null ) {
+ setFoundNodes0( new HashSet<Long>() );
}
- getFoundNodes().add( node.getId() );
- getControlPanel().setSearchFoundCountsOnLabel( getFoundNodes().size() );
+ getFoundNodes0().add( node.getId() );
+ getControlPanel().setSearchFoundCountsOnLabel0( getFoundNodes0().size() );
}
}
_current_external_nodes_data_buffer = sb;
}
- final void setFoundNodes( final Set<Long> found_nodes ) {
- _found_nodes = found_nodes;
+ final void setFoundNodes0( final Set<Long> found_nodes ) {
+ _found_nodes_0 = found_nodes;
+ }
+
+ final void setFoundNodes1( final Set<Long> found_nodes ) {
+ _found_nodes_1 = found_nodes;
}
final void setInOvRect( final boolean in_ov_rect ) {
&& ( getCopiedAndPastedNodes() != null )
&& !to_pdf
&& !to_graphics_file && getCopiedAndPastedNodes().contains( node.getId() ) ) {
- g.setColor( getTreeColorSet().getFoundColor() );
+ g.setColor( getTreeColorSet().getFoundColor0() );
}
else if ( getControlPanel().isColorBranches() && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
g.setColor( PhylogenyMethods.getBranchColorValue( node ) );
repaint();
}
+ final private void colorizeNodes( final Color c,
+ final PhylogenyNode node,
+ final List<PhylogenyNode> additional_nodes ) {
+ _control_panel.setColorBranches( true );
+ if ( _control_panel.getColorBranchesCb() != null ) {
+ _control_panel.getColorBranchesCb().setSelected( true );
+ }
+ if ( node != null ) {
+ colorizeNodesHelper( c, node );
+ }
+ if ( additional_nodes != null ) {
+ for( final PhylogenyNode n : additional_nodes ) {
+ colorizeNodesHelper( c, n );
+ }
+ }
+ repaint();
+ }
+
+ private final static void colorizeNodesHelper( final Color c, final PhylogenyNode node ) {
+ NodeVisualData v;
+ if ( node.getNodeData().getNodeVisualData() != null ) {
+ v = node.getNodeData().getNodeVisualData();
+ }
+ else {
+ v = new NodeVisualData();
+ }
+ v.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,
}
_color_chooser.setPreviewPanel( new JPanel() );
SubtreeColorizationActionListener al;
- if ( ( getFoundNodes() != null ) && !getFoundNodes().isEmpty() ) {
- final List<PhylogenyNode> additional_nodes = getFoundNodesAsListOfPhylogenyNodes();
+ if ( ( getFoundNodes0() != null ) && !getFoundNodes0().isEmpty() ) {
+ final List<PhylogenyNode> additional_nodes = getFoundNodes0AsListOfPhylogenyNodes();
al = new SubtreeColorizationActionListener( _color_chooser, node, additional_nodes );
}
else {
dialog.setVisible( true );
}
- private List<PhylogenyNode> getFoundNodesAsListOfPhylogenyNodes() {
- final List<PhylogenyNode> additional_nodes = new ArrayList<PhylogenyNode>();
- for( final Long id : getFoundNodes() ) {
- additional_nodes.add( _phylogeny.getNode( id ) );
+ private void colorNodeFont( final PhylogenyNode node ) {
+ _color_chooser.setPreviewPanel( new JPanel() );
+ NodeColorizationActionListener al;
+ if ( ( getFoundNodes0() != null ) && !getFoundNodes0().isEmpty() ) {
+ final List<PhylogenyNode> additional_nodes = getFoundNodes0AsListOfPhylogenyNodes();
+ al = new NodeColorizationActionListener( _color_chooser, node, additional_nodes );
+ }
+ else {
+ al = new NodeColorizationActionListener( _color_chooser, node );
+ }
+ final JDialog dialog = JColorChooser
+ .createDialog( this, "Subtree colorization", true, _color_chooser, al, null );
+ 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().getFontObject();
+ }
+ if ( f != null ) {
+ fc.setFont( f );
+ }
+ else {
+ fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() );
+ }
+ fc.showDialog( this, "Select Font" );
+ if ( fc.getFont() != null ) {
+ NodeVisualData v = node.getNodeData().getNodeVisualData();
+ Font ff = fc.getFont();
+ v.setFont( ff.getFamily() );
+ v.setFontSize( ( byte ) ( ff.getSize() ) );
+ if ( ff.getStyle() == Font.BOLD && ff.getStyle() == Font.ITALIC ) {
+ v.setFontType( FontType.BOLD_ITALIC );
+ }
+ else if ( ff.getStyle() == Font.ITALIC ) {
+ v.setFontType( FontType.ITALIC );
+ }
+ else if ( ff.getStyle() == Font.BOLD ) {
+ v.setFontType( FontType.BOLD );
+ }
+ else {
+ v.setFontType( FontType.NORMAL );
+ }
}
- return additional_nodes;
}
final private void copySubtree( final PhylogenyNode node ) {
JOptionPane.ERROR_MESSAGE );
}
+ private final Color getColorForFoundNode( final PhylogenyNode n ) {
+ if ( isInCurrentExternalNodes( n ) ) {
+ return getTreeColorSet().getFoundColor0();
+ }
+ else if ( isInFoundNodes0( n ) && !isInFoundNodes1( n ) ) {
+ return getTreeColorSet().getFoundColor0();
+ }
+ else if ( !isInFoundNodes0( n ) && isInFoundNodes1( n ) ) {
+ return getTreeColorSet().getFoundColor1();
+ }
+ else {
+ return getTreeColorSet().getFoundColor0and1();
+ }
+ }
+
final private Set<Long> getCopiedAndPastedNodes() {
return getMainPanel().getCopiedAndPastedNodes();
}
return getMainPanel().getCutOrCopiedTree();
}
+ private List<PhylogenyNode> getFoundNodes0AsListOfPhylogenyNodes() {
+ final List<PhylogenyNode> additional_nodes = new ArrayList<PhylogenyNode>();
+ for( final Long id : getFoundNodes0() ) {
+ additional_nodes.add( _phylogeny.getNode( id ) );
+ }
+ return additional_nodes;
+ }
+
+ private List<PhylogenyNode> getFoundNodes1AsListOfPhylogenyNodes() {
+ final List<PhylogenyNode> additional_nodes = new ArrayList<PhylogenyNode>();
+ for( final Long id : getFoundNodes1() ) {
+ additional_nodes.add( _phylogeny.getNode( id ) );
+ }
+ return additional_nodes;
+ }
+
final private float getLastDragPointX() {
return _last_drag_point_x;
}
return _ov_y_start;
}
+ final private List<Accession> getPdbAccs( final PhylogenyNode node ) {
+ final List<Accession> pdb_ids = new ArrayList<Accession>();
+ if ( node.getNodeData().isHasSequence() ) {
+ final Sequence seq = node.getNodeData().getSequence();
+ if ( !ForesterUtil.isEmpty( seq.getCrossReferences() ) ) {
+ final SortedSet<Accession> cross_refs = seq.getCrossReferences();
+ for( final Accession acc : cross_refs ) {
+ if ( acc.getSource().equalsIgnoreCase( "pdb" ) ) {
+ pdb_ids.add( acc );
+ }
+ }
+ }
+ }
+ return pdb_ids;
+ }
+
final private double getScaleDistance() {
return _scale_distance;
}
case COLOR_SUBTREE:
colorSubtree( node );
break;
+ case COLOR_NODE_FONT:
+ colorNodeFont( node );
+ break;
+ case CHANGE_NODE_FONT:
+ changeNodeFont( node );
+ break;
case OPEN_SEQ_WEB:
openSeqWeb( node );
break;
return null;
}
- final private List<Accession> getPdbAccs( final PhylogenyNode node ) {
- final List<Accession> pdb_ids = new ArrayList<Accession>();
- if ( node.getNodeData().isHasSequence() ) {
- final Sequence seq = node.getNodeData().getSequence();
- if ( !ForesterUtil.isEmpty( seq.getCrossReferences() ) ) {
- final SortedSet<Accession> cross_refs = seq.getCrossReferences();
- for( final Accession acc : cross_refs ) {
- if ( acc.getSource().equalsIgnoreCase( "pdb" ) ) {
- pdb_ids.add( acc );
- }
- }
- }
- }
- return pdb_ids;
- }
-
final private boolean isCanOpenTaxWeb( final PhylogenyNode node ) {
if ( node.getNodeData().isHasTaxonomy()
&& ( ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getScientificName() ) )
return ( ( getCurrentExternalNodes() != null ) && getCurrentExternalNodes().contains( node.getId() ) );
}
- final private boolean isInFoundNodes( final PhylogenyNode node ) {
- return ( ( getFoundNodes() != null ) && getFoundNodes().contains( node.getId() ) );
+ private boolean isInFoundNodes( final PhylogenyNode n ) {
+ return isInFoundNodes0( n ) || isInFoundNodes1( n );
+ }
+
+ final private boolean isInFoundNodes0( final PhylogenyNode node ) {
+ return ( ( getFoundNodes0() != null ) && getFoundNodes0().contains( node.getId() ) );
+ }
+
+ final private boolean isInFoundNodes1( final PhylogenyNode node ) {
+ return ( ( getFoundNodes1() != null ) && getFoundNodes1().contains( node.getId() ) );
}
final private boolean isInOv() {
}
}
- final private void openSeqWeb( final PhylogenyNode node ) {
- if ( ForesterUtil.isEmpty( isCanOpenSeqWeb( node ) ) ) {
- cannotOpenBrowserWarningMessage( "sequence" );
- return;
- }
- final String uri_str = TreePanelUtil.createUriForSeqWeb( node, getConfiguration(), this );
- if ( !ForesterUtil.isEmpty( uri_str ) ) {
- try {
- AptxUtil.launchWebBrowser( new URI( uri_str ),
- isApplet(),
- isApplet() ? obtainApplet() : null,
- "_aptx_seq" );
- }
- catch ( final IOException e ) {
- AptxUtil.showErrorMessage( this, e.toString() );
- e.printStackTrace();
- }
- catch ( final URISyntaxException e ) {
- AptxUtil.showErrorMessage( this, e.toString() );
- e.printStackTrace();
- }
- }
- else {
- cannotOpenBrowserWarningMessage( "sequence" );
- }
- }
-
final private void openPdbWeb( final PhylogenyNode node ) {
final List<Accession> pdb_ids = getPdbAccs( node );
if ( ForesterUtil.isEmpty( pdb_ids ) ) {
}
}
+ final private void openSeqWeb( final PhylogenyNode node ) {
+ if ( ForesterUtil.isEmpty( isCanOpenSeqWeb( node ) ) ) {
+ cannotOpenBrowserWarningMessage( "sequence" );
+ return;
+ }
+ final String uri_str = TreePanelUtil.createUriForSeqWeb( node, getConfiguration(), this );
+ if ( !ForesterUtil.isEmpty( uri_str ) ) {
+ try {
+ AptxUtil.launchWebBrowser( new URI( uri_str ),
+ isApplet(),
+ isApplet() ? obtainApplet() : null,
+ "_aptx_seq" );
+ }
+ catch ( final IOException e ) {
+ AptxUtil.showErrorMessage( this, e.toString() );
+ e.printStackTrace();
+ }
+ catch ( final URISyntaxException e ) {
+ AptxUtil.showErrorMessage( this, e.toString() );
+ e.printStackTrace();
+ }
+ }
+ else {
+ cannotOpenBrowserWarningMessage( "sequence" );
+ }
+ }
+
final private void openTaxWeb( final PhylogenyNode node ) {
if ( !isCanOpenTaxWeb( node ) ) {
cannotOpenBrowserWarningMessage( "taxonomic" );
}
}
if ( node.isExternal() ) {
- paintNodeBox( x2, y2, node, g, to_pdf, to_graphics_file, isInFoundNodes( node )
- || isInCurrentExternalNodes( node ) );
+ paintNodeBox( x2, y2, node, g, to_pdf, to_graphics_file );
}
}
c = Color.BLACK;
}
else if ( is_in_found_nodes ) {
- c = getTreeColorSet().getFoundColor();
+ c = getColorForFoundNode( node );
}
else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
c = getTaxonomyBasedColor( node );
_polygon.lineTo( node.getXcoord() + 1, node.getYcoord() - d );
_polygon.lineTo( node.getXcoord() + 1, node.getYcoord() + d );
_polygon.closePath();
- if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.SOLID ) {
+ if ( getOptions().getDefaultNodeFill() == NodeVisualData.NodeFill.SOLID ) {
g.setColor( c );
g.fill( _polygon );
}
- else if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.NONE ) {
+ else if ( getOptions().getDefaultNodeFill() == NodeVisualData.NodeFill.NONE ) {
g.setColor( getBackground() );
g.fill( _polygon );
g.setColor( c );
}
}
- 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 );
- }
-
final private void paintGainedAndLostCharacters( final Graphics2D g,
final PhylogenyNode node,
final String gained,
final PhylogenyNode node,
final Graphics2D g,
final boolean to_pdf,
- final boolean to_graphics_file,
- final boolean is_in_found_nodes ) {
+ final boolean to_graphics_file ) {
if ( node.isCollapse() ) {
return;
}
// if this node should be highlighted, do so
if ( ( _highlight_node == node ) && !to_pdf && !to_graphics_file ) {
- g.setColor( getTreeColorSet().getFoundColor() );
+ g.setColor( getTreeColorSet().getFoundColor0() );
drawOval( x - 8, y - 8, 16, 16, g );
drawOval( x - 9, y - 8, 17, 17, g );
drawOval( x - 9, y - 9, 18, 18, g );
}
- if ( is_in_found_nodes ) {
- paintFoundNode( ForesterUtil.roundToInt( x ), ForesterUtil.roundToInt( 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() ) {
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() == NodeFill.NONE ) {
+ Color background = getBackground();
+ if ( to_pdf ) {
+ background = Color.WHITE;
}
- 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 );
+ drawOvalGradient( x - half_box_size,
+ y - half_box_size,
+ box_size,
+ box_size,
+ g,
+ background,
+ background,
+ outline_color );
+ }
+ else if ( getOptions().getDefaultNodeFill() == NodeVisualData.NodeFill.SOLID ) {
+ 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 ) {
+ 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 ) {
+ 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() == NodeVisualData.NodeFill.SOLID ) {
+ g.setColor( outline_color );
+ drawRectFilled( x - half_box_size, y - half_box_size, box_size, box_size, g );
}
}
}
g.setColor( Color.BLACK );
}
else if ( is_in_found_nodes ) {
- g.setColor( getTreeColorSet().getFoundColor() );
+ g.setColor( getColorForFoundNode( node ) );
}
else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
g.setColor( getTaxonomyBasedColor( node ) );
g.setColor( Color.BLACK );
}
else if ( is_in_found_nodes ) {
- g.setColor( getTreeColorSet().getFoundColor() );
+ g.setColor( getColorForFoundNode( node ) );
}
else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
g.setColor( getTaxonomyBasedColor( node ) );
return;
}
if ( isInFoundNodes( node ) || isInCurrentExternalNodes( node ) ) {
- g.setColor( getTreeColorSet().getFoundColor() );
- drawRectFilled( node.getXSecondary() - 1, node.getYSecondary() - 1, 3, 3, g );
+ g.setColor( getColorForFoundNode( node ) );
+ 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() ) {
child_node.setYcoord( y2 );
y2 += _y_distance * child_node.getNumberOfExternalNodes();
}
- paintNodeBox( node.getXcoord(), node.getYcoord(), node, g, to_pdf, to_graphics_file, isInFoundNodes( node )
- || isInCurrentExternalNodes( node ) );
+ paintNodeBox( node.getXcoord(), node.getYcoord(), node, g, to_pdf, to_graphics_file );
}
if ( dynamically_hide
&& !is_in_found_nodes
final float height = getOvMaxHeight() / h_ratio;
final float x = getVisibleRect().x + getOvXPosition() + ( getOvMaxWidth() / x_ratio );
final float y = getVisibleRect().y + getOvYPosition() + ( getOvMaxHeight() / y_ratio );
- g.setColor( getTreeColorSet().getFoundColor() );
+ g.setColor( getTreeColorSet().getFoundColor0() );
getOvRectangle().setRect( x, y, width, height );
final Stroke s = g.getStroke();
g.setStroke( STROKE_1 );
final double w = PhylogenyMethods.getBranchWidthValue( root );
drawRectFilled( x1 - d, root.getYcoord() - ( w / 2 ), d, w, g );
}
- paintNodeBox( x1, root.getYcoord(), root, g, to_pdf, to_graphics_file, isInFoundNodes( root ) );
+ paintNodeBox( x1, root.getYcoord(), root, g, to_pdf, to_graphics_file );
}
final private void paintScale( final Graphics2D g,
}
else if ( is_in_found_nodes ) {
g.setFont( getTreeFontSet().getLargeItalicFont().deriveFont( TreeFontSet.BOLD_AND_ITALIC ) );
- g.setColor( getTreeColorSet().getFoundColor() );
+ g.setColor( getColorForFoundNode( node ) );
}
else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
g.setColor( getTaxonomyBasedColor( node ) );
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 )
- || isInCurrentExternalNodes( desc ) );
+ paintNodeBox( new_x, new_y, desc, g, to_pdf, to_graphics_file );
}
if ( n.isRoot() ) {
- paintNodeBox( n.getXcoord(), n.getYcoord(), n, g, to_pdf, to_graphics_file, isInFoundNodes( n ) );
+ paintNodeBox( n.getXcoord(), n.getYcoord(), n, g, to_pdf, to_graphics_file );
}
}
desc.setXSecondary( new_x );
desc.setYSecondary( new_y );
if ( isInFoundNodes( desc ) || isInCurrentExternalNodes( desc ) ) {
- g.setColor( getTreeColorSet().getFoundColor() );
- drawRectFilled( desc.getXSecondary() - 1, desc.getYSecondary() - 1, 3, 3, g );
+ g.setColor( getColorForFoundNode( desc ) );
+ 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 );
private void showExtDescNodeData( final PhylogenyNode node ) {
final List<String> data = new ArrayList<String>();
final List<PhylogenyNode> nodes = node.getAllExternalDescendants();
- if ( ( getFoundNodes() != null ) && !getFoundNodes().isEmpty() ) {
- for( final PhylogenyNode n : getFoundNodesAsListOfPhylogenyNodes() ) {
+ if ( ( getFoundNodes0() != null ) && !getFoundNodes0().isEmpty() ) {
+ for( final PhylogenyNode n : getFoundNodes0AsListOfPhylogenyNodes() ) {
+ if ( !nodes.contains( n ) ) {
+ nodes.add( n );
+ }
+ }
+ }
+ if ( ( getFoundNodes1() != null ) && !getFoundNodes1().isEmpty() ) {
+ for( final PhylogenyNode n : getFoundNodes1AsListOfPhylogenyNodes() ) {
if ( !nodes.contains( n ) ) {
nodes.add( n );
}
else {
setCurrentExternalNodesDataBuffer( sb );
String title;
- if ( ( getFoundNodes() != null ) && !getFoundNodes().isEmpty() ) {
+ if ( ( getFoundNodes0() != null ) && !getFoundNodes0().isEmpty() ) {
title = ( getOptions().getExtDescNodeDataToReturn() == NODE_DATA.UNKNOWN ? "Data"
: obtainTitleForExtDescNodeData() )
+ " for "
_rollover_popup
.setBorder( BorderFactory.createLineBorder( getTreeColorSet().getBranchColor() ) );
_rollover_popup.setBackground( getTreeColorSet().getBackgroundColor() );
- if ( isInFoundNodes( node ) ) {
- _rollover_popup.setForeground( getTreeColorSet().getFoundColor() );
+ if ( isInFoundNodes0( node ) && !isInFoundNodes1( node ) ) {
+ _rollover_popup.setForeground( getTreeColorSet().getFoundColor0() );
+ }
+ else if ( !isInFoundNodes0( node ) && isInFoundNodes1( node ) ) {
+ _rollover_popup.setForeground( getTreeColorSet().getFoundColor1() );
+ }
+ else if ( isInFoundNodes0( node ) && isInFoundNodes1( node ) ) {
+ _rollover_popup.setForeground( getTreeColorSet().getFoundColor0and1() );
}
else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
_rollover_popup.setForeground( getTaxonomyBasedColor( node ) );
final private class SubtreeColorizationActionListener implements ActionListener {
+ List<PhylogenyNode> _additional_nodes = null;
JColorChooser _chooser = null;
PhylogenyNode _node = null;
- List<PhylogenyNode> _additional_nodes = null;
SubtreeColorizationActionListener( final JColorChooser chooser, final PhylogenyNode node ) {
_chooser = chooser;
}
}
}
+
+ final private class NodeColorizationActionListener implements ActionListener {
+
+ List<PhylogenyNode> _additional_nodes = null;
+ JColorChooser _chooser = null;
+ PhylogenyNode _node = null;
+
+ NodeColorizationActionListener( final JColorChooser chooser, final PhylogenyNode node ) {
+ _chooser = chooser;
+ _node = node;
+ }
+
+ NodeColorizationActionListener( final JColorChooser chooser,
+ final PhylogenyNode node,
+ final List<PhylogenyNode> additional_nodes ) {
+ _chooser = chooser;
+ _node = node;
+ _additional_nodes = additional_nodes;
+ }
+
+ @Override
+ public void actionPerformed( final ActionEvent e ) {
+ final Color c = _chooser.getColor();
+ if ( c != null ) {
+ colorizeNodes( c, _node, _additional_nodes );
+ }
+ }
+ }
}
git://source.jalview.org / jalview.git / blobdiff