X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FTreePanel.java;h=3b3977da6a90ea0cc802dc4c2998626e4726b206;hb=886c0c0a7a7cef72503df9f21762db1dab594362;hp=9e88db2c2b772bd782aebcdcb8fd04f1ce67f86b;hpb=31a3cd8e86021dc25295567db88c11e833d14291;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/TreePanel.java b/forester/java/src/org/forester/archaeopteryx/TreePanel.java index 9e88db2..3b3977d 100644 --- a/forester/java/src/org/forester/archaeopteryx/TreePanel.java +++ b/forester/java/src/org/forester/archaeopteryx/TreePanel.java @@ -49,6 +49,7 @@ import java.awt.event.MouseEvent; import java.awt.event.MouseWheelEvent; import java.awt.event.MouseWheelListener; import java.awt.font.FontRenderContext; +import java.awt.font.TextAttribute; import java.awt.font.TextLayout; import java.awt.geom.AffineTransform; import java.awt.geom.Arc2D; @@ -68,6 +69,7 @@ import java.io.UnsupportedEncodingException; import java.net.URI; import java.net.URISyntaxException; import java.net.URLEncoder; +import java.text.AttributedString; import java.text.DecimalFormat; import java.text.DecimalFormatSymbols; import java.text.NumberFormat; @@ -76,12 +78,13 @@ import java.util.Collections; import java.util.HashMap; import java.util.HashSet; import java.util.Hashtable; +import java.util.Iterator; import java.util.List; +import java.util.Map; import java.util.Set; import java.util.SortedSet; import javax.swing.BorderFactory; -import javax.swing.JApplet; import javax.swing.JColorChooser; import javax.swing.JDialog; import javax.swing.JMenuItem; @@ -114,20 +117,18 @@ import org.forester.phylogeny.data.BranchColor; import org.forester.phylogeny.data.Confidence; import org.forester.phylogeny.data.DomainArchitecture; import org.forester.phylogeny.data.Event; -import org.forester.phylogeny.data.NodeData.NODE_DATA; +import org.forester.phylogeny.data.NodeDataField; import org.forester.phylogeny.data.NodeVisualData; 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; +import org.forester.phylogeny.data.ProteinDomain; import org.forester.phylogeny.data.Sequence; import org.forester.phylogeny.data.SequenceRelation; import org.forester.phylogeny.data.Taxonomy; import org.forester.phylogeny.data.Uri; import org.forester.phylogeny.iterators.PhylogenyNodeIterator; import org.forester.phylogeny.iterators.PreorderTreeIterator; -import org.forester.util.BasicDescriptiveStatistics; import org.forester.util.DescriptiveStatistics; import org.forester.util.ForesterConstants; import org.forester.util.ForesterUtil; @@ -136,130 +137,221 @@ import org.forester.util.TaxonomyUtil; public final class TreePanel extends JPanel implements ActionListener, MouseWheelListener, Printable { - public final static boolean SPECIAL_DOMAIN_COLORING = true; - 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 ); - 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 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 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, - 12 ); - private static final float ROUNDED_D = 8; - private final static long serialVersionUID = -978349745916505029L; - private static final BasicStroke STROKE_0025 = new BasicStroke( 0.025f ); - 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 static final String SHOW_ONLY_THIS_CONF_TYPE = "posterior probability"; //TODO remove me - HashMap _nodeid_dist_to_leaf = new HashMap(); - final private Arc2D _arc = new Arc2D.Double(); - private AffineTransform _at; - private int _circ_max_depth; - final private Set _collapsed_external_nodeid_set = new HashSet(); - private JColorChooser _color_chooser = null; - private Configuration _configuration = null; - private ControlPanel _control_panel = null; - private final CubicCurve2D _cubic_curve = new CubicCurve2D.Float(); - private Set _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 _found_nodes_0 = null; - private Set _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 final Line2D _line = new Line2D.Float(); - private int _longest_ext_node_info = 0; - private PhylogenyNode _ext_node_with_longest_txt_info = null; - 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_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 final boolean _phy_has_branch_lengths; - private Phylogeny _phylogeny = null; - private final Path2D.Float _polygon = new Path2D.Float(); - private final StringBuffer _popup_buffer = new StringBuffer(); - private final QuadCurve2D _quad_curve = new QuadCurve2D.Float(); - private Sequence _query_sequence = null; - 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; - private DescriptiveStatistics _statistics_for_vector_data; - 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 _urt_nodeid_angle_map = new HashMap(); - final private HashMap _urt_nodeid_index_map = new HashMap(); - 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 int _length_of_longest_text; - private int _longest_domain; - // private Image offscreenImage; - // private Graphics offscreenGraphics; - // private Dimension offscreenDimension; + final private class NodeColorizationActionListener implements ActionListener { + + List _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 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 ); + } + } + } + + final private class SubtreeColorizationActionListener implements ActionListener { + + List _additional_nodes = null; + JColorChooser _chooser = null; + PhylogenyNode _node = null; + + SubtreeColorizationActionListener( final JColorChooser chooser, final PhylogenyNode node ) { + _chooser = chooser; + _node = node; + } + + SubtreeColorizationActionListener( final JColorChooser chooser, + final PhylogenyNode node, + final List 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 ) { + colorizeSubtree( c, _node, _additional_nodes ); + } + } + } + public final static boolean SPECIAL_DOMAIN_COLORING = true; + 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 ); + 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 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 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, 12 ); + private static final float ROUNDED_D = 8; + private final static long serialVersionUID = -978349745916505029L; + private static final BasicStroke STROKE_0025 = new BasicStroke( 0.025f ); + 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 BasicStroke STROKE_01_DASHED = new BasicStroke( 0.1f, + BasicStroke.CAP_SQUARE, + BasicStroke.JOIN_ROUND, + 0, + new float[] { + 2.0f }, + 0f ); + private static final BasicStroke STROKE_005_DASHED = new BasicStroke( 0.05f, + BasicStroke.CAP_SQUARE, + BasicStroke.JOIN_ROUND, + 0, + new float[] { + 2.0f }, + 0f ); + private static final BasicStroke STROKE_001_DASHED = new BasicStroke( 0.01f, + BasicStroke.CAP_SQUARE, + BasicStroke.JOIN_ROUND, + 0, + new float[] { + 2.0f }, + 0f ); + private static final double TWO_PI = 2 * Math.PI; + private final static int WIGGLE = 3; + private static final String SHOW_ONLY_THIS_CONF_TYPE = null; //TODO remove me + HashMap _nodeid_dist_to_leaf = new HashMap(); + final private Arc2D _arc = new Arc2D.Double(); + private AffineTransform _at; + private int _clicked_x; + private int _circ_max_depth; + final private Set _collapsed_external_nodeid_set = new HashSet(); + private JColorChooser _color_chooser = null; + private Configuration _configuration = null; + private ControlPanel _control_panel = null; + private final CubicCurve2D _cubic_curve = new CubicCurve2D.Float(); + private Set _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 = AptxConstants.DOMAIN_STRUCTURE_E_VALUE_THR_DEFAULT_EXP; + private double _domain_structure_width = AptxConstants.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 _found_nodes_0 = null; + private Set _found_nodes_1 = null; + private final FontRenderContext _frc = new FontRenderContext( null, + false, + false ); + private float _furthest_node_x; + 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 final Line2D _line = new Line2D.Float(); + private int _longest_ext_node_info = 0; + private PhylogenyNode _ext_node_with_longest_txt_info = null; + 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_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 boolean _partition_tree = false; + private final boolean _phy_has_branch_lengths; + private Phylogeny _phylogeny = null; + private final Path2D.Float _polygon = new Path2D.Float(); + private final StringBuffer _popup_buffer = new StringBuffer(); + private final QuadCurve2D _quad_curve = new QuadCurve2D.Float(); + private Sequence _query_sequence = null; + 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 float _root_x; + private final StringBuilder _sb = new StringBuilder(); + private double _scale_distance = 0.0; + private String _scale_label = null; + private DescriptiveStatistics _statistics_for_vector_data; + 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 _urt_nodeid_angle_map = new HashMap(); + final private HashMap _urt_nodeid_index_map = new HashMap(); + 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 int _length_of_longest_text; + private int _longest_domain; + private Map _attributed_string_map = null; + private int _depth_collapse_level = -1; + private int _rank_collapse_level = -1; + + + static { final DecimalFormatSymbols dfs = new DecimalFormatSymbols(); dfs.setDecimalSeparator( '.' ); @@ -295,7 +387,6 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee init(); // if ( !_phylogeny.isEmpty() ) { _phylogeny.recalculateNumberOfExternalDescendants( true ); - checkForVectorProperties( _phylogeny ); // } setBackground( getTreeColorSet().getBackgroundColor() ); final MouseListener mouse_listener = new MouseListener( this ); @@ -304,8 +395,8 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee addMouseWheelListener( this ); calculateScaleDistance(); FORMATTER_CONFIDENCE.setMaximumFractionDigits( configuration.getNumberOfDigitsAfterCommaForConfidenceValues() ); - FORMATTER_BRANCH_LENGTH.setMaximumFractionDigits( configuration - .getNumberOfDigitsAfterCommaForBranchLengthValues() ); + FORMATTER_BRANCH_LENGTH + .setMaximumFractionDigits( configuration.getNumberOfDigitsAfterCommaForBranchLengthValues() ); } @Override @@ -337,14 +428,18 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } /** - * Get a pointer to the phylogeny - * + * Get a pointer to the phylogeny + * * @return a pointer to the phylogeny */ public final Phylogeny getPhylogeny() { return _phylogeny; } + public final TreeColorSet getTreeColorSet() { + return getMainPanel().getTreeColorSet(); + } + @Override final public void mouseWheelMoved( final MouseWheelEvent e ) { final int notches = e.getWheelRotation(); @@ -360,14 +455,31 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee repaint(); } } - if ( e.isControlDown() ) { + if ( e.isControlDown() && e.isShiftDown() ) { if ( notches < 0 ) { getTreeFontSet().increaseFontSize(); - getControlPanel().displayedPhylogenyMightHaveChanged( true ); } else { getTreeFontSet().decreaseFontSize( 1, false ); - getControlPanel().displayedPhylogenyMightHaveChanged( true ); + } + getControlPanel().displayedPhylogenyMightHaveChanged( true ); + resetPreferredSize(); + updateOvSizes(); + repaint(); + } + else if ( e.isShiftDown() && e.isAltDown() ) { + if ( notches < 0 ) { + for( int i = 0; i < ( -notches ); ++i ) { + getControlPanel().zoomInX( AptxConstants.WHEEL_ZOOM_IN_FACTOR, AptxConstants.WHEEL_ZOOM_IN_FACTOR ); + getControlPanel().displayedPhylogenyMightHaveChanged( false ); + } + } + else { + for( int i = 0; i < notches; ++i ) { + getControlPanel().zoomOutX( AptxConstants.WHEEL_ZOOM_OUT_FACTOR, + AptxConstants.WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR ); + getControlPanel().displayedPhylogenyMightHaveChanged( false ); + } } } else if ( e.isShiftDown() ) { @@ -392,13 +504,13 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee else { if ( notches < 0 ) { for( int i = 0; i < ( -notches ); ++i ) { - getControlPanel().zoomInY( Constants.WHEEL_ZOOM_IN_FACTOR ); + getControlPanel().zoomInY( AptxConstants.WHEEL_ZOOM_IN_FACTOR ); getControlPanel().displayedPhylogenyMightHaveChanged( false ); } } else { for( int i = 0; i < notches; ++i ) { - getControlPanel().zoomOutY( Constants.WHEEL_ZOOM_OUT_FACTOR ); + getControlPanel().zoomOutY( AptxConstants.WHEEL_ZOOM_OUT_FACTOR ); getControlPanel().displayedPhylogenyMightHaveChanged( false ); } } @@ -407,17 +519,17 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee else { if ( notches < 0 ) { for( int i = 0; i < ( -notches ); ++i ) { - getControlPanel().zoomInX( Constants.WHEEL_ZOOM_IN_FACTOR, - Constants.WHEEL_ZOOM_IN_X_CORRECTION_FACTOR ); - getControlPanel().zoomInY( Constants.WHEEL_ZOOM_IN_FACTOR ); + getControlPanel().zoomInX( AptxConstants.WHEEL_ZOOM_IN_FACTOR, + AptxConstants.WHEEL_ZOOM_IN_X_CORRECTION_FACTOR ); + getControlPanel().zoomInY( AptxConstants.WHEEL_ZOOM_IN_FACTOR ); getControlPanel().displayedPhylogenyMightHaveChanged( false ); } } else { for( int i = 0; i < notches; ++i ) { - getControlPanel().zoomOutY( Constants.WHEEL_ZOOM_OUT_FACTOR ); - getControlPanel().zoomOutX( Constants.WHEEL_ZOOM_OUT_FACTOR, - Constants.WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR ); + getControlPanel().zoomOutY( AptxConstants.WHEEL_ZOOM_OUT_FACTOR ); + getControlPanel().zoomOutX( AptxConstants.WHEEL_ZOOM_OUT_FACTOR, + AptxConstants.WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR ); getControlPanel().displayedPhylogenyMightHaveChanged( false ); } } @@ -429,20 +541,9 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee @Override final public void paintComponent( final Graphics g ) { - // Dimension currentSize = getSize(); - // if ( offscreenImage == null || !currentSize.equals( offscreenDimension ) ) { - // call the 'java.awt.Component.createImage(...)' method to get an - // image - // offscreenImage = createImage( currentSize.width, currentSize.height ); - // offscreenGraphics = offscreenImage.getGraphics(); - // offscreenDimension = currentSize; - // } - // super.paintComponent( g ); //why? - //final Graphics2D g2d = ( Graphics2D ) offscreenGraphics; final Graphics2D g2d = ( Graphics2D ) g; g2d.setRenderingHints( _rendering_hints ); paintPhylogeny( g2d, false, false, 0, 0, 0, 0 ); - //g.drawImage( offscreenImage, 0, 0, this ); } @Override @@ -471,7 +572,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee /** * Set a phylogeny tree. - * + * * @param t * an instance of a Phylogeny */ @@ -490,5505 +591,5800 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee paint( g ); } - final void calcMaxDepth() { - if ( _phylogeny != null ) { - _circ_max_depth = PhylogenyMethods.calculateMaxDepth( _phylogeny ); - } - } - - /** - * Set parameters for printing the displayed tree - * - */ - final void calcParametersForPainting( final int x, final int y, final boolean recalc_longest_ext_node_info ) { - // updateStyle(); not needed? - if ( ( _phylogeny != null ) && !_phylogeny.isEmpty() ) { - initNodeData(); - if ( recalc_longest_ext_node_info ) { - calculateLongestExtNodeInfo(); - if ( getOptions().isAllowFontSizeChange() ) { - if ( ( getLongestExtNodeInfo() > ( x * 0.6 ) ) - && ( getTreeFontSet().getLargeFont().getSize() > ( 2 + TreeFontSet.FONT_SIZE_CHANGE_STEP ) ) ) { - while ( ( getLongestExtNodeInfo() > ( x * 0.7 ) ) - && ( getTreeFontSet().getLargeFont().getSize() > 2 ) ) { - getMainPanel().getTreeFontSet().decreaseFontSize( getConfiguration().getMinBaseFontSize(), - true ); - calculateLongestExtNodeInfo(); - } - } - else { - while ( ( getLongestExtNodeInfo() < ( x * 0.6 ) ) - && ( getTreeFontSet().getLargeFont().getSize() <= ( getTreeFontSet() - .getLargeFontMemory().getSize() - TreeFontSet.FONT_SIZE_CHANGE_STEP ) ) ) { - getMainPanel().getTreeFontSet().increaseFontSize(); - calculateLongestExtNodeInfo(); - } - } - } - _length_of_longest_text = calcLengthOfLongestText(); - } - int ext_nodes = _phylogeny.getRoot().getNumberOfExternalNodes(); - final int max_depth = PhylogenyMethods.calculateMaxDepth( _phylogeny ); - if ( ext_nodes == 1 ) { - ext_nodes = max_depth; - if ( ext_nodes < 1 ) { - ext_nodes = 1; - } - } - updateOvSizes(); - float xdist = 0; - float ov_xdist = 0; - if ( !isNonLinedUpCladogram() && !isUniformBranchLengthsForCladogram() ) { - xdist = ( float ) ( ( x - getLongestExtNodeInfo() - TreePanel.MOVE ) / ( ext_nodes + 3.0 ) ); - ov_xdist = ( float ) ( getOvMaxWidth() / ( ext_nodes + 3.0 ) ); - } - else { - xdist = ( ( x - getLongestExtNodeInfo() - TreePanel.MOVE ) / ( max_depth + 1 ) ); - ov_xdist = ( getOvMaxWidth() / ( max_depth + 1 ) ); - } - float ydist = ( float ) ( ( y - TreePanel.MOVE ) / ( ext_nodes * 2.0 ) ); - if ( xdist < 0.0 ) { - xdist = 0.0f; - } - if ( ov_xdist < 0.0 ) { - ov_xdist = 0.0f; - } - if ( ydist < 0.0 ) { - ydist = 0.0f; - } - setXdistance( xdist ); - setYdistance( ydist ); - setOvXDistance( ov_xdist ); - final double height = _phylogeny.getHeight(); - if ( height > 0 ) { - final float corr = ( float ) ( ( x - TreePanel.MOVE - getLongestExtNodeInfo() - getXdistance() ) / height ); - setXcorrectionFactor( corr > 0 ? corr : 0 ); - final float ov_corr = ( float ) ( ( getOvMaxWidth() - getOvXDistance() ) / height ); - setOvXcorrectionFactor( ov_corr > 0 ? ov_corr : 0 ); - } - else { - setXcorrectionFactor( 0 ); - setOvXcorrectionFactor( 0 ); - } - _circ_max_depth = max_depth; - setUpUrtFactor(); - // - if ( getOptions().isAllowFontSizeChange() ) { - if ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) - && ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) { - // int dynamic_hiding_factor = calcDynamicHidingFactor(); - // if ( dynamic_hiding_factor > 1 ) { - // while ( dynamic_hiding_factor > 1 - // && getTreeFontSet()._fm_large.getHeight() > TreeFontSet.SMALL_FONTS_BASE ) { - // getTreeFontSet().decreaseFontSize( 1, true ); - // dynamic_hiding_factor = calcDynamicHidingFactor(); - // } - // } - // else if ( getTreeFontSet().isDecreasedSizeBySystem() ) { - // while ( dynamic_hiding_factor < 1 && getTreeFontSet()._fm_large.getHeight() < 12 ) { - // getTreeFontSet().increaseFontSize(); - // dynamic_hiding_factor = calcDynamicHidingFactor(); - // } - // } - } + 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 ) ); + if ( a.length > 2 ) { + for( int i = 2; i < a.length; i++ ) { + sb.append( " " ); + sb.append( a[ i ] ); } - // } } - final void calculateLongestExtNodeInfo() { - if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) { + final private void addEmptyNode( final PhylogenyNode node ) { + if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) { + errorMessageNoCutCopyPasteInUnrootedDisplay(); return; } - int max_length = ForesterUtil.roundToInt( ( getSize().getWidth() - MOVE ) - * Constants.EXT_NODE_INFO_LENGTH_MAX_RATIO ); - if ( max_length < 40 ) { - max_length = 40; + final String label = createASimpleTextRepresentationOfANode( node ); + String msg = ""; + if ( ForesterUtil.isEmpty( label ) ) { + msg = "How to add the new, empty node?"; } - int longest = 30; - int longest_txt = 0; - _longest_domain = 0; - PhylogenyNode longest_txt_node = _phylogeny.getFirstExternalNode(); - for( final PhylogenyNode node : _phylogeny.getExternalNodes() ) { - int sum = 0; - if ( node.isCollapse() ) { - continue; - } - final StringBuilder sb = new StringBuilder(); - nodeDataAsSB( node, sb ); - if ( node.getNodeData().isHasTaxonomy() ) { - nodeTaxonomyDataAsSB( node.getNodeData().getTaxonomy(), sb ); - } - final int txt = sb.length(); - if ( txt > longest_txt ) { - longest_txt = txt; - longest_txt_node = node; - } - boolean use_vis = false; - final Graphics2D g = ( Graphics2D ) getGraphics(); - if ( getControlPanel().isUseVisualStyles() ) { - use_vis = setFont( g, node, false ); - } - if ( !use_vis ) { - sum = getFontMetricsForLargeDefaultFont().stringWidth( sb.toString() ); - } - else { - sum = getFontMetrics( g.getFont() ).stringWidth( sb.toString() ); - } - if ( getControlPanel().isShowBinaryCharacters() && node.getNodeData().isHasBinaryCharacters() ) { - sum += getFontMetricsForLargeDefaultFont().stringWidth( node.getNodeData().getBinaryCharacters() - .getGainedCharactersAsStringBuffer().toString() ); - } - if ( getControlPanel().isShowVectorData() && ( node.getNodeData().getVector() != null ) - && ( node.getNodeData().getVector().size() > 0 ) ) { - if ( getConfiguration() != null ) { - sum += getConfiguration().getVectorDataWidth() + 10; - } - else { - sum += RenderableVector.VECTOR_DEFAULT_WIDTH + 10; - } - } - if ( getControlPanel().isShowDomainArchitectures() && node.getNodeData().isHasSequence() - && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) { - // FIXME - // TODO this might need some clean up - final DomainArchitecture d = node.getNodeData().getSequence().getDomainArchitecture(); - sum += ( ( _domain_structure_width / ( ( RenderableDomainArchitecture ) d ).getOriginalSize() - .getWidth() ) * d.getTotalLength() ) + 10; - if ( d.getTotalLength() > _longest_domain ) { - _longest_domain = d.getTotalLength(); - } - } - if ( getControlPanel().isShowMolSequences() && ( node.getNodeData().isHasSequence() ) - && ( node.getNodeData().getSequence().isMolecularSequenceAligned() ) - && ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) ) { - // FIXME - sum += RenderableMsaSequence.DEFAULT_WIDTH + 30; - } - if ( sum >= max_length ) { - _longest_ext_node_info = max_length; + else { + msg = "How to add the new, empty node to node" + label + "?"; + } + final Object[] options = { "As sibling", "As descendant", "Cancel" }; + final int r = JOptionPane.showOptionDialog( this, + msg, + "Addition of Empty New Node", + JOptionPane.CLOSED_OPTION, + JOptionPane.QUESTION_MESSAGE, + null, + options, + options[ 2 ] ); + boolean add_as_sibling = true; + if ( r == 1 ) { + add_as_sibling = false; + } + else if ( r != 0 ) { + return; + } + final Phylogeny phy = new Phylogeny(); + phy.setRoot( new PhylogenyNode() ); + phy.setRooted( true ); + if ( add_as_sibling ) { + if ( node.isRoot() ) { + JOptionPane.showMessageDialog( this, + "Cannot add sibling to root", + "Attempt to add sibling to root", + JOptionPane.ERROR_MESSAGE ); return; } - if ( sum > longest ) { - longest = sum; - } - } - _ext_node_with_longest_txt_info = longest_txt_node; - if ( longest >= max_length ) { - _longest_ext_node_info = max_length; + phy.addAsSibling( node ); } else { - _longest_ext_node_info = longest; + phy.addAsChild( node ); } + setNodeInPreorderToNull(); + _phylogeny.externalNodesHaveChanged(); + _phylogeny.clearHashIdToNodeMap(); + _phylogeny.recalculateNumberOfExternalDescendants( true ); + resetNodeIdToDistToLeafMap(); + setEdited( true ); + repaint(); } - final void calculateScaleDistance() { - if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) { - return; + final private void addToCurrentExternalNodes( final long i ) { + if ( _current_external_nodes == null ) { + _current_external_nodes = new HashSet(); } - final double height = getMaxDistanceToRoot(); - if ( height > 0 ) { - if ( ( height <= 0.5 ) ) { - setScaleDistance( 0.01 ); - } - else if ( height <= 5.0 ) { - setScaleDistance( 0.1 ); - } - else if ( height <= 50.0 ) { - setScaleDistance( 1 ); - } - else if ( height <= 500.0 ) { - setScaleDistance( 10 ); - } - else { - setScaleDistance( 100 ); - } + _current_external_nodes.add( i ); + } + + final private void assignGraphicsForBranchWithColorForParentBranch( final PhylogenyNode node, + final boolean is_vertical, + final Graphics g, + final boolean to_pdf, + final boolean to_graphics_file ) { + final NodeClickAction action = _control_panel.getActionWhenNodeClicked(); + if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) { + g.setColor( Color.BLACK ); } - else { - setScaleDistance( 0.0 ); + else if ( ( ( action == NodeClickAction.COPY_SUBTREE ) || ( action == NodeClickAction.CUT_SUBTREE ) + || ( action == NodeClickAction.DELETE_NODE_OR_SUBTREE ) || ( action == NodeClickAction.PASTE_SUBTREE ) + || ( action == NodeClickAction.ADD_NEW_NODE ) ) && ( getCutOrCopiedTree() != null ) + && ( getCopiedAndPastedNodes() != null ) && !to_pdf && !to_graphics_file + && getCopiedAndPastedNodes().contains( node.getId() ) ) { + g.setColor( getTreeColorSet().getFoundColor0() ); } - String scale_label = String.valueOf( getScaleDistance() ); - if ( !ForesterUtil.isEmpty( _phylogeny.getDistanceUnit() ) ) { - scale_label += " [" + _phylogeny.getDistanceUnit() + "]"; + else if ( getControlPanel().isUseVisualStyles() && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) { + g.setColor( PhylogenyMethods.getBranchColorValue( node ) ); } - setScaleLabel( scale_label ); - } - - final Color calculateTaxonomyBasedColor( final Taxonomy tax ) { - 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(); + else if ( to_pdf ) { + g.setColor( getTreeColorSet().getBranchColorForPdf() ); } else { - if ( ForesterUtil.isEmpty( tax.getTaxonomyCode() ) && ForesterUtil.isEmpty( tax.getScientificName() ) ) { - return getTreeColorSet().getTaxonomyColor(); - } - Color c = null; - if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) { - c = getControlPanel().getSpeciesColors().get( tax.getTaxonomyCode() ); - } - if ( ( c == null ) && !ForesterUtil.isEmpty( tax.getScientificName() ) ) { - c = getControlPanel().getSpeciesColors().get( tax.getScientificName() ); - } - if ( c == null ) { - if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) { - c = AptxUtil.calculateColorFromString( tax.getTaxonomyCode(), true ); - getControlPanel().getSpeciesColors().put( tax.getTaxonomyCode(), c ); - } - else { - c = AptxUtil.calculateColorFromString( tax.getScientificName(), true ); - getControlPanel().getSpeciesColors().put( tax.getScientificName(), c ); - } - } - return c; + g.setColor( getTreeColorSet().getBranchColor() ); } } - 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 = AptxUtil.calculateColorFromString( seq_name, false ); - getControlPanel().getSequenceColors().put( seq_name, c ); + final private void blast( final PhylogenyNode node ) { + if ( !isCanBlast( node ) ) { + JOptionPane.showMessageDialog( this, + "Insufficient information present", + "Cannot Blast", + JOptionPane.INFORMATION_MESSAGE ); + return; } - return c; - } - - void checkForVectorProperties( final Phylogeny phy ) { - final DescriptiveStatistics stats = new BasicDescriptiveStatistics(); - for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) { - final PhylogenyNode node = iter.next(); - if ( node.getNodeData().getProperties() != null ) { - final PropertiesMap pm = node.getNodeData().getProperties(); - final double[] vector = new double[ pm.getProperties().size() ]; - int counter = 0; - for( final String ref : pm.getProperties().keySet() ) { - if ( ref.startsWith( PhyloXmlUtil.VECTOR_PROPERTY_REF ) ) { - final Property p = pm.getProperty( ref ); - final String value_str = p.getValue(); - final String index_str = ref - .substring( PhyloXmlUtil.VECTOR_PROPERTY_REF.length(), ref.length() ); - double d = -100; - try { - d = Double.parseDouble( value_str ); - } - catch ( final NumberFormatException e ) { - JOptionPane.showMessageDialog( this, "Could not parse \"" + value_str - + "\" into a decimal value", "Problem with Vector Data", JOptionPane.ERROR_MESSAGE ); - return; + else { + final String query = Blast.obtainQueryForBlast( node ); + System.out.println( "query for BLAST is: " + query ); + char type = '?'; + if ( !ForesterUtil.isEmpty( query ) ) { + if ( node.getNodeData().isHasSequence() ) { + if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getType() ) ) { + if ( node.getNodeData().getSequence().getType().toLowerCase() + .equals( PhyloXmlUtil.SEQ_TYPE_PROTEIN ) ) { + type = 'p'; } - int i = -1; - try { - i = Integer.parseInt( index_str ); + else { + type = 'n'; } - catch ( final NumberFormatException e ) { - JOptionPane.showMessageDialog( this, - "Could not parse \"" + index_str - + "\" into index for vector data", - "Problem with Vector Data", - JOptionPane.ERROR_MESSAGE ); - return; + } + else if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) { + if ( ForesterUtil + .seqIsLikelyToBeAa( node.getNodeData().getSequence().getMolecularSequence() ) ) { + type = 'p'; } - if ( i < 0 ) { - JOptionPane.showMessageDialog( this, - "Attempt to use negative index for vector data", - "Problem with Vector Data", - JOptionPane.ERROR_MESSAGE ); - return; + else { + type = 'n'; } - vector[ i ] = d; - ++counter; - stats.addValue( d ); } } - final List vector_l = new ArrayList( counter ); - for( int i = 0; i < counter; ++i ) { - vector_l.add( vector[ i ] ); + if ( type == '?' ) { + if ( SequenceAccessionTools.isProteinDbQuery( query ) ) { + type = 'p'; + } + else { + type = 'n'; + } + } + try { + Blast.openNcbiBlastWeb( query, type == 'n', this ); + } + catch ( final Exception e ) { + e.printStackTrace(); } - node.getNodeData().setVector( vector_l ); } } - if ( stats.getN() > 0 ) { - _statistics_for_vector_data = stats; - } } - void clearCurrentExternalNodesDataBuffer() { - setCurrentExternalNodesDataBuffer( new StringBuilder() ); + private final int calcDynamicHidingFactor() { + return ( int ) ( 0.5 + ( getFontMetricsForLargeDefaultFont().getHeight() / ( 1.5 * getYdistance() ) ) ); + } + + final private int calcLengthOfLongestText() { + final StringBuilder sb = new StringBuilder(); + if ( _ext_node_with_longest_txt_info != null ) { + nodeDataAsSB( _ext_node_with_longest_txt_info, sb ); + if ( _ext_node_with_longest_txt_info.getNodeData().isHasTaxonomy() ) { + nodeTaxonomyDataAsSB( _ext_node_with_longest_txt_info.getNodeData().getTaxonomy(), sb ); + } + } + return getFontMetricsForLargeDefaultFont().stringWidth( sb.toString() ); } /** - * Collapse the tree from the given node - * + * Calculate the length of the distance between the given node and its + * parent. + * * @param node - * a PhylogenyNode + * @param ext_node_x + * @factor + * @return the distance value */ - final void collapse( final PhylogenyNode node ) { - if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) { - JOptionPane.showMessageDialog( this, - "Cannot collapse in unrooted display type", - "Attempt to collapse in unrooted display", - JOptionPane.WARNING_MESSAGE ); - return; + final private float calculateBranchLengthToParent( final PhylogenyNode node, final float factor ) { + if ( getControlPanel().isDrawPhylogram() ) { + if ( node.getDistanceToParent() < 0.0 ) { + return 0.0f; + } + return ( float ) ( getXcorrectionFactor() * node.getDistanceToParent() ); } - if ( !node.isExternal() && !node.isRoot() ) { - final boolean collapse = !node.isCollapse(); - TreePanelUtil.collapseSubtree( node, collapse ); - updateSetOfCollapsedExternalNodes(); - _phylogeny.recalculateNumberOfExternalDescendants( true ); - resetNodeIdToDistToLeafMap(); - calculateLongestExtNodeInfo(); - setNodeInPreorderToNull(); - _control_panel.displayedPhylogenyMightHaveChanged( true ); - resetPreferredSize(); - updateOvSizes(); - _main_panel.adjustJScrollPane(); - repaint(); + else { + if ( ( factor == 0 ) || isNonLinedUpCladogram() ) { + return getXdistance(); + } + return getXdistance() * factor; } } - final void collapseSpeciesSpecificSubtrees() { - if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) { - return; + final private Color calculateColorForAnnotation( final SortedSet ann ) { + Color c = getTreeColorSet().getAnnotationColor(); + if ( getControlPanel().isColorAccordingToAnnotation() && ( getControlPanel().getAnnotationColors() != null ) ) { + final StringBuilder sb = new StringBuilder(); + for( final Annotation a : ann ) { + sb.append( !ForesterUtil.isEmpty( a.getRefValue() ) ? a.getRefValue() : a.getDesc() ); + } + final String ann_str = sb.toString(); + if ( !ForesterUtil.isEmpty( ann_str ) ) { + c = getControlPanel().getAnnotationColors().get( ann_str ); + if ( c == null ) { + c = AptxUtil.calculateColorFromString( ann_str, false ); + getControlPanel().getAnnotationColors().put( ann_str, c ); + } + if ( c == null ) { + c = getTreeColorSet().getAnnotationColor(); + } + } } - setWaitCursor(); - TreePanelUtil.collapseSpeciesSpecificSubtrees( _phylogeny ); - updateSetOfCollapsedExternalNodes(); - _phylogeny.recalculateNumberOfExternalDescendants( true ); - resetNodeIdToDistToLeafMap(); - calculateLongestExtNodeInfo(); - setNodeInPreorderToNull(); - resetPreferredSize(); - _main_panel.adjustJScrollPane(); - setArrowCursor(); - repaint(); + return c; } - final void colorRank( final String rank ) { - if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) { - return; - } - setWaitCursor(); - AptxUtil.removeBranchColors( _phylogeny ); - final int colorizations = TreePanelUtil.colorPhylogenyAccordingToRanks( _phylogeny, rank, this ); - if ( colorizations > 0 ) { - _control_panel.setColorBranches( true ); - if ( _control_panel.getUseVisualStylesCb() != null ) { - _control_panel.getUseVisualStylesCb().setSelected( true ); - } - if ( _control_panel.getColorAccSpeciesCb() != null ) { - _control_panel.getColorAccSpeciesCb().setSelected( false ); + final private float calculateOvBranchLengthToParent( final PhylogenyNode node, final int factor ) { + if ( getControlPanel().isDrawPhylogram() ) { + if ( node.getDistanceToParent() < 0.0 ) { + return 0.0f; } - _options.setColorLabelsSameAsParentBranch( true ); - if ( getMainPanel().getMainFrame()._color_labels_same_as_parent_branch != null ) { - getMainPanel().getMainFrame()._color_labels_same_as_parent_branch.setSelected( true ); + return ( float ) ( getOvXcorrectionFactor() * node.getDistanceToParent() ); + } + else { + if ( ( factor == 0 ) || isNonLinedUpCladogram() ) { + return getOvXDistance(); } - _control_panel.repaint(); + return getOvXDistance() * factor; } - setArrowCursor(); - repaint(); - if ( colorizations > 0 ) { - String msg = "Taxonomy colorization via " + rank + " completed:\n"; - if ( colorizations > 1 ) { - msg += "colorized " + colorizations + " subtrees"; - } - else { - msg += "colorized one subtree"; - } - setEdited( true ); - JOptionPane.showMessageDialog( this, - msg, - "Taxonomy Colorization Completed (" + rank + ")", - JOptionPane.INFORMATION_MESSAGE ); + } + + final private void cannotOpenBrowserWarningMessage( final String type_type ) { + JOptionPane.showMessageDialog( this, + "Cannot launch web browser for " + type_type + " data of this node", + "Cannot launch web browser", + JOptionPane.WARNING_MESSAGE ); + } + + 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 ( f != null ) { + fc.setFont( f ); } else { - String msg = "Could not taxonomy colorize any subtree via " + rank + ".\n"; - msg += "Possible solutions (given that suitable taxonomic information is present):\n"; - msg += "select a different rank (e.g. phylum, genus, ...)\n"; - msg += " and/or\n"; - msg += "execute:\n"; - msg += "1. \"" + MainFrameApplication.OBTAIN_DETAILED_TAXONOMIC_INFORMATION + "\" (Tools)\n"; - msg += "2. \"" + MainFrameApplication.INFER_ANCESTOR_TAXONOMIES + "\" (Analysis)"; - JOptionPane.showMessageDialog( this, msg, "Taxonomy Colorization Failed", JOptionPane.WARNING_MESSAGE ); + fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() ); + } + List nodes = new ArrayList(); + if ( ( getFoundNodes0() != null ) || ( getFoundNodes1() != null ) ) { + nodes = getFoundNodesAsListOfPhylogenyNodes(); + } + if ( !nodes.contains( node ) ) { + nodes.add( node ); + } + final int count = nodes.size(); + String title = "Change the font for "; + if ( count == 1 ) { + title += "one node"; + } + else { + title += ( count + " nodes" ); + } + fc.showDialog( this, title ); + if ( ( fc.getFont() != null ) && !ForesterUtil.isEmpty( fc.getFont().getFamily().trim() ) ) { + 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 ); + } } + setEdited( true ); + repaint(); } - final void confColor() { - if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) { - return; - } - setWaitCursor(); - AptxUtil.removeBranchColors( _phylogeny ); - TreePanelUtil.colorPhylogenyAccordingToConfidenceValues( _phylogeny, this ); + final private void colorizeNodes( final Color c, + final PhylogenyNode node, + final List additional_nodes ) { _control_panel.setColorBranches( true ); if ( _control_panel.getUseVisualStylesCb() != null ) { _control_panel.getUseVisualStylesCb().setSelected( true ); } - setArrowCursor(); + if ( node != null ) { + colorizeNodesHelper( c, node ); + } + if ( additional_nodes != null ) { + for( final PhylogenyNode n : additional_nodes ) { + colorizeNodesHelper( c, n ); + } + } repaint(); } - final void decreaseDomainStructureEvalueThreshold() { - if ( _domain_structure_e_value_thr_exp > -20 ) { - _domain_structure_e_value_thr_exp -= 1; + final private void colorizeSubtree( final Color c, + final PhylogenyNode node, + final List additional_nodes ) { + _control_panel.setColorBranches( true ); + if ( _control_panel.getUseVisualStylesCb() != null ) { + _control_panel.getUseVisualStylesCb().setSelected( true ); } - } - - /** - * Find the node, if any, at the given location - * - * @param x - * @param y - * @return pointer to the node at x,y, null if not found - */ - final PhylogenyNode findNode( final int x, final int y ) { - if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) { - return null; + if ( node != null ) { + for( final PreorderTreeIterator it = new PreorderTreeIterator( node ); it.hasNext(); ) { + it.next().getBranchData().setBranchColor( new BranchColor( c ) ); + } } - 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 ) ) { - return node; + if ( additional_nodes != null ) { + for( final PhylogenyNode an : additional_nodes ) { + for( final PreorderTreeIterator it = new PreorderTreeIterator( an ); it.hasNext(); ) { + it.next().getBranchData().setBranchColor( new BranchColor( c ) ); + } } } - return null; + repaint(); } - final Configuration getConfiguration() { - return _configuration; + private void colorNodeFont( final PhylogenyNode node ) { + _color_chooser.setPreviewPanel( new JPanel() ); + NodeColorizationActionListener al; + int count = 1; + if ( ( getFoundNodes0() != null ) || ( getFoundNodes1() != null ) ) { + final List additional_nodes = getFoundNodesAsListOfPhylogenyNodes(); + al = new NodeColorizationActionListener( _color_chooser, node, additional_nodes ); + count = additional_nodes.size(); + if ( !additional_nodes.contains( node ) ) { + count++; + } + } + else { + al = new NodeColorizationActionListener( _color_chooser, node ); + } + String title = "Change the (node and font) color for "; + if ( count == 1 ) { + title += "one node"; + } + else { + title += ( count + " nodes" ); + } + final JDialog dialog = JColorChooser.createDialog( this, title, true, _color_chooser, al, null ); + setEdited( true ); + dialog.setVisible( true ); } - final ControlPanel getControlPanel() { - return _control_panel; + 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; + } + _color_chooser.setPreviewPanel( new JPanel() ); + final SubtreeColorizationActionListener al; + final boolean color_found = getOptions().isColorAllFoundNodesWhenColoringSubtree(); + if ( color_found && ( ( getFoundNodes0() != null ) || ( getFoundNodes1() != null ) ) ) { + final List additional_nodes = getFoundNodesAsListOfPhylogenyNodes(); + al = new SubtreeColorizationActionListener( _color_chooser, node, additional_nodes ); + } + else { + al = new SubtreeColorizationActionListener( _color_chooser, node ); + } + final JDialog dialog = JColorChooser.createDialog( this, + "Subtree colorization", + true, + _color_chooser, + al, + null ); + setEdited( true ); + dialog.setVisible( true ); } - String getCurrentExternalNodesDataBufferAsString() { - return _current_external_nodes_data_buffer.toString(); + final private void copySubtree( final PhylogenyNode node ) { + if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) { + errorMessageNoCutCopyPasteInUnrootedDisplay(); + return; + } + setNodeInPreorderToNull(); + setCutOrCopiedTree( _phylogeny.copy( node ) ); + final List nodes = PhylogenyMethods.getAllDescendants( node ); + final Set node_ids = new HashSet( nodes.size() ); + for( final PhylogenyNode n : nodes ) { + node_ids.add( n.getId() ); + } + node_ids.add( node.getId() ); + setCopiedAndPastedNodes( node_ids ); + repaint(); } - int getCurrentExternalNodesDataBufferChangeCounter() { - return _current_external_nodes_data_buffer_change_counter; + final private String createASimpleTextRepresentationOfANode( final PhylogenyNode node ) { + final String tax = PhylogenyMethods.getSpecies( node ); + String label = node.getName(); + if ( !ForesterUtil.isEmpty( label ) && !ForesterUtil.isEmpty( tax ) ) { + label = label + " " + tax; + } + else if ( !ForesterUtil.isEmpty( tax ) ) { + label = tax; + } + else { + label = ""; + } + if ( !ForesterUtil.isEmpty( label ) ) { + label = " [" + label + "]"; + } + return label; } - final int getDomainStructureEvalueThreshold() { - return _domain_structure_e_value_thr_exp; + final private void cutSubtree( final PhylogenyNode node ) { + if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) { + errorMessageNoCutCopyPasteInUnrootedDisplay(); + return; + } + if ( node.isRoot() ) { + JOptionPane.showMessageDialog( this, + "Cannot cut entire tree as subtree", + "Attempt to cut entire tree", + JOptionPane.ERROR_MESSAGE ); + return; + } + final String label = createASimpleTextRepresentationOfANode( node ); + final int r = JOptionPane.showConfirmDialog( null, + "Cut subtree" + label + "?", + "Confirm Cutting of Subtree", + JOptionPane.YES_NO_OPTION ); + if ( r != JOptionPane.OK_OPTION ) { + return; + } + setNodeInPreorderToNull(); + setCopiedAndPastedNodes( null ); + setCutOrCopiedTree( _phylogeny.copy( node ) ); + _phylogeny.deleteSubtree( node, true ); + _phylogeny.clearHashIdToNodeMap(); + _phylogeny.recalculateNumberOfExternalDescendants( true ); + resetNodeIdToDistToLeafMap(); + setEdited( true ); + repaint(); } - final Set getFoundNodes0() { - return _found_nodes_0; + final private void cycleColors() { + getMainPanel().getTreeColorSet().cycleColorScheme(); + for( final TreePanel tree_panel : getMainPanel().getTreePanels() ) { + tree_panel.setBackground( getMainPanel().getTreeColorSet().getBackgroundColor() ); + } } - final Set getFoundNodes1() { - return _found_nodes_1; + final private void decreaseOvSize() { + if ( ( getOvMaxWidth() > 20 ) && ( getOvMaxHeight() > 20 ) ) { + setOvMaxWidth( getOvMaxWidth() - 5 ); + setOvMaxHeight( getOvMaxHeight() - 5 ); + updateOvSettings(); + getControlPanel().displayedPhylogenyMightHaveChanged( false ); + } } - final Color getGraphicsForNodeBoxWithColorForParentBranch( final PhylogenyNode node ) { - if ( getControlPanel().isUseVisualStyles() && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) { - return ( PhylogenyMethods.getBranchColorValue( node ) ); + final private void deleteNodeOrSubtree( final PhylogenyNode node ) { + if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) { + errorMessageNoCutCopyPasteInUnrootedDisplay(); + return; + } + if ( node.isRoot() && ( node.getNumberOfDescendants() != 1 ) ) { + JOptionPane.showMessageDialog( this, + "Cannot delete entire tree", + "Attempt to delete entire tree", + JOptionPane.ERROR_MESSAGE ); + return; + } + final String label = createASimpleTextRepresentationOfANode( node ); + final Object[] options = { "Node only", "Entire subtree", "Cancel" }; + final int r = JOptionPane.showOptionDialog( this, + "Delete" + label + "?", + "Delete Node/Subtree", + JOptionPane.CLOSED_OPTION, + JOptionPane.QUESTION_MESSAGE, + null, + options, + options[ 2 ] ); + setNodeInPreorderToNull(); + boolean node_only = true; + if ( r == 1 ) { + node_only = false; + } + else if ( r != 0 ) { + return; + } + if ( node_only ) { + PhylogenyMethods.removeNode( node, _phylogeny ); } else { - return ( getTreeColorSet().getBranchColor() ); + _phylogeny.deleteSubtree( node, true ); } + _phylogeny.externalNodesHaveChanged(); + _phylogeny.clearHashIdToNodeMap(); + _phylogeny.recalculateNumberOfExternalDescendants( true ); + resetNodeIdToDistToLeafMap(); + setEdited( true ); + repaint(); } - final int getLongestExtNodeInfo() { - return _longest_ext_node_info; + final private void displayNodePopupMenu( final PhylogenyNode node, final int x, final int y ) { + makePopupMenus( node ); + _node_popup_menu.putClientProperty( NODE_POPMENU_NODE_CLIENT_PROPERTY, node ); + _node_popup_menu.show( this, x, y ); } - final Options getOptions() { - if ( _options == null ) { - _options = getControlPanel().getOptions(); + final private void drawArc( final double x, + final double y, + final double width, + final double heigth, + final double start_angle, + final double arc_angle, + final Graphics2D g ) { + _arc.setArc( x, y, width, heigth, _180_OVER_PI * start_angle, _180_OVER_PI * arc_angle, Arc2D.OPEN ); + g.draw( _arc ); + } + + final private void drawLine( final double x1, + final double y1, + final double x2, + final double y2, + final Graphics2D g ) { + if ( ( x1 == x2 ) && ( y1 == y2 ) ) { + return; } - return _options; + _line.setLine( x1, y1, x2, y2 ); + g.draw( _line ); } - final Rectangle2D getOvRectangle() { - return _ov_rectangle; + final private void drawOval( final double x, + final double y, + final double width, + final double heigth, + final Graphics2D g ) { + _ellipse.setFrame( x, y, width, heigth ); + g.draw( _ellipse ); } - final Rectangle getOvVirtualRectangle() { - return _ov_virtual_rectangle; + final private void drawOvalFilled( final double x, + final double y, + final double width, + final double heigth, + final Graphics2D g ) { + _ellipse.setFrame( x, y, width, heigth ); + g.fill( _ellipse ); } - final PHYLOGENY_GRAPHICS_TYPE getPhylogenyGraphicsType() { - return _graphics_type; + 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( x, y, color_1, ( x + width ), ( y + heigth ), color_2, false ) ); + g.fill( _ellipse ); + if ( color_border != null ) { + g.setPaint( color_border ); + g.draw( _ellipse ); + } } - final double getStartingAngle() { - return _urt_starting_angle; + final private void drawRect( final float x, + final float y, + final float width, + final float heigth, + final Graphics2D g ) { + _rectangle.setFrame( x, y, width, heigth ); + g.draw( _rectangle ); } - DescriptiveStatistics getStatisticsForExpressionValues() { - return _statistics_for_vector_data; + final private void drawRectFilled( final double x, + final double y, + final double width, + final double heigth, + final Graphics2D g ) { + _rectangle.setFrame( x, y, width, heigth ); + g.fill( _rectangle ); } - final Color getTaxonomyBasedColor( final PhylogenyNode node ) { - if ( node.isExternal() && node.getNodeData().isHasTaxonomy() ) { - return calculateTaxonomyBasedColor( node.getNodeData().getTaxonomy() ); + 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( x, y, color_1, ( x + width ), ( y + heigth ), color_2, false ) ); + g.fill( _rectangle ); + if ( color_border != null ) { + g.setPaint( color_border ); + g.draw( _rectangle ); } - // return non-colorized color - return getTreeColorSet().getTaxonomyColor(); } - final Color getSequenceBasedColor( final PhylogenyNode node ) { - if ( node.getNodeData().isHasSequence() ) { - return calculateSequenceBasedColor( node.getNodeData().getSequence() ); + private double drawTaxonomyImage( final double x, final double y, final PhylogenyNode node, final Graphics2D g ) { + final List us = new ArrayList(); + for( final Taxonomy t : node.getNodeData().getTaxonomies() ) { + for( final Uri uri : t.getUris() ) { + us.add( uri ); + } } - // return non-colorized color - return getTreeColorSet().getSequenceColor(); + double offset = 0; + for( final Uri uri : us ) { + if ( uri != null ) { + final String uri_str = uri.getValue().toString().toLowerCase(); + if ( getImageMap().containsKey( uri_str ) ) { + final BufferedImage bi = getImageMap().get( uri_str ); + if ( ( bi != null ) && ( bi.getHeight() > 5 ) && ( bi.getWidth() > 5 ) ) { + double scaling_factor = 1; + if ( getOptions().isAllowMagnificationOfTaxonomyImages() + || ( bi.getHeight() > ( 1.8 * getYdistance() ) ) ) { + scaling_factor = ( 1.8 * getYdistance() ) / bi.getHeight(); + } + // y = y - ( 0.9 * getYdistance() ); + final double hs = bi.getHeight() * scaling_factor; + double ws = ( bi.getWidth() * scaling_factor ) + offset; + final double my_y = y - ( 0.5 * hs ); + final int x_w = ( int ) ( x + ws + 0.5 ); + final int y_h = ( int ) ( my_y + hs + 0.5 ); + if ( ( ( x_w - x ) > 7 ) && ( ( y_h - my_y ) > 7 ) ) { + g.drawImage( bi, + ( int ) ( x + 0.5 + offset ), + ( int ) ( my_y + 0.5 ), + x_w, + y_h, + 0, + 0, + bi.getWidth(), + bi.getHeight(), + null ); + ws += 8; + } + else { + ws = 0.0; + } + offset = ws; + } + } + } + } + return offset; } - public final TreeColorSet getTreeColorSet() { - return getMainPanel().getTreeColorSet(); + final private void errorMessageNoCutCopyPasteInUnrootedDisplay() { + JOptionPane.showMessageDialog( this, + "Cannot cut, copy, paste, add, or delete subtrees/nodes in unrooted display", + "Attempt to cut/copy/paste/add/delete in unrooted display", + JOptionPane.ERROR_MESSAGE ); } - final File getTreeFile() { - return _treefile; + 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 float getXcorrectionFactor() { - return _x_correction_factor; + final private Set getCopiedAndPastedNodes() { + return getMainPanel().getCopiedAndPastedNodes(); } - final float getXdistance() { - return _x_distance; + final private Set getCurrentExternalNodes() { + return _current_external_nodes; } - final float getYdistance() { - return _y_distance; + final private Phylogeny getCutOrCopiedTree() { + return getMainPanel().getCutOrCopiedTree(); } - final void increaseDomainStructureEvalueThreshold() { - if ( _domain_structure_e_value_thr_exp < 3 ) { - _domain_structure_e_value_thr_exp += 1; - } + private FontMetrics getFontMetricsForLargeDefaultFont() { + return getTreeFontSet().getFontMetricsLarge(); } - final void initNodeData() { - if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) { - return; + final private float getLastDragPointX() { + return _last_drag_point_x; + } + + final private float getLastDragPointY() { + return _last_drag_point_y; + } + + final private double getMaxDistanceToRoot() { + if ( _max_distance_to_root < 0 ) { + recalculateMaxDistanceToRoot(); } - double _max_original_domain_structure_width = 0.0; - for( final PhylogenyNode node : _phylogeny.getExternalNodes() ) { - if ( node.getNodeData().isHasSequence() - && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) { - RenderableDomainArchitecture rds = null; - if ( !( node.getNodeData().getSequence().getDomainArchitecture() instanceof RenderableDomainArchitecture ) ) { - if ( SPECIAL_DOMAIN_COLORING ) { - rds = new RenderableDomainArchitecture( node.getNodeData().getSequence() - .getDomainArchitecture(), node.getName() ); - } - else { - rds = new RenderableDomainArchitecture( node.getNodeData().getSequence() - .getDomainArchitecture() ); - } - node.getNodeData().getSequence().setDomainArchitecture( rds ); - } - else { - rds = ( RenderableDomainArchitecture ) node.getNodeData().getSequence().getDomainArchitecture(); - } - if ( getControlPanel().isShowDomainArchitectures() ) { - final double dsw = rds.getOriginalSize().getWidth(); - if ( dsw > _max_original_domain_structure_width ) { - _max_original_domain_structure_width = dsw; + return _max_distance_to_root; + } + + final private float getOvMaxHeight() { + return _ov_max_height; + } + + final private float getOvMaxWidth() { + return _ov_max_width; + } + + final private float getOvXcorrectionFactor() { + return _ov_x_correction_factor; + } + + final private float getOvXDistance() { + return _ov_x_distance; + } + + final private int getOvXPosition() { + return _ov_x_position; + } + + final private float getOvYDistance() { + return _ov_y_distance; + } + + final private int getOvYPosition() { + return _ov_y_position; + } + + final private int getOvYStart() { + return _ov_y_start; + } + + final private List getPdbAccs( final PhylogenyNode node ) { + final List pdb_ids = new ArrayList(); + if ( node.getNodeData().isHasSequence() ) { + final Sequence seq = node.getNodeData().getSequence(); + if ( !ForesterUtil.isEmpty( seq.getCrossReferences() ) ) { + final SortedSet cross_refs = seq.getCrossReferences(); + for( final Accession acc : cross_refs ) { + if ( acc.getSource().equalsIgnoreCase( "pdb" ) ) { + pdb_ids.add( acc ); } } } } - if ( getControlPanel().isShowDomainArchitectures() ) { - final float ds_factor_width = ( float ) ( _domain_structure_width / _max_original_domain_structure_width ); - for( final PhylogenyNode node : _phylogeny.getExternalNodes() ) { - if ( node.getNodeData().isHasSequence() - && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) { - final RenderableDomainArchitecture rds = ( RenderableDomainArchitecture ) node.getNodeData() - .getSequence().getDomainArchitecture(); - rds.setRenderingFactorWidth( ds_factor_width ); - rds.setParameter( _domain_structure_e_value_thr_exp ); - } - } - } + return pdb_ids; } - final boolean inOv( final MouseEvent e ) { - return ( ( e.getX() > ( getVisibleRect().x + getOvXPosition() + 1 ) ) - && ( e.getX() < ( ( getVisibleRect().x + getOvXPosition() + getOvMaxWidth() ) - 1 ) ) - && ( e.getY() > ( getVisibleRect().y + getOvYPosition() + 1 ) ) && ( e.getY() < ( ( getVisibleRect().y - + getOvYPosition() + getOvMaxHeight() ) - 1 ) ) ); + final private double getScaleDistance() { + return _scale_distance; } - final boolean inOvRectangle( final MouseEvent e ) { - return ( ( e.getX() >= ( getOvRectangle().getX() - 1 ) ) - && ( e.getX() <= ( getOvRectangle().getX() + getOvRectangle().getWidth() + 1 ) ) - && ( e.getY() >= ( getOvRectangle().getY() - 1 ) ) && ( e.getY() <= ( getOvRectangle().getY() - + getOvRectangle().getHeight() + 1 ) ) ); + final private String getScaleLabel() { + return _scale_label; } - final boolean isApplet() { - return getMainPanel() instanceof MainPanelApplets; + final private TreeFontSet getTreeFontSet() { + return getMainPanel().getTreeFontSet(); } - final boolean isCanCollapse() { - return ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ); + final private float getUrtFactor() { + return _urt_factor; } - final boolean isCanColorSubtree() { - return ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ); + final private float getUrtFactorOv() { + return _urt_factor_ov; } - final boolean isCanCopy() { - return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable() ); + final private void handleClickToAction( final NodeClickAction action, final PhylogenyNode node ) { + switch ( action ) { + case SHOW_DATA: + showNodeFrame( node ); + break; + case COLLAPSE: + collapse( node ); + break; + case REROOT: + reRoot( node ); + break; + case SUBTREE: + subTree( node ); + break; + case SWAP: + swap( node ); + break; + 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; + case BLAST: + blast( node ); + break; + case OPEN_TAX_WEB: + openTaxWeb( node ); + break; + case OPEN_PDB_WEB: + openPdbWeb( node ); + break; + case CUT_SUBTREE: + cutSubtree( node ); + break; + case COPY_SUBTREE: + copySubtree( node ); + break; + case PASTE_SUBTREE: + pasteSubtree( node ); + break; + case DELETE_NODE_OR_SUBTREE: + deleteNodeOrSubtree( node ); + break; + case ADD_NEW_NODE: + addEmptyNode( node ); + break; + case EDIT_NODE_DATA: + showNodeEditFrame( node ); + break; + case SELECT_NODES: + selectNode( node ); + break; + case SORT_DESCENDENTS: + sortDescendants( node ); + break; + case GET_EXT_DESC_DATA: + showExtDescNodeData( node, '_' ); + break; + case UNCOLLAPSE_ALL: + uncollapseAll( node ); + break; + case ORDER_SUBTREE: + orderSubtree( node ); + break; + default: + throw new IllegalArgumentException( "unknown action: " + action ); + } } - final boolean isCanCut( final PhylogenyNode node ) { - return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable() && !node - .isRoot() ); + final private void increaseCurrentExternalNodesDataBufferChangeCounter() { + _current_external_nodes_data_buffer_change_counter++; } - final boolean isCanDelete() { - return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable() ); + final private void increaseOvSize() { + if ( ( getOvMaxWidth() < ( getMainPanel().getCurrentScrollPane().getViewport().getVisibleRect().getWidth() + / 2 ) ) + && ( getOvMaxHeight() < ( getMainPanel().getCurrentScrollPane().getViewport().getVisibleRect() + .getHeight() / 2 ) ) ) { + setOvMaxWidth( getOvMaxWidth() + 5 ); + setOvMaxHeight( getOvMaxHeight() + 5 ); + updateOvSettings(); + getControlPanel().displayedPhylogenyMightHaveChanged( false ); + } } - final boolean isCanPaste() { - return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable() - && ( getCutOrCopiedTree() != null ) && !getCutOrCopiedTree().isEmpty() ); + final private void init() { + _color_chooser = new JColorChooser(); + _rollover_popup = new JTextArea(); + _rollover_popup.setFont( POPUP_FONT ); + resetNodeIdToDistToLeafMap(); + setTextAntialias(); + setTreeFile( null ); + setEdited( false ); + initializeOvSettings(); + resetDepthCollapseDepthValue(); + resetRankCollapseRankValue(); + setStartingAngle( ( TWO_PI * 3 ) / 4 ); + final ImageLoader il = new ImageLoader( this ); + new Thread( il ).start(); } - final boolean isCanReroot() { - return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( _subtree_index < 1 ) ); + final private void initializeOvSettings() { + setOvMaxHeight( getConfiguration().getOvMaxHeight() ); + setOvMaxWidth( getConfiguration().getOvMaxWidth() ); } - final boolean isCanSubtree( final PhylogenyNode node ) { - return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && !node.isExternal() && ( !node - .isRoot() || ( _subtree_index > 0 ) ) ); + final private boolean inOvVirtualRectangle( final int x, final int y ) { + return ( ( x >= ( getOvVirtualRectangle().x - 1 ) ) + && ( x <= ( getOvVirtualRectangle().x + getOvVirtualRectangle().width + 1 ) ) + && ( y >= ( getOvVirtualRectangle().y - 1 ) ) + && ( y <= ( getOvVirtualRectangle().y + getOvVirtualRectangle().height + 1 ) ) ); } - final boolean isCurrentTreeIsSubtree() { - return ( _subtree_index > 0 ); + final private boolean inOvVirtualRectangle( final MouseEvent e ) { + return ( inOvVirtualRectangle( e.getX(), e.getY() ) ); } - final boolean isEdited() { - return _edited; + final private boolean isCanBlast( final PhylogenyNode node ) { + if ( !node.getNodeData().isHasSequence() && ForesterUtil.isEmpty( node.getName() ) ) { + return false; + } + return Blast.isContainsQueryForBlast( node ); } - final boolean isInOvRect() { - return _in_ov_rect; + final private String isCanOpenSeqWeb( final PhylogenyNode node ) { + final Accession a = SequenceAccessionTools.obtainAccessorFromDataFields( node ); + if ( a != null ) { + return a.getValue(); + } + return null; } - final boolean isOvOn() { - return _ov_on; + final private boolean isCanOpenTaxWeb( final PhylogenyNode node ) { + if ( node.getNodeData().isHasTaxonomy() && ( ( !ForesterUtil + .isEmpty( node.getNodeData().getTaxonomy().getScientificName() ) ) + || ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getTaxonomyCode() ) ) + || ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getCommonName() ) ) + || ( ( node.getNodeData().getTaxonomy().getIdentifier() != null ) + && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getIdentifier().getValue() ) ) ) ) { + return true; + } + else { + return false; + } } - final boolean isPhyHasBranchLengths() { - return _phy_has_branch_lengths; + final private boolean isInCurrentExternalNodes( final PhylogenyNode node ) { + return ( ( getCurrentExternalNodes() != null ) && getCurrentExternalNodes().contains( node.getId() ) ); } - final void midpointRoot() { - if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) { - return; - } - if ( !_phylogeny.isRerootable() ) { - JOptionPane.showMessageDialog( this, - "This is not rerootable", - "Not rerootable", - JOptionPane.WARNING_MESSAGE ); - return; - } - setNodeInPreorderToNull(); - setWaitCursor(); - PhylogenyMethods.midpointRoot( _phylogeny ); - resetNodeIdToDistToLeafMap(); - setArrowCursor(); - setEdited( true ); - repaint(); + private boolean isInFoundNodes( final PhylogenyNode n ) { + return isInFoundNodes0( n ) || isInFoundNodes1( n ); } - final void mouseClicked( final MouseEvent e ) { - if ( getOptions().isShowOverview() && isOvOn() && isInOv() ) { - final double w_ratio = getVisibleRect().width / getOvRectangle().getWidth(); - final double h_ratio = getVisibleRect().height / getOvRectangle().getHeight(); - double x = ( e.getX() - getVisibleRect().x - getOvXPosition() - ( getOvRectangle().getWidth() / 2.0 ) ) - * w_ratio; - double y = ( e.getY() - getVisibleRect().y - getOvYPosition() - ( getOvRectangle().getHeight() / 2.0 ) ) - * h_ratio; - if ( x < 0 ) { - x = 0; - } - if ( y < 0 ) { - y = 0; - } - final double max_x = getWidth() - getVisibleRect().width; - final double max_y = getHeight() - getVisibleRect().height; - if ( x > max_x ) { - x = max_x; + 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() { + return _in_ov; + } + + final private boolean isNodeDataInvisible( final PhylogenyNode node ) { + int y_dist = 40; + if ( getControlPanel().isShowTaxonomyImages() ) { + y_dist = 40 + ( int ) getYdistance(); + } + return ( ( node.getYcoord() < ( getVisibleRect().getMinY() - y_dist ) ) + || ( node.getYcoord() > ( getVisibleRect().getMaxY() + y_dist ) ) + || ( ( node.getParent() != null ) && ( node.getParent().getXcoord() > getVisibleRect().getMaxX() ) ) ); + } + + final private boolean isNodeDataInvisibleUnrootedCirc( final PhylogenyNode node ) { + return ( ( node.getYcoord() < ( getVisibleRect().getMinY() - 20 ) ) + || ( node.getYcoord() > ( getVisibleRect().getMaxY() + 20 ) ) + || ( node.getXcoord() < ( getVisibleRect().getMinX() - 20 ) ) + || ( node.getXcoord() > ( getVisibleRect().getMaxX() + 20 ) ) ); + } + + final private boolean isNonLinedUpCladogram() { + return getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP; + } + + final private void keyPressedCalls( final KeyEvent e ) { + if ( isOvOn() && ( getMousePosition() != null ) && ( getMousePosition().getLocation() != null ) ) { + if ( inOvVirtualRectangle( getMousePosition().x, getMousePosition().y ) ) { + if ( !isInOvRect() ) { + setInOvRect( true ); + } } - if ( y > max_y ) { - y = max_y; + else if ( isInOvRect() ) { + setInOvRect( false ); + } + } + if ( e.isAltDown() ) { + if ( ( e.getKeyCode() == KeyEvent.VK_DELETE ) || ( e.getKeyCode() == KeyEvent.VK_HOME ) + || ( e.getKeyCode() == KeyEvent.VK_C ) || ( e.getKeyCode() == KeyEvent.VK_BACK_SPACE ) ) { + getControlPanel().showWhole(); + } + else if ( e.isShiftDown() + && ( ( e.getKeyCode() == KeyEvent.VK_SUBTRACT ) || ( e.getKeyCode() == KeyEvent.VK_MINUS ) ) ) { + getMainPanel().getTreeFontSet().decreaseFontSize( 1, false ); + getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true ); + } + else if ( e.isShiftDown() && plusPressed( e.getKeyCode() ) ) { + getMainPanel().getTreeFontSet().increaseFontSize(); + getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true ); + } + else if ( e.getKeyCode() == KeyEvent.VK_O ) { + getControlPanel().orderPressed( this ); + } + else if ( e.getKeyCode() == KeyEvent.VK_R ) { + getControlPanel().returnedToSuperTreePressed(); + } + else if ( e.getKeyCode() == KeyEvent.VK_U ) { + getControlPanel().uncollapseAll( this ); + getControlPanel().displayedPhylogenyMightHaveChanged( false ); + } + else if ( e.getKeyCode() == KeyEvent.VK_UP ) { + getMainPanel().getControlPanel().zoomInY( AptxConstants.WHEEL_ZOOM_IN_FACTOR ); + getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false ); + } + else if ( e.getKeyCode() == KeyEvent.VK_DOWN ) { + getMainPanel().getControlPanel().zoomOutY( AptxConstants.WHEEL_ZOOM_OUT_FACTOR ); + getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false ); + } + else if ( e.getKeyCode() == KeyEvent.VK_LEFT ) { + getMainPanel().getControlPanel().zoomOutX( AptxConstants.WHEEL_ZOOM_OUT_FACTOR, + AptxConstants.WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR ); + getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false ); + } + else if ( e.getKeyCode() == KeyEvent.VK_RIGHT ) { + getMainPanel().getControlPanel().zoomInX( AptxConstants.WHEEL_ZOOM_IN_FACTOR, + AptxConstants.WHEEL_ZOOM_IN_FACTOR ); + getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false ); + } + else if ( ( e.getKeyCode() == KeyEvent.VK_SUBTRACT ) || ( e.getKeyCode() == KeyEvent.VK_MINUS ) ) { + getMainPanel().getControlPanel().zoomOutY( AptxConstants.WHEEL_ZOOM_OUT_FACTOR ); + getMainPanel().getControlPanel().zoomOutX( AptxConstants.WHEEL_ZOOM_OUT_FACTOR, + AptxConstants.WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR ); + getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false ); + } + else if ( plusPressed( e.getKeyCode() ) ) { + getMainPanel().getControlPanel().zoomInX( AptxConstants.WHEEL_ZOOM_IN_FACTOR, + AptxConstants.WHEEL_ZOOM_IN_FACTOR ); + getMainPanel().getControlPanel().zoomInY( AptxConstants.WHEEL_ZOOM_IN_FACTOR ); + getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false ); } - getMainPanel().getCurrentScrollPane().getViewport() - .setViewPosition( new Point( ForesterUtil.roundToInt( x ), ForesterUtil.roundToInt( y ) ) ); - setInOvRect( true ); - repaint(); } else { - final PhylogenyNode node = findNode( e.getX(), e.getY() ); - if ( node != null ) { - if ( !node.isRoot() && node.getParent().isCollapse() ) { - return; + if ( ( e.getKeyCode() == KeyEvent.VK_UP ) || ( e.getKeyCode() == KeyEvent.VK_DOWN ) + || ( e.getKeyCode() == KeyEvent.VK_LEFT ) || ( e.getKeyCode() == KeyEvent.VK_RIGHT ) ) { + final int d = 80; + int dx = 0; + int dy = -d; + if ( e.getKeyCode() == KeyEvent.VK_DOWN ) { + dy = d; + } + else if ( e.getKeyCode() == KeyEvent.VK_LEFT ) { + dx = -d; + dy = 0; + } + else if ( e.getKeyCode() == KeyEvent.VK_RIGHT ) { + dx = d; + dy = 0; + } + final Point scroll_position = getMainPanel().getCurrentScrollPane().getViewport().getViewPosition(); + scroll_position.x = scroll_position.x + dx; + scroll_position.y = scroll_position.y + dy; + if ( scroll_position.x <= 0 ) { + scroll_position.x = 0; } - _highlight_node = node; - // Check if shift key is down - if ( ( e.getModifiers() & InputEvent.SHIFT_MASK ) != 0 ) { - // Yes, so add to _found_nodes - if ( getFoundNodes0() == null ) { - setFoundNodes0( new HashSet() ); + else { + final int max_x = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getMaximum() + - getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getVisibleAmount(); + if ( scroll_position.x >= max_x ) { + scroll_position.x = max_x; } - getFoundNodes0().add( node.getId() ); - // Check if control key is down } - else if ( ( e.getModifiers() & InputEvent.CTRL_MASK ) != 0 ) { - // Yes, so pop-up menu - displayNodePopupMenu( node, e.getX(), e.getY() ); - // Handle unadorned click + if ( scroll_position.y <= 0 ) { + scroll_position.y = 0; } else { - // Check for right mouse button - if ( e.getModifiers() == 4 ) { - displayNodePopupMenu( node, e.getX(), e.getY() ); + final int max_y = getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getMaximum() + - getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getVisibleAmount(); + if ( scroll_position.y >= max_y ) { + scroll_position.y = max_y; } - else { - // if not in _found_nodes, clear _found_nodes - handleClickToAction( _control_panel.getActionWhenNodeClicked(), node ); + } + repaint(); + getMainPanel().getCurrentScrollPane().getViewport().setViewPosition( scroll_position ); + } + else if ( e.getKeyCode() == KeyEvent.VK_S ) { + if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) + || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) { + setStartingAngle( ( getStartingAngle() % TWO_PI ) + ANGLE_ROTATION_UNIT ); + getControlPanel().displayedPhylogenyMightHaveChanged( false ); + } + } + else if ( e.getKeyCode() == KeyEvent.VK_A ) { + if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) + || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) { + setStartingAngle( ( getStartingAngle() % TWO_PI ) - ANGLE_ROTATION_UNIT ); + if ( getStartingAngle() < 0 ) { + setStartingAngle( TWO_PI + getStartingAngle() ); } + getControlPanel().displayedPhylogenyMightHaveChanged( false ); } } - else { - // no node was clicked - _highlight_node = null; + else if ( e.getKeyCode() == KeyEvent.VK_D ) { + boolean selected = false; + if ( getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.HORIZONTAL ) { + getOptions().setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL ); + selected = true; + } + else { + getOptions().setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL ); + } + getMainPanel().getMainFrame().getlabelDirectionCbmi().setSelected( selected ); + repaint(); } - } - repaint(); - } - - final void mouseDragInBrowserPanel( final MouseEvent e ) { - setCursor( MOVE_CURSOR ); - final Point scroll_position = getMainPanel().getCurrentScrollPane().getViewport().getViewPosition(); - scroll_position.x -= ( e.getX() - getLastDragPointX() ); - scroll_position.y -= ( e.getY() - getLastDragPointY() ); - if ( scroll_position.x < 0 ) { - scroll_position.x = 0; - } - else { - final int max_x = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getMaximum() - - getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getVisibleAmount(); - if ( scroll_position.x > max_x ) { - scroll_position.x = max_x; + else if ( e.getKeyCode() == KeyEvent.VK_X ) { + switchDisplaygetPhylogenyGraphicsType(); + repaint(); } - } - if ( scroll_position.y < 0 ) { - scroll_position.y = 0; - } - else { - final int max_y = getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getMaximum() - - getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getVisibleAmount(); - if ( scroll_position.y > max_y ) { - scroll_position.y = max_y; + else if ( e.getKeyCode() == KeyEvent.VK_C ) { + cycleColors(); + repaint(); } - } - if ( isOvOn() || getOptions().isShowScale() ) { - repaint(); - } - getMainPanel().getCurrentScrollPane().getViewport().setViewPosition( scroll_position ); - } - - final void mouseDragInOvRectangle( final MouseEvent e ) { - setCursor( HAND_CURSOR ); - final double w_ratio = getVisibleRect().width / getOvRectangle().getWidth(); - final double h_ratio = getVisibleRect().height / getOvRectangle().getHeight(); - final Point scroll_position = getMainPanel().getCurrentScrollPane().getViewport().getViewPosition(); - double dx = ( ( w_ratio * e.getX() ) - ( w_ratio * getLastDragPointX() ) ); - double dy = ( ( h_ratio * e.getY() ) - ( h_ratio * getLastDragPointY() ) ); - scroll_position.x = ForesterUtil.roundToInt( scroll_position.x + dx ); - scroll_position.y = ForesterUtil.roundToInt( scroll_position.y + dy ); - if ( scroll_position.x <= 0 ) { - scroll_position.x = 0; - dx = 0; - } - else { - final int max_x = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getMaximum() - - getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getVisibleAmount(); - if ( scroll_position.x >= max_x ) { - dx = 0; - scroll_position.x = max_x; + else if ( getOptions().isShowOverview() && isOvOn() && ( e.getKeyCode() == KeyEvent.VK_O ) ) { + MainFrame.cycleOverview( getOptions(), this ); + repaint(); + } + else if ( getOptions().isShowOverview() && isOvOn() && ( e.getKeyCode() == KeyEvent.VK_I ) ) { + increaseOvSize(); + } + else if ( getOptions().isShowOverview() && isOvOn() && ( e.getKeyCode() == KeyEvent.VK_U ) ) { + decreaseOvSize(); } } - if ( scroll_position.y <= 0 ) { - dy = 0; - scroll_position.y = 0; + if ( e.getKeyCode() == KeyEvent.VK_HOME || e.getKeyCode() == KeyEvent.VK_ESCAPE ) { + getControlPanel().showWhole(); } - else { - final int max_y = getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getMaximum() - - getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getVisibleAmount(); - if ( scroll_position.y >= max_y ) { - dy = 0; - scroll_position.y = max_y; - } + else if ( e.getKeyCode() == KeyEvent.VK_PAGE_UP ) { + getMainPanel().getTreeFontSet().increaseFontSize(); + getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true ); } - repaint(); - getMainPanel().getCurrentScrollPane().getViewport().setViewPosition( scroll_position ); - setLastMouseDragPointX( ( float ) ( e.getX() + dx ) ); - setLastMouseDragPointY( ( float ) ( e.getY() + dy ) ); + else if ( e.getKeyCode() == KeyEvent.VK_PAGE_DOWN ) { + getMainPanel().getTreeFontSet().decreaseFontSize( 1, false ); + getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true ); + } + e.consume(); } - final void mouseMoved( final MouseEvent e ) { - requestFocusInWindow(); - if ( _current_external_nodes != null ) { - _current_external_nodes = null; - repaint(); - } - if ( getControlPanel().isNodeDescPopup() ) { - if ( _node_desc_popup != null ) { - _node_desc_popup.hide(); - _node_desc_popup = null; - } - } - if ( getOptions().isShowOverview() && isOvOn() ) { - if ( inOvVirtualRectangle( e ) ) { - if ( !isInOvRect() ) { - setInOvRect( true ); - repaint(); + final private void makePopupMenus( final PhylogenyNode node ) { + _node_popup_menu = new JPopupMenu(); + final List clickto_names = _main_panel.getControlPanel().getSingleClickToNames(); + _node_popup_menu_items = new JMenuItem[ clickto_names.size() ]; + for( int i = 0; i < clickto_names.size(); i++ ) { + final String title = clickto_names.get( i ); + _node_popup_menu_items[ i ] = new JMenuItem( title ); + if ( title.equals( Configuration.clickto_options[ Configuration.open_seq_web ][ 0 ] ) ) { + final String id = isCanOpenSeqWeb( node ); + if ( !ForesterUtil.isEmpty( id ) ) { + _node_popup_menu_items[ i ].setText( _node_popup_menu_items[ i ].getText() + " [" + id + "]" ); + _node_popup_menu_items[ i ].setEnabled( true ); } - } - else { - if ( isInOvRect() ) { - setInOvRect( false ); - repaint(); + else { + _node_popup_menu_items[ i ].setEnabled( false ); } } - } - if ( inOv( e ) && getOptions().isShowOverview() && isOvOn() ) { - if ( !isInOv() ) { - setInOv( true ); - } - } - else { - if ( isInOv() ) { - setInOv( false ); - } - final PhylogenyNode node = findNode( e.getX(), e.getY() ); - if ( ( node != null ) && ( node.isRoot() || !node.getParent().isCollapse() ) ) { - if ( ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.GET_EXT_DESC_DATA ) ) { - for( final PhylogenyNode n : node.getAllExternalDescendants() ) { - addToCurrentExternalNodes( n.getId() ); + else if ( title.equals( Configuration.clickto_options[ Configuration.open_pdb_web ][ 0 ] ) ) { + final List accs = getPdbAccs( node ); + _node_popup_menu_items[ i ] = new JMenuItem( title ); + if ( !ForesterUtil.isEmpty( accs ) ) { + if ( accs.size() == 1 ) { + _node_popup_menu_items[ i ].setText( _node_popup_menu_items[ i ].getText() + " [" + + TreePanelUtil.pdbAccToString( accs, 0 ) + "]" ); + _node_popup_menu_items[ i ].setEnabled( true ); + } + else if ( accs.size() == 2 ) { + _node_popup_menu_items[ i ].setText( _node_popup_menu_items[ i ].getText() + " [" + + TreePanelUtil.pdbAccToString( accs, 0 ) + ", " + + TreePanelUtil.pdbAccToString( accs, 1 ) + "]" ); + _node_popup_menu_items[ i ].setEnabled( true ); + } + else if ( accs.size() == 3 ) { + _node_popup_menu_items[ i ].setText( _node_popup_menu_items[ i ].getText() + " [" + + TreePanelUtil.pdbAccToString( accs, 0 ) + ", " + + TreePanelUtil.pdbAccToString( accs, 1 ) + ", " + + TreePanelUtil.pdbAccToString( accs, 2 ) + "]" ); + _node_popup_menu_items[ i ].setEnabled( true ); + } + else { + _node_popup_menu_items[ i ].setText( _node_popup_menu_items[ i ].getText() + " [" + + TreePanelUtil.pdbAccToString( accs, 0 ) + ", " + + TreePanelUtil.pdbAccToString( accs, 1 ) + ", " + + TreePanelUtil.pdbAccToString( accs, 2 ) + ", + " + ( accs.size() - 3 ) + " more]" ); + _node_popup_menu_items[ i ].setEnabled( true ); } - setCursor( HAND_CURSOR ); - repaint(); - } - else if ( ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.CUT_SUBTREE ) - || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.COPY_SUBTREE ) - || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.PASTE_SUBTREE ) - || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.DELETE_NODE_OR_SUBTREE ) - || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.REROOT ) - || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.ADD_NEW_NODE ) ) { - setCursor( CUT_CURSOR ); } else { - setCursor( HAND_CURSOR ); - if ( getControlPanel().isNodeDescPopup() ) { - showNodeDataPopup( e, node ); - } + _node_popup_menu_items[ i ].setEnabled( false ); } } - else { - setCursor( ARROW_CURSOR ); - } - } - } - - final void mouseReleasedInBrowserPanel( final MouseEvent e ) { - setCursor( ARROW_CURSOR ); - } - - final void multiplyUrtFactor( final float f ) { - _urt_factor *= f; - } - - final JApplet obtainApplet() { - return ( ( MainPanelApplets ) getMainPanel() ).getApplet(); - } - - final void paintBranchCircular( final PhylogenyNode p, - final PhylogenyNode c, - final Graphics2D g, - final boolean radial_labels, - final boolean to_pdf, - final boolean to_graphics_file ) { - final double angle = _urt_nodeid_angle_map.get( c.getId() ); - final double root_x = _root.getXcoord(); - final double root_y = _root.getYcoord(); - final double dx = root_x - p.getXcoord(); - final double dy = root_y - p.getYcoord(); - final double parent_radius = Math.sqrt( ( dx * dx ) + ( dy * dy ) ); - final double arc = ( _urt_nodeid_angle_map.get( p.getId() ) ) - angle; - assignGraphicsForBranchWithColorForParentBranch( c, false, g, to_pdf, to_graphics_file ); - if ( ( c.isFirstChildNode() || c.isLastChildNode() ) - && ( ( Math.abs( parent_radius * arc ) > 1.5 ) || to_pdf || to_graphics_file ) ) { - final double r2 = 2.0 * parent_radius; - drawArc( root_x - parent_radius, root_y - parent_radius, r2, r2, ( -angle - arc ), arc, g ); - } - drawLine( c.getXcoord(), - c.getYcoord(), - 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 ); - if ( c.isExternal() ) { - 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; + else if ( title.startsWith( Configuration.clickto_options[ Configuration.get_ext_desc_data ][ 0 ] ) ) { + _node_popup_menu_items[ i ] + .setText( Configuration.clickto_options[ Configuration.get_ext_desc_data ][ 0 ] + ": " + + getOptions().getExtDescNodeDataToReturn().toString() ); } - paintNodeDataUnrootedCirc( g, c, to_pdf, to_graphics_file, radial_labels, 0, is_in_found_nodes ); - } - } - - final void paintBranchCircularLite( final PhylogenyNode p, final PhylogenyNode c, final Graphics2D g ) { - final double angle = _urt_nodeid_angle_map.get( c.getId() ); - final double root_x = _root.getXSecondary(); - final double root_y = _root.getYSecondary(); - final double dx = root_x - p.getXSecondary(); - final double dy = root_y - p.getYSecondary(); - final double arc = ( _urt_nodeid_angle_map.get( p.getId() ) ) - angle; - final double parent_radius = Math.sqrt( ( dx * dx ) + ( dy * dy ) ); - g.setColor( getTreeColorSet().getOvColor() ); - if ( ( c.isFirstChildNode() || c.isLastChildNode() ) && ( Math.abs( arc ) > 0.02 ) ) { - final double r2 = 2.0 * parent_radius; - drawArc( root_x - parent_radius, root_y - parent_radius, r2, r2, ( -angle - arc ), arc, g ); - } - drawLine( c.getXSecondary(), - c.getYSecondary(), - root_x + ( Math.cos( angle ) * parent_radius ), - root_y + ( Math.sin( angle ) * parent_radius ), - 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 ); - } - } - - final void paintCircular( final Phylogeny phy, - final double starting_angle, - final int center_x, - final int center_y, - final int radius, - final Graphics2D g, - final boolean to_pdf, - final boolean to_graphics_file ) { - 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; - double current_angle = starting_angle; - int i = 0; - for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) { - final PhylogenyNode n = it.next(); - 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 if ( title.equals( Configuration.clickto_options[ Configuration.open_tax_web ][ 0 ] ) ) { + _node_popup_menu_items[ i ].setEnabled( isCanOpenTaxWeb( node ) ); } - else { - //TODO remove me - System.out.println( "is collapse" + n.getName() ); + else if ( title.equals( Configuration.clickto_options[ Configuration.blast ][ 0 ] ) ) { + _node_popup_menu_items[ i ].setEnabled( isCanBlast( node ) ); } - } - 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 ); - } - - final void paintCircularLite( final Phylogeny phy, - final double starting_angle, - final int center_x, - final int center_y, - final int radius, - final Graphics2D g ) { - final int circ_num_ext_nodes = phy.getNumberOfExternalNodes(); - _root = phy.getRoot(); - _root.setXSecondary( center_x ); - _root.setYSecondary( center_y ); - double current_angle = starting_angle; - for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) { - final PhylogenyNode n = it.next(); - 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 ); - } - paintCircularsLite( phy.getRoot(), phy, center_x, center_y, radius, g ); - } - - final void paintPhylogeny( final Graphics2D g, - final boolean to_pdf, - final boolean to_graphics_file, - final int graphics_file_width, - final int graphics_file_height, - final int graphics_file_x, - final int graphics_file_y ) { - if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) { - return; - } - if ( _control_panel.isShowSequenceRelations() ) { - _query_sequence = _control_panel.getSelectedQuerySequence(); - } - // Color the background - if ( !to_pdf ) { - final Rectangle r = getVisibleRect(); - if ( !getOptions().isBackgroundColorGradient() || getOptions().isPrintBlackAndWhite() ) { - g.setColor( getTreeColorSet().getBackgroundColor() ); - if ( !to_graphics_file ) { - g.fill( r ); + else if ( title.equals( Configuration.clickto_options[ Configuration.delete_subtree_or_node ][ 0 ] ) ) { + if ( !getOptions().isEditable() ) { + continue; } - else { - if ( getOptions().isPrintBlackAndWhite() ) { - g.setColor( Color.WHITE ); - } - g.fillRect( graphics_file_x, graphics_file_y, graphics_file_width, graphics_file_height ); + _node_popup_menu_items[ i ].setEnabled( isCanDelete() ); + } + else if ( title.equals( Configuration.clickto_options[ Configuration.cut_subtree ][ 0 ] ) ) { + if ( !getOptions().isEditable() ) { + continue; } + _node_popup_menu_items[ i ].setEnabled( isCanCut( node ) ); } - else { - if ( !to_graphics_file ) { - g.setPaint( new GradientPaint( r.x, r.y, getTreeColorSet().getBackgroundColor(), r.x, r.y - + r.height, getTreeColorSet().getBackgroundColorGradientBottom() ) ); - g.fill( r ); + else if ( title.equals( Configuration.clickto_options[ Configuration.copy_subtree ][ 0 ] ) ) { + if ( !getOptions().isEditable() ) { + continue; } - else { - g.setPaint( new GradientPaint( graphics_file_x, - graphics_file_y, - getTreeColorSet().getBackgroundColor(), - graphics_file_x, - graphics_file_y + graphics_file_height, - getTreeColorSet().getBackgroundColorGradientBottom() ) ); - g.fillRect( graphics_file_x, graphics_file_y, graphics_file_width, graphics_file_height ); + _node_popup_menu_items[ i ].setEnabled( isCanCopy() ); + } + else if ( title.equals( Configuration.clickto_options[ Configuration.paste_subtree ][ 0 ] ) ) { + if ( !getOptions().isEditable() ) { + continue; } + _node_popup_menu_items[ i ].setEnabled( isCanPaste() ); } - setupStroke( g ); - } - else { - g.setStroke( new BasicStroke( getOptions().getPrintLineWidth() ) ); - } - if ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) - && ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) { - _external_node_index = 0; - // Position starting X of tree - if ( !_phylogeny.isRooted() /*|| ( _subtree_index > 0 )*/) { - _phylogeny.getRoot().setXcoord( TreePanel.MOVE ); + else if ( title.equals( Configuration.clickto_options[ Configuration.edit_node_data ][ 0 ] ) ) { + if ( !getOptions().isEditable() ) { + continue; + } } - else if ( ( _phylogeny.getRoot().getDistanceToParent() > 0.0 ) && getControlPanel().isDrawPhylogram() ) { - _phylogeny.getRoot().setXcoord( ( float ) ( TreePanel.MOVE + ( _phylogeny.getRoot() - .getDistanceToParent() * getXcorrectionFactor() ) ) ); + else if ( title.equals( Configuration.clickto_options[ Configuration.add_new_node ][ 0 ] ) ) { + if ( !getOptions().isEditable() ) { + continue; + } } - else { - _phylogeny.getRoot().setXcoord( TreePanel.MOVE + getXdistance() ); + else if ( title.equals( Configuration.clickto_options[ Configuration.reroot ][ 0 ] ) ) { + _node_popup_menu_items[ i ].setEnabled( isCanReroot() ); } - // Position starting Y of tree - _phylogeny.getRoot().setYcoord( ( getYdistance() * _phylogeny.getRoot().getNumberOfExternalNodes() ) - + ( TreePanel.MOVE / 2.0f ) ); - final int dynamic_hiding_factor = calcDynamicHidingFactor(); - if ( getControlPanel().isDynamicallyHideData() ) { - if ( dynamic_hiding_factor > 1 ) { - getControlPanel().setDynamicHidingIsOn( true ); - } - else { - getControlPanel().setDynamicHidingIsOn( false ); - } + else if ( title.equals( Configuration.clickto_options[ Configuration.collapse_uncollapse ][ 0 ] ) ) { + _node_popup_menu_items[ i ].setEnabled( ( isCanCollapse() && !node.isExternal() ) ); } - if ( _nodes_in_preorder == null ) { - _nodes_in_preorder = new PhylogenyNode[ _phylogeny.getNodeCount() ]; - int i = 0; - for( final PhylogenyNodeIterator it = _phylogeny.iteratorPreorder(); it.hasNext(); ) { - _nodes_in_preorder[ i++ ] = it.next(); - } + else if ( title.equals( Configuration.clickto_options[ Configuration.color_subtree ][ 0 ] ) ) { + _node_popup_menu_items[ i ].setEnabled( isCanColorSubtree() ); } - final boolean disallow_shortcutting = ( dynamic_hiding_factor < 40 ) - || getControlPanel().isUseVisualStyles() || getOptions().isShowDefaultNodeShapesForMarkedNodes() - || ( ( getFoundNodes0() != null ) && !getFoundNodes0().isEmpty() ) - || ( ( getFoundNodes1() != null ) && !getFoundNodes1().isEmpty() ) - || ( ( getCurrentExternalNodes() != null ) && !getCurrentExternalNodes().isEmpty() ) - || to_graphics_file || to_pdf; - for( final PhylogenyNode element : _nodes_in_preorder ) { - paintNodeRectangular( g, - element, - to_pdf, - getControlPanel().isDynamicallyHideData() && ( dynamic_hiding_factor > 1 ), - dynamic_hiding_factor, - to_graphics_file, - disallow_shortcutting ); + else if ( title.equals( Configuration.clickto_options[ Configuration.subtree ][ 0 ] ) ) { + _node_popup_menu_items[ i ].setEnabled( isCanSubtree( node ) ); } - if ( getOptions().isShowScale() && getControlPanel().isDrawPhylogram() && ( getScaleDistance() > 0.0 ) ) { - if ( !( to_graphics_file || to_pdf ) ) { - paintScale( g, - getVisibleRect().x, - getVisibleRect().y + getVisibleRect().height, - to_pdf, - to_graphics_file ); - } - else { - paintScale( g, graphics_file_x, graphics_file_y + graphics_file_height, to_pdf, to_graphics_file ); - } + else if ( title.equals( Configuration.clickto_options[ Configuration.swap ][ 0 ] ) ) { + _node_popup_menu_items[ i ].setEnabled( node.getNumberOfDescendants() == 2 ); } - if ( getOptions().isShowOverview() && isOvOn() && !to_graphics_file && !to_pdf ) { - paintPhylogenyLite( g ); + else if ( title.equals( Configuration.clickto_options[ Configuration.sort_descendents ][ 0 ] ) ) { + _node_popup_menu_items[ i ].setEnabled( node.getNumberOfDescendants() > 1 ); } - } - else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) { - if ( getControlPanel().getDynamicallyHideData() != null ) { - getControlPanel().setDynamicHidingIsOn( false ); + else if ( title.equals( Configuration.clickto_options[ Configuration.uncollapse_all ][ 0 ] ) ) { + _node_popup_menu_items[ i ].setEnabled( isCanUncollapseAll( node ) ); } - final double angle = getStartingAngle(); - final boolean radial_labels = getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL; - _dynamic_hiding_factor = 0; - if ( getControlPanel().isDynamicallyHideData() ) { - _dynamic_hiding_factor = ( int ) ( ( getFontMetricsForLargeDefaultFont().getHeight() * 1.5 * getPhylogeny() - .getNumberOfExternalNodes() ) / ( TWO_PI * 10 ) ); + _node_popup_menu_items[ i ].addActionListener( this ); + _node_popup_menu.add( _node_popup_menu_items[ i ] ); + } + } + + private final void nodeDataAsSB( final PhylogenyNode node, final StringBuilder sb ) { + if ( node != null ) { + if ( getControlPanel().isShowNodeNames() && ( !ForesterUtil.isEmpty( node.getName() ) ) ) { + if ( sb.length() > 0 ) { + sb.append( " " ); + } + sb.append( node.getName() ); } - if ( getControlPanel().getDynamicallyHideData() != null ) { - if ( _dynamic_hiding_factor > 1 ) { - getControlPanel().setDynamicHidingIsOn( true ); + 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() ); } - else { - getControlPanel().setDynamicHidingIsOn( false ); + if ( getControlPanel().isShowGeneNames() + && ( node.getNodeData().getSequence().getGeneName().length() > 0 ) ) { + if ( sb.length() > 0 ) { + sb.append( " " ); + } + sb.append( node.getNodeData().getSequence().getGeneName() ); } - } - paintUnrooted( _phylogeny.getRoot(), - angle, - ( float ) ( angle + ( 2 * Math.PI ) ), - radial_labels, - g, - to_pdf, - to_graphics_file ); - if ( getOptions().isShowScale() ) { - if ( !( to_graphics_file || to_pdf ) ) { - paintScale( g, - getVisibleRect().x, - getVisibleRect().y + getVisibleRect().height, - to_pdf, - to_graphics_file ); + if ( getControlPanel().isShowSeqNames() + && ( node.getNodeData().getSequence().getName().length() > 0 ) ) { + if ( sb.length() > 0 ) { + sb.append( " " ); + } + sb.append( node.getNodeData().getSequence().getName() ); } - else { - paintScale( g, graphics_file_x, graphics_file_y + graphics_file_height, to_pdf, to_graphics_file ); + 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 ( getOptions().isShowOverview() && isOvOn() && !to_graphics_file && !to_pdf ) { - g.setColor( getTreeColorSet().getOvColor() ); - paintUnrootedLite( _phylogeny.getRoot(), - angle, - angle + ( 2 * Math.PI ), - g, - ( getUrtFactorOv() / ( getVisibleRect().width / getOvMaxWidth() ) ) ); - paintOvRectangle( g ); + if ( getControlPanel().isShowProperties() && node.getNodeData().isHasProperties() ) { + if ( sb.length() > 0 ) { + sb.append( " " ); + } + sb.append( propertiesToString( node ) ); } } - else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) { - final int radius = ( int ) ( ( Math.min( getPreferredSize().getWidth(), getPreferredSize().getHeight() ) / 2 ) - ( MOVE + getLongestExtNodeInfo() ) ); - final int d = radius + MOVE + getLongestExtNodeInfo(); - _dynamic_hiding_factor = 0; - if ( getControlPanel().isDynamicallyHideData() && ( radius > 0 ) ) { - _dynamic_hiding_factor = ( int ) ( ( getFontMetricsForLargeDefaultFont().getHeight() * 1.5 * getPhylogeny() - .getNumberOfExternalNodes() ) / ( TWO_PI * radius ) ); + } + + private final void nodeTaxonomyDataAsSB( final Taxonomy taxonomy, final StringBuilder sb ) { + if ( _control_panel.isShowTaxonomyRank() && !ForesterUtil.isEmpty( taxonomy.getRank() ) ) { + sb.append( "[" ); + sb.append( taxonomy.getRank() ); + sb.append( "] " ); + } + 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( ") " ); } - if ( getControlPanel().getDynamicallyHideData() != null ) { - if ( _dynamic_hiding_factor > 1 ) { - getControlPanel().setDynamicHidingIsOn( true ); + else if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) { + if ( getOptions().isAbbreviateScientificTaxonNames() + && ( taxonomy.getScientificName().indexOf( ' ' ) > 0 ) ) { + abbreviateScientificName( taxonomy.getScientificName(), sb ); } else { - getControlPanel().setDynamicHidingIsOn( false ); + sb.append( taxonomy.getScientificName() ); } + sb.append( " " ); } - paintCircular( _phylogeny, getStartingAngle(), d, d, radius > 0 ? radius : 0, g, to_pdf, to_graphics_file ); - if ( getOptions().isShowOverview() && isOvOn() && !to_graphics_file && !to_pdf ) { - final int radius_ov = ( int ) ( getOvMaxHeight() < getOvMaxWidth() ? getOvMaxHeight() / 2 - : getOvMaxWidth() / 2 ); - double x_scale = 1.0; - double y_scale = 1.0; - int x_pos = getVisibleRect().x + getOvXPosition(); - int y_pos = getVisibleRect().y + getOvYPosition(); - if ( getWidth() > getHeight() ) { - x_scale = ( double ) getHeight() / getWidth(); - x_pos = ForesterUtil.roundToInt( x_pos / x_scale ); + 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 { - y_scale = ( double ) getWidth() / getHeight(); - y_pos = ForesterUtil.roundToInt( y_pos / y_scale ); + sb.append( taxonomy.getScientificName() ); } - _at = g.getTransform(); - g.scale( x_scale, y_scale ); - paintCircularLite( _phylogeny, - getStartingAngle(), - x_pos + radius_ov, - y_pos + radius_ov, - ( int ) ( radius_ov - ( getLongestExtNodeInfo() / ( getVisibleRect().width / getOvRectangle() - .getWidth() ) ) ), - g ); - g.setTransform( _at ); - paintOvRectangle( g ); + sb.append( " " ); + } + } + else if ( _control_panel.isShowTaxonomyCommonNames() ) { + if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) { + sb.append( taxonomy.getCommonName() ); + sb.append( " " ); } } } - final void recalculateMaxDistanceToRoot() { - _max_distance_to_root = PhylogenyMethods.calculateMaxDistanceToRoot( getPhylogeny() ); + private final String obtainTitleForExtDescNodeData() { + return getOptions().getExtDescNodeDataToReturn().toString(); } - /** - * Remove all edit-node frames - */ - final void removeAllEditNodeJFrames() { - for( int i = 0; i <= ( TreePanel.MAX_NODE_FRAMES - 1 ); i++ ) { - if ( _node_frames[ i ] != null ) { - _node_frames[ i ].dispose(); - _node_frames[ i ] = null; - } + final private void openPdbWeb( final PhylogenyNode node ) { + final List pdb_ids = getPdbAccs( node ); + if ( ForesterUtil.isEmpty( pdb_ids ) ) { + cannotOpenBrowserWarningMessage( "PDB" ); + return; } - _node_frame_index = 0; - } - - /** - * Remove a node-edit frame. - */ - final void removeEditNodeFrame( final int i ) { - _node_frame_index--; - _node_frames[ i ] = null; - if ( i < _node_frame_index ) { - for( int j = 0; j < ( _node_frame_index - 1 ); j++ ) { - _node_frames[ j ] = _node_frames[ j + 1 ]; + final List uri_strs = TreePanelUtil.createUrisForPdbWeb( node, pdb_ids, getConfiguration(), this ); + if ( !ForesterUtil.isEmpty( uri_strs ) ) { + for( final String uri_str : uri_strs ) { + try { + AptxUtil.launchWebBrowser( new URI( uri_str ), "_aptx_seq" ); + } + catch ( final IOException e ) { + AptxUtil.showErrorMessage( this, e.toString() ); + e.printStackTrace(); + } + catch ( final URISyntaxException e ) { + AptxUtil.showErrorMessage( this, e.toString() ); + e.printStackTrace(); + } } - _node_frames[ _node_frame_index ] = null; + } + else { + cannotOpenBrowserWarningMessage( "PDB" ); } } - final void reRoot( final PhylogenyNode node ) { - if ( !getPhylogeny().isRerootable() ) { - JOptionPane.showMessageDialog( this, - "This is not rerootable", - "Not rerootable", - JOptionPane.WARNING_MESSAGE ); + final private void openSeqWeb( final PhylogenyNode node ) { + if ( ForesterUtil.isEmpty( isCanOpenSeqWeb( node ) ) ) { + cannotOpenBrowserWarningMessage( "sequence" ); return; } - if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) { - JOptionPane.showMessageDialog( this, - "Cannot reroot in unrooted display type", - "Attempt to reroot tree in unrooted display", - JOptionPane.WARNING_MESSAGE ); - return; + final String uri_str = TreePanelUtil.createUriForSeqWeb( node, getConfiguration(), this ); + if ( !ForesterUtil.isEmpty( uri_str ) ) { + try { + AptxUtil.launchWebBrowser( new URI( uri_str ), "_aptx_seq" ); + } + catch ( final IOException e ) { + AptxUtil.showErrorMessage( this, e.toString() ); + e.printStackTrace(); + } + catch ( final URISyntaxException e ) { + AptxUtil.showErrorMessage( this, e.toString() ); + e.printStackTrace(); + } } - getPhylogeny().reRoot( node ); - getPhylogeny().recalculateNumberOfExternalDescendants( true ); - resetNodeIdToDistToLeafMap(); - setNodeInPreorderToNull(); - resetPreferredSize(); - getMainPanel().adjustJScrollPane(); - setEdited( true ); - repaint(); - if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) { - getControlPanel().showWhole(); + else { + cannotOpenBrowserWarningMessage( "sequence" ); } } - final void resetNodeIdToDistToLeafMap() { - _nodeid_dist_to_leaf = new HashMap(); - } - - final void resetPreferredSize() { - if ( ( getPhylogeny() == null ) || getPhylogeny().isEmpty() ) { + final private void openTaxWeb( final PhylogenyNode node ) { + if ( !isCanOpenTaxWeb( node ) ) { + cannotOpenBrowserWarningMessage( "taxonomic" ); return; } - int x = 0; - int y = 0; - y = TreePanel.MOVE - + ForesterUtil.roundToInt( getYdistance() * getPhylogeny().getRoot().getNumberOfExternalNodes() * 2 ); - if ( getControlPanel().isDrawPhylogram() ) { - x = TreePanel.MOVE - + getLongestExtNodeInfo() - + ForesterUtil - .roundToInt( ( getXcorrectionFactor() * getPhylogeny().getHeight() ) + getXdistance() ); + String uri_str = null; + final Taxonomy tax = node.getNodeData().getTaxonomy(); + if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getValue() ) + && tax.getIdentifier().getValue().startsWith( "http://" ) ) { + try { + uri_str = new URI( tax.getIdentifier().getValue() ).toString(); + } + catch ( final URISyntaxException e ) { + AptxUtil.showErrorMessage( this, e.toString() ); + uri_str = null; + e.printStackTrace(); + } } - else { - if ( !isNonLinedUpCladogram() && !isUniformBranchLengthsForCladogram() ) { - x = TreePanel.MOVE - + getLongestExtNodeInfo() - + ForesterUtil.roundToInt( getXdistance() - * ( getPhylogeny().getRoot().getNumberOfExternalNodes() + 2 ) ); + else if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getValue() ) + && !ForesterUtil.isEmpty( tax.getIdentifier().getProvider() ) + && ( tax.getIdentifier().getProvider().equalsIgnoreCase( "ncbi" ) + || tax.getIdentifier().getProvider().equalsIgnoreCase( "uniprot" ) ) ) { + try { + uri_str = "http://www.uniprot.org/taxonomy/" + + URLEncoder.encode( tax.getIdentifier().getValue(), ForesterConstants.UTF_8 ); } - else { - x = TreePanel.MOVE - + getLongestExtNodeInfo() - + ForesterUtil.roundToInt( getXdistance() - * ( PhylogenyMethods.calculateMaxDepth( getPhylogeny() ) + 1 ) ); + catch ( final UnsupportedEncodingException e ) { + AptxUtil.showErrorMessage( this, e.toString() ); + e.printStackTrace(); } } - setPreferredSize( new Dimension( x, y ) ); - } - - final void selectNode( final PhylogenyNode node ) { - if ( ( getFoundNodes0() != null ) && getFoundNodes0().contains( node.getId() ) ) { - getFoundNodes0().remove( node.getId() ); - getControlPanel().setSearchFoundCountsOnLabel0( getFoundNodes0().size() ); - if ( getFoundNodes0().size() < 1 ) { - getControlPanel().searchReset0(); + else if ( !ForesterUtil.isEmpty( tax.getScientificName() ) ) { + try { + uri_str = "http://www.uniprot.org/taxonomy/?query=" + + URLEncoder.encode( tax.getScientificName(), ForesterConstants.UTF_8 ); + } + catch ( final UnsupportedEncodingException e ) { + AptxUtil.showErrorMessage( this, e.toString() ); + e.printStackTrace(); } } - else { - getControlPanel().getSearchFoundCountsLabel0().setVisible( true ); - getControlPanel().getSearchResetButton0().setEnabled( true ); - getControlPanel().getSearchResetButton0().setVisible( true ); - if ( getFoundNodes0() == null ) { - setFoundNodes0( new HashSet() ); + else if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) { + try { + uri_str = "http://www.uniprot.org/taxonomy/?query=" + + URLEncoder.encode( tax.getTaxonomyCode(), ForesterConstants.UTF_8 ); + } + catch ( final UnsupportedEncodingException e ) { + AptxUtil.showErrorMessage( this, e.toString() ); + e.printStackTrace(); } - getFoundNodes0().add( node.getId() ); - getControlPanel().setSearchFoundCountsOnLabel0( getFoundNodes0().size() ); + } + else if ( !ForesterUtil.isEmpty( tax.getCommonName() ) ) { + try { + uri_str = "http://www.uniprot.org/taxonomy/?query=" + + URLEncoder.encode( tax.getCommonName(), ForesterConstants.UTF_8 ); + } + catch ( final UnsupportedEncodingException e ) { + AptxUtil.showErrorMessage( this, e.toString() ); + e.printStackTrace(); + } + } + if ( !ForesterUtil.isEmpty( uri_str ) ) { + try { + AptxUtil.launchWebBrowser( new URI( uri_str ), "_aptx_tax" ); + } + catch ( final IOException e ) { + AptxUtil.showErrorMessage( this, e.toString() ); + e.printStackTrace(); + } + catch ( final URISyntaxException e ) { + AptxUtil.showErrorMessage( this, e.toString() ); + e.printStackTrace(); + } + } + else { + cannotOpenBrowserWarningMessage( "taxonomic" ); } } - final void setArrowCursor() { - setCursor( ARROW_CURSOR ); - repaint(); - } - - final void setControlPanel( final ControlPanel atv_control ) { - _control_panel = atv_control; - } - - void setCurrentExternalNodesDataBuffer( final StringBuilder sb ) { - increaseCurrentExternalNodesDataBufferChangeCounter(); - _current_external_nodes_data_buffer = sb; - } - - final void setFoundNodes0( final Set found_nodes ) { - _found_nodes_0 = found_nodes; - } - - final void setFoundNodes1( final Set found_nodes ) { - _found_nodes_1 = found_nodes; - } - - final void setInOvRect( final boolean in_ov_rect ) { - _in_ov_rect = in_ov_rect; - } - - final void setLargeFonts() { - getTreeFontSet().largeFonts(); - } - - final void setLastMouseDragPointX( final float x ) { - _last_drag_point_x = x; - } - - final void setLastMouseDragPointY( final float y ) { - _last_drag_point_y = y; - } - - final void setMediumFonts() { - getTreeFontSet().mediumFonts(); - } - - final void setNodeInPreorderToNull() { - _nodes_in_preorder = null; - } - - final void setOvOn( final boolean ov_on ) { - _ov_on = ov_on; - } - - final void setPhylogenyGraphicsType( final PHYLOGENY_GRAPHICS_TYPE graphics_type ) { - _graphics_type = graphics_type; - setTextAntialias(); - } - - final void setSmallFonts() { - getTreeFontSet().smallFonts(); - } - - final void setStartingAngle( final double starting_angle ) { - _urt_starting_angle = starting_angle; - } - - void setStatisticsForExpressionValues( final DescriptiveStatistics statistics_for_expression_values ) { - _statistics_for_vector_data = statistics_for_expression_values; - } - - final void setSuperTinyFonts() { - getTreeFontSet().superTinyFonts(); - } - - final void setTextAntialias() { - if ( ( _phylogeny != null ) && !_phylogeny.isEmpty() ) { - if ( _phylogeny.getNumberOfExternalNodes() <= LIMIT_FOR_HQ_RENDERING ) { - _rendering_hints.put( RenderingHints.KEY_RENDERING, RenderingHints.VALUE_RENDER_QUALITY ); + final private void paintBranchLength( final Graphics2D g, + final PhylogenyNode node, + final boolean to_pdf, + final boolean to_graphics_file ) { + g.setFont( getTreeFontSet().getSmallFont() ); + if ( to_pdf || ( to_graphics_file && getOptions().isPrintBlackAndWhite() ) ) { + g.setColor( Color.BLACK ); + } + else { + g.setColor( getTreeColorSet().getBranchLengthColor() ); + } + 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().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().getSmallMaxDescent(), + g ); } else { - _rendering_hints.put( RenderingHints.KEY_RENDERING, RenderingHints.VALUE_RENDER_SPEED ); + TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), + node.getParent().getXcoord() + 3, + node.getYcoord() - getTreeFontSet().getSmallMaxDescent(), + g ); } } - if ( getMainPanel().getOptions().isAntialiasScreen() ) { - _rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON ); - // try { - _rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_LCD_HRGB ); - // } - // catch ( final Throwable e ) { - // _rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_ON ); - //} - } else { - _rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_OFF ); - _rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_OFF ); + TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), + 3, + node.getYcoord() - getTreeFontSet().getSmallMaxDescent(), + g ); } } - final void setTinyFonts() { - getTreeFontSet().tinyFonts(); + final private void paintBranchLite( final Graphics2D g, + final float x1, + final float x2, + final float y1, + final float y2, + final PhylogenyNode node ) { + g.setColor( getTreeColorSet().getOvColor() ); + if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR ) { + drawLine( x1, y1, x2, y2, g ); + } + else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CONVEX ) { + _quad_curve.setCurve( x1, y1, x1, y2, x2, y2 ); + ( g ).draw( _quad_curve ); + } + else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CURVED ) { + final float dx = x2 - x1; + final float dy = y2 - y1; + _cubic_curve.setCurve( x1, + y1, + x1 + ( dx * 0.4f ), + y1 + ( dy * 0.2f ), + x1 + ( dx * 0.6f ), + y1 + ( dy * 0.8f ), + x2, + y2 ); + ( g ).draw( _cubic_curve ); + } + else { + final float x2a = x2; + final float x1a = x1; + // draw the vertical line + if ( node.isFirstChildNode() || node.isLastChildNode() ) { + drawLine( x1, y1, x1, y2, g ); + } + // draw the horizontal line + drawLine( x1a, y2, x2a, y2, g ); + } } - final void setTreeFile( final File treefile ) { - _treefile = treefile; - } - - final void setXcorrectionFactor( final float f ) { - _x_correction_factor = f; - } - - final void setXdistance( final float x ) { - _x_distance = x; + /** + * Paint a branch which consists of a vertical and a horizontal bar + * @param is_ind_found_nodes + */ + final private void paintBranchRectangular( final Graphics2D g, + final float x1, + final float x2, + final float y1, + final float y2, + final PhylogenyNode node, + final boolean to_pdf, + final boolean to_graphics_file ) { + assignGraphicsForBranchWithColorForParentBranch( node, false, g, to_pdf, to_graphics_file ); + if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR ) { + drawLine( x1, y1, x2, y2, g ); + } + else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CONVEX ) { + _quad_curve.setCurve( x1, y1, x1, y2, x2, y2 ); + g.draw( _quad_curve ); + } + else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CURVED ) { + final float dx = x2 - x1; + final float dy = y2 - y1; + _cubic_curve.setCurve( x1, + y1, + x1 + ( dx * 0.4f ), + y1 + ( dy * 0.2f ), + x1 + ( dx * 0.6f ), + y1 + ( dy * 0.8f ), + x2, + y2 ); + g.draw( _cubic_curve ); + } + else { + 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 ) ) { + 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.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 ); + } + } + else { + drawLine( x1, y1, x1, y2, g ); + } + } + } + // draw the horizontal line + if ( !to_graphics_file && !to_pdf && ( ( y2 < ( getVisibleRect().getMinY() - 20 ) ) + || ( y2 > ( getVisibleRect().getMaxY() + 20 ) ) ) ) { + return; + } + float x1_r = 0; + 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 { + 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 ); + } + } + else { + drawRectFilled( x1a, y2 - ( w / 2 ), x2a - x1a, w, g ); + } + } + if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) { + if ( x1_r > x2a ) { + x1_r = x2a; + } + if ( y2 > y2_r ) { + final double diff = y2 - y2_r; + _arc.setArc( x1, y2_r - diff, 2 * ( x1_r - x1 ), 2 * diff, 180, 90, Arc2D.OPEN ); + } + else { + _arc.setArc( x1, y2, 2 * ( x1_r - x1 ), 2 * ( y2_r - y2 ), 90, 90, Arc2D.OPEN ); + } + g.draw( _arc ); + } + } + if ( node.isExternal() ) { + paintNodeBox( x2, y2, node, g, to_pdf, to_graphics_file ); + } } - final void setYdistance( final float y ) { - _y_distance = y; + final private double paintCirculars( final PhylogenyNode n, + final Phylogeny phy, + final float center_x, + final float center_y, + final double radius, + final boolean radial_labels, + final Graphics2D g, + final boolean to_pdf, + final boolean to_graphics_file ) { + if ( n.isExternal() || n.isCollapse() ) { //~~circ collapse + if ( !_urt_nodeid_angle_map.containsKey( n.getId() ) ) { + System.out.println( "no " + n + " =====>>>>>>> ERROR!" );//TODO + } + return _urt_nodeid_angle_map.get( n.getId() ); + } + else { + final List descs = n.getDescendants(); + double sum = 0; + for( final PhylogenyNode desc : descs ) { + sum += paintCirculars( desc, + phy, + center_x, + center_y, + radius, + radial_labels, + g, + to_pdf, + to_graphics_file ); + } + double r = 0; + if ( !n.isRoot() ) { + r = 1 - ( ( ( double ) _circ_max_depth - n.calculateDepth() ) / _circ_max_depth ); + } + final double theta = sum / descs.size(); + n.setXcoord( ( float ) ( center_x + ( r * radius * Math.cos( theta ) ) ) ); + n.setYcoord( ( float ) ( center_y + ( r * radius * Math.sin( theta ) ) ) ); + _urt_nodeid_angle_map.put( n.getId(), theta ); + for( final PhylogenyNode desc : descs ) { + paintBranchCircular( n, desc, g, radial_labels, to_pdf, to_graphics_file ); + } + return theta; + } } - final void sortDescendants( final PhylogenyNode node ) { - if ( !node.isExternal() ) { - DESCENDANT_SORT_PRIORITY pri = DESCENDANT_SORT_PRIORITY.NODE_NAME; - if ( getControlPanel().isShowTaxonomyScientificNames() || getControlPanel().isShowTaxonomyCode() ) { - pri = DESCENDANT_SORT_PRIORITY.TAXONOMY; + final private void paintCircularsLite( final PhylogenyNode n, + final Phylogeny phy, + final int center_x, + final int center_y, + final int radius, + final Graphics2D g ) { + if ( n.isExternal() ) { + return; + } + else { + final List descs = n.getDescendants(); + for( final PhylogenyNode desc : descs ) { + paintCircularsLite( desc, phy, center_x, center_y, radius, g ); } - else if ( getControlPanel().isShowSeqNames() || getControlPanel().isShowSeqSymbols() - || getControlPanel().isShowGeneNames() ) { - pri = DESCENDANT_SORT_PRIORITY.SEQUENCE; + float r = 0; + if ( !n.isRoot() ) { + r = 1 - ( ( ( float ) _circ_max_depth - n.calculateDepth() ) / _circ_max_depth ); + } + final double theta = _urt_nodeid_angle_map.get( n.getId() ); + n.setXSecondary( ( float ) ( center_x + ( radius * r * Math.cos( theta ) ) ) ); + n.setYSecondary( ( float ) ( center_y + ( radius * r * Math.sin( theta ) ) ) ); + for( final PhylogenyNode desc : descs ) { + paintBranchCircularLite( n, desc, g ); } - PhylogenyMethods.sortNodeDescendents( node, pri ); - setNodeInPreorderToNull(); - _phylogeny.externalNodesHaveChanged(); - _phylogeny.clearHashIdToNodeMap(); - _phylogeny.recalculateNumberOfExternalDescendants( true ); - resetNodeIdToDistToLeafMap(); - setEdited( true ); } - repaint(); } - final void subTree( final PhylogenyNode node ) { - if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) { - JOptionPane.showMessageDialog( this, - "Cannot get a sub/super tree in unrooted display", - "Attempt to get sub/super tree in unrooted display", - JOptionPane.WARNING_MESSAGE ); - return; + final private void paintCollapsedNode( final Graphics2D g, + final PhylogenyNode node, + final boolean to_graphics_file, + final boolean to_pdf, + final boolean is_in_found_nodes ) { + //// + //// TODO + //// + Color c = null; + int res[] = null; + if ( _found_nodes_0 != null || _found_nodes_1 != null ) { + res = calcFoundNodesInSubtree( node ); } - if ( node.isExternal() ) { - JOptionPane.showMessageDialog( this, - "Cannot get a subtree of a external node", - "Attempt to get subtree of external node", - JOptionPane.WARNING_MESSAGE ); - return; + if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) { + c = Color.BLACK; } - if ( node.isRoot() && !isCurrentTreeIsSubtree() ) { - JOptionPane.showMessageDialog( this, - "Cannot get a subtree of the root node", - "Attempt to get subtree of root node", - JOptionPane.WARNING_MESSAGE ); - return; + //TODO + //FIXME + // else if ( is_in_found_nodes ) { + // c = getColorForFoundNode( node ); + // } + // else if ( getControlPanel().isColorAccordingToSequence() ) { + // c = getSequenceBasedColor( node ); + // } + // else if ( getControlPanel().isColorAccordingToTaxonomy() ) { + // c = getTaxonomyBasedColor( node ); + // } + else if ( getOptions().isColorLabelsSameAsParentBranch() && getControlPanel().isUseVisualStyles() + && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) { + c = PhylogenyMethods.getBranchColorValue( node ); } - setNodeInPreorderToNull(); - if ( !node.isExternal() && !node.isRoot() && ( _subtree_index <= ( TreePanel.MAX_SUBTREES - 1 ) ) ) { - _sub_phylogenies[ _subtree_index ] = _phylogeny; - _sub_phylogenies_temp_roots[ _subtree_index ] = node; - ++_subtree_index; - _phylogeny = TreePanelUtil.subTree( node, _phylogeny ); - updateSubSuperTreeButton(); + else if ( to_pdf ) { + g.setColor( getTreeColorSet().getBranchColorForPdf() ); } - else if ( node.isRoot() && isCurrentTreeIsSubtree() ) { - superTree(); + else { + c = getTreeColorSet().getCollapseFillColor(); } - _main_panel.getControlPanel().showWhole(); - repaint(); - } - - final void superTree() { - setNodeInPreorderToNull(); - final PhylogenyNode temp_root = _sub_phylogenies_temp_roots[ _subtree_index - 1 ]; - for( final PhylogenyNode n : temp_root.getDescendants() ) { - n.setParent( temp_root ); - } - _sub_phylogenies[ _subtree_index ] = null; - _sub_phylogenies_temp_roots[ _subtree_index ] = null; - _phylogeny = _sub_phylogenies[ --_subtree_index ]; - updateSubSuperTreeButton(); - } - - final void swap( final PhylogenyNode node ) { - if ( node.isExternal() || ( node.getNumberOfDescendants() < 2 ) ) { - return; - } - if ( node.getNumberOfDescendants() > 2 ) { - JOptionPane.showMessageDialog( this, - "Cannot swap descendants of nodes with more than 2 descendants", - "Cannot swap descendants", - JOptionPane.ERROR_MESSAGE ); - return; + double d = node.getAllExternalDescendants().size(); + float xxx; + double s = 0; + if ( getControlPanel().isDrawPhylogram() ) { + if ( d > 1000 ) { + d = 0.75 * _y_distance; + } + else { + d = 0.25 * Math.log10( d ) * _y_distance; + } + final float half_box_size = 0.5f * getOptions().getDefaultNodeShapeSize(); + if ( d < half_box_size ) { + d = half_box_size; + } + _polygon.reset(); + final float xx = node.getXcoord() - ( getOptions().getDefaultNodeShapeSize() ); + xxx = xx > ( node.getParent().getXcoord() + 1 ) ? xx : node.getParent().getXcoord() + 1; + _polygon.moveTo( xxx, node.getYcoord() + 0.5 ); + _polygon.lineTo( xxx, node.getYcoord() - 0.5 ); + s = _options.isCollapsedWithAverageHeigh() + ? PhylogenyMethods.calculateAverageTreeHeight( node ) * _x_correction_factor : 1; + _polygon.lineTo( node.getXcoord() + s, node.getYcoord() - d ); + _polygon.lineTo( node.getXcoord() + s, node.getYcoord() + d ); + _polygon.closePath(); } - if ( !node.isExternal() ) { - node.swapChildren(); - setNodeInPreorderToNull(); - _phylogeny.externalNodesHaveChanged(); - _phylogeny.clearHashIdToNodeMap(); - _phylogeny.recalculateNumberOfExternalDescendants( true ); - resetNodeIdToDistToLeafMap(); - setEdited( true ); + else { + if ( d > 1000 ) { + d = _y_distance; + } + else { + d = ( Math.log10( d ) * _y_distance ) / 2.5; + } + final int box_size = getOptions().getDefaultNodeShapeSize() + 1; + if ( d < box_size ) { + d = box_size; + } + final float xx = node.getXcoord() - ( 2 * box_size ); + xxx = xx > ( node.getParent().getXcoord() + 1 ) ? xx : node.getParent().getXcoord() + 1; + _polygon.reset(); + _polygon.moveTo( xxx, node.getYcoord() ); + _polygon.lineTo( node.getXcoord() + 1, node.getYcoord() - d ); + _polygon.lineTo( node.getXcoord() + 1, node.getYcoord() + d ); + _polygon.closePath(); } - repaint(); - } - - final void taxColor() { - if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) { - return; + if ( getOptions().getDefaultNodeFill() == NodeVisualData.NodeFill.SOLID ) { + g.setColor( c ); + g.fill( _polygon ); } - setWaitCursor(); - TreePanelUtil.colorPhylogenyAccordingToExternalTaxonomy( _phylogeny, this ); - _control_panel.setColorBranches( true ); - if ( _control_panel.getUseVisualStylesCb() != null ) { - _control_panel.getUseVisualStylesCb().setSelected( true ); + else if ( getOptions().getDefaultNodeFill() == NodeVisualData.NodeFill.NONE ) { + g.setColor( getBackground() ); + g.fill( _polygon ); + g.setColor( c ); + g.draw( _polygon ); } - setEdited( true ); - setArrowCursor(); - repaint(); - } - - final void updateOvSettings() { - switch ( getOptions().getOvPlacement() ) { - case LOWER_LEFT: - setOvXPosition( OV_BORDER ); - setOvYPosition( ForesterUtil.roundToInt( getVisibleRect().height - OV_BORDER - getOvMaxHeight() ) ); - setOvYStart( ForesterUtil.roundToInt( getOvYPosition() + ( getOvMaxHeight() / 2 ) ) ); - break; - case LOWER_RIGHT: - setOvXPosition( ForesterUtil.roundToInt( getVisibleRect().width - OV_BORDER - getOvMaxWidth() ) ); - setOvYPosition( ForesterUtil.roundToInt( getVisibleRect().height - OV_BORDER - getOvMaxHeight() ) ); - setOvYStart( ForesterUtil.roundToInt( getOvYPosition() + ( getOvMaxHeight() / 2 ) ) ); - break; - case UPPER_RIGHT: - setOvXPosition( ForesterUtil.roundToInt( getVisibleRect().width - OV_BORDER - getOvMaxWidth() ) ); - setOvYPosition( OV_BORDER ); - setOvYStart( ForesterUtil.roundToInt( OV_BORDER + ( getOvMaxHeight() / 2 ) ) ); - break; - default: - setOvXPosition( OV_BORDER ); - setOvYPosition( OV_BORDER ); - setOvYStart( ForesterUtil.roundToInt( OV_BORDER + ( getOvMaxHeight() / 2 ) ) ); - break; + else if ( getOptions().getDefaultNodeFill() == NodeFill.GRADIENT ) { + g.setPaint( new GradientPaint( xxx, + node.getYcoord(), + getBackground(), + node.getXcoord(), + ( 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, s ); } - final void updateOvSizes() { - if ( ( getWidth() > ( 1.05 * getVisibleRect().width ) ) || ( getHeight() > ( 1.05 * getVisibleRect().height ) ) ) { - setOvOn( true ); - float l = getLongestExtNodeInfo(); - final float w_ratio = getOvMaxWidth() / getWidth(); - l *= w_ratio; - final int ext_nodes = _phylogeny.getRoot().getNumberOfExternalNodes(); - setOvYDistance( getOvMaxHeight() / ( 2 * ext_nodes ) ); - float ov_xdist = 0; - if ( !isNonLinedUpCladogram() && !isUniformBranchLengthsForCladogram() ) { - ov_xdist = ( ( getOvMaxWidth() - l ) / ( ext_nodes ) ); - } - else { - ov_xdist = ( ( getOvMaxWidth() - l ) / ( PhylogenyMethods.calculateMaxDepth( _phylogeny ) ) ); + final private void paintConfidenceValues( final Graphics2D g, + final PhylogenyNode node, + final boolean to_pdf, + final boolean to_graphics_file ) { + final List confidences = node.getBranchData().getConfidences(); + boolean not_first = false; + Collections.sort( confidences ); + final StringBuilder sb = new StringBuilder(); + for( final Confidence confidence : confidences ) { + if ( ForesterUtil.isEmpty( SHOW_ONLY_THIS_CONF_TYPE ) || ( !ForesterUtil.isEmpty( confidence.getType() ) + && confidence.getType().equalsIgnoreCase( SHOW_ONLY_THIS_CONF_TYPE ) ) ) { + final double value = confidence.getValue(); + if ( value != Confidence.CONFIDENCE_DEFAULT_VALUE ) { + if ( value < getOptions().getMinConfidenceValue() ) { + return; + } + if ( not_first ) { + sb.append( "/" ); + } + else { + not_first = true; + } + sb.append( FORMATTER_CONFIDENCE.format( ForesterUtil + .round( value, getOptions().getNumberOfDigitsAfterCommaForConfidenceValues() ) ) ); + if ( getOptions().isShowConfidenceStddev() ) { + if ( confidence.getStandardDeviation() != Confidence.CONFIDENCE_DEFAULT_VALUE ) { + sb.append( "(" ); + sb.append( FORMATTER_CONFIDENCE + .format( ForesterUtil.round( confidence.getStandardDeviation(), + getOptions() + .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) ); + sb.append( ")" ); + } + } + } } - float ydist = ( float ) ( ( getOvMaxWidth() / ( ext_nodes * 2.0 ) ) ); - if ( ov_xdist < 0.0 ) { - ov_xdist = 0.0f; + } + if ( sb.length() > 0 ) { + 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; } - if ( ydist < 0.0 ) { - ydist = 0.0f; + else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) { + x += ROUNDED_D; } - setOvXDistance( ov_xdist ); - final double height = _phylogeny.getHeight(); - if ( height > 0 ) { - final float ov_corr = ( float ) ( ( ( getOvMaxWidth() - l ) - getOvXDistance() ) / height ); - setOvXcorrectionFactor( ov_corr > 0 ? ov_corr : 0 ); + if ( to_pdf || ( to_graphics_file && getOptions().isPrintBlackAndWhite() ) ) { + g.setColor( Color.BLACK ); } else { - setOvXcorrectionFactor( 0 ); + g.setColor( getTreeColorSet().getConfidenceColor() ); } - } - else { - setOvOn( false ); + final String conf_str = sb.toString(); + TreePanel.drawString( conf_str, + parent_x + ( ( x - parent_x + - getTreeFontSet().getFontMetricsSmall().stringWidth( conf_str ) ) / 2 ), + ( node.getYcoord() + getTreeFontSet().getSmallMaxAscent() ) - 1, + g ); } } - void updateSetOfCollapsedExternalNodes() { - final Phylogeny phy = getPhylogeny(); - _collapsed_external_nodeid_set.clear(); - if ( phy != null ) { - 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() ); - ext_node.setCollapse( true ); - continue E; - } - n = n.getParent(); - } + final private void paintGainedAndLostCharacters( final Graphics2D g, + final PhylogenyNode node, + final String gained, + final String lost ) { + if ( node.getParent() != null ) { + final float parent_x = node.getParent().getXcoord(); + final float x = node.getXcoord(); + g.setFont( getTreeFontSet().getLargeFont() ); + g.setColor( getTreeColorSet().getGainedCharactersColor() ); + if ( AptxConstants.SPECIAL_CUSTOM ) { + g.setColor( Color.BLUE ); } + TreePanel.drawString( gained, + 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 - getFontMetricsForLargeDefaultFont().stringWidth( lost ) ) + / 2 ), + ( node.getYcoord() + getFontMetricsForLargeDefaultFont().getMaxAscent() ), + g ); } } - final void updateSubSuperTreeButton() { - if ( _subtree_index < 1 ) { - getControlPanel().deactivateButtonToReturnToSuperTree(); - } - else { - getControlPanel().activateButtonToReturnToSuperTree( _subtree_index ); - } - } - - final void zoomInDomainStructure() { - if ( _domain_structure_width < 2000 ) { - _domain_structure_width *= 1.2; - } - } - - final void zoomOutDomainStructure() { - if ( _domain_structure_width > 20 ) { - _domain_structure_width *= 0.8; - } - } - - 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 ) ); - if ( a.length > 2 ) { - for( int i = 2; i < a.length; i++ ) { - sb.append( " " ); - sb.append( a[ i ] ); + private void paintMolecularSequences( final Graphics2D g, final PhylogenyNode node, final boolean to_pdf ) { + final RenderableMsaSequence rs = RenderableMsaSequence + .createInstance( node.getNodeData().getSequence().getMolecularSequence(), + node.getNodeData().getSequence().getType(), + getConfiguration() ); + if ( rs != null ) { + final int default_height = 8; + final float y = getYdistance(); + final int h = ( y / 2 ) < default_height ? ForesterUtil.roundToInt( y * 2 ) : default_height; + rs.setRenderingHeight( h > 1 ? h : 1 ); + if ( getControlPanel().isDrawPhylogram() ) { + rs.render( ( float ) ( ( getMaxDistanceToRoot() * getXcorrectionFactor() ) + _length_of_longest_text ), + node.getYcoord() - ( h / 2.0f ), + g, + this, + to_pdf ); + } + else { + rs.render( getPhylogeny().getFirstExternalNode().getXcoord() + _length_of_longest_text, + node.getYcoord() - ( h / 2.0f ), + g, + this, + to_pdf ); } } } - final private void addEmptyNode( final PhylogenyNode node ) { - if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) { - errorMessageNoCutCopyPasteInUnrootedDisplay(); + /** + * Draw a box at the indicated node. + * + * @param x + * @param y + * @param node + * @param g + */ + final private void paintNodeBox( final float x, + final float y, + final PhylogenyNode node, + final Graphics2D g, + final boolean to_pdf, + final boolean to_graphics_file ) { + if ( node.isCollapse() ) { return; } - final String label = createASimpleTextRepresentationOfANode( node ); - String msg = ""; - if ( ForesterUtil.isEmpty( label ) ) { - msg = "How to add the new, empty node?"; - } - else { - msg = "How to add the new, empty node to node" + label + "?"; + // if this node should be highlighted, do so + if ( ( _highlight_node == node ) && !to_pdf && !to_graphics_file ) { + 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 ); } - final Object[] options = { "As sibling", "As descendant", "Cancel" }; - final int r = JOptionPane.showOptionDialog( this, - msg, - "Addition of Empty New Node", - JOptionPane.CLOSED_OPTION, - JOptionPane.QUESTION_MESSAGE, - null, - options, - options[ 2 ] ); - boolean add_as_sibling = true; - if ( r == 1 ) { - add_as_sibling = false; - } - else if ( r != 0 ) { - return; - } - final Phylogeny phy = new Phylogeny(); - phy.setRoot( new PhylogenyNode() ); - phy.setRooted( true ); - if ( add_as_sibling ) { - if ( node.isRoot() ) { - JOptionPane.showMessageDialog( this, - "Cannot add sibling to root", - "Attempt to add sibling to root", - JOptionPane.ERROR_MESSAGE ); - return; + if ( ( isInFoundNodes( node ) || isInCurrentExternalNodes( node ) ) + || ( getOptions().isShowDefaultNodeShapesExternal() && node.isExternal() ) + || ( getOptions().isShowDefaultNodeShapesInternal() && node.isInternal() ) + || ( getOptions().isShowDefaultNodeShapesForMarkedNodes() + && ( node.getNodeData().getNodeVisualData() != null ) + && ( !node.getNodeData().getNodeVisualData().isEmpty() ) ) + || ( 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() ) ) ) { + NodeVisualData vis = null; + if ( getControlPanel().isUseVisualStyles() && ( node.getNodeData().getNodeVisualData() != null ) + && ( !node.getNodeData().getNodeVisualData().isEmpty() ) ) { + vis = node.getNodeData().getNodeVisualData(); } - phy.addAsSibling( node ); - } - else { - phy.addAsChild( node ); - } - setNodeInPreorderToNull(); - _phylogeny.externalNodesHaveChanged(); - _phylogeny.clearHashIdToNodeMap(); - _phylogeny.recalculateNumberOfExternalDescendants( true ); - resetNodeIdToDistToLeafMap(); - setEdited( true ); - repaint(); - } - - final private void addToCurrentExternalNodes( final long i ) { - if ( _current_external_nodes == null ) { - _current_external_nodes = new HashSet(); - } - _current_external_nodes.add( i ); - } - - final private void assignGraphicsForBranchWithColorForParentBranch( final PhylogenyNode node, - final boolean is_vertical, - final Graphics g, - final boolean to_pdf, - final boolean to_graphics_file ) { - final NodeClickAction action = _control_panel.getActionWhenNodeClicked(); - if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) { - g.setColor( Color.BLACK ); - } - else if ( ( ( action == NodeClickAction.COPY_SUBTREE ) || ( action == NodeClickAction.CUT_SUBTREE ) - || ( action == NodeClickAction.DELETE_NODE_OR_SUBTREE ) || ( action == NodeClickAction.PASTE_SUBTREE ) || ( action == NodeClickAction.ADD_NEW_NODE ) ) - && ( getCutOrCopiedTree() != null ) - && ( getCopiedAndPastedNodes() != null ) - && !to_pdf - && !to_graphics_file && getCopiedAndPastedNodes().contains( node.getId() ) ) { - g.setColor( getTreeColorSet().getFoundColor0() ); - } - else if ( getControlPanel().isUseVisualStyles() && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) { - g.setColor( PhylogenyMethods.getBranchColorValue( node ) ); - } - else if ( to_pdf ) { - g.setColor( getTreeColorSet().getBranchColorForPdf() ); - } - else { - g.setColor( getTreeColorSet().getBranchColor() ); - } - } - - final private void blast( final PhylogenyNode node ) { - if ( !isCanBlast( node ) ) { - JOptionPane.showMessageDialog( this, - "Insufficient information present", - "Cannot Blast", - JOptionPane.INFORMATION_MESSAGE ); - return; - } - else { - final String query = Blast.obtainQueryForBlast( node ); - System.out.println( "query for BLAST is: " + query ); - char type = '?'; - if ( !ForesterUtil.isEmpty( query ) ) { - if ( node.getNodeData().isHasSequence() ) { - if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getType() ) ) { - if ( node.getNodeData().getSequence().getType().toLowerCase() - .equals( PhyloXmlUtil.SEQ_TYPE_PROTEIN ) ) { - type = 'p'; - } - else { - type = 'n'; - } - } - else if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) { - if ( ForesterUtil.seqIsLikelyToBeAa( node.getNodeData().getSequence().getMolecularSequence() ) ) { - type = 'p'; - } - else { - type = 'n'; - } + 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().getDuplicationBoxColor(); + } + else if ( event.isSpeciation() ) { + outline_color = getTreeColorSet().getSpecBoxColor(); + } + else if ( event.isSpeciationOrDuplication() ) { + outline_color = getTreeColorSet().getDuplicationOrSpeciationColor(); + } + } + if ( outline_color == null ) { + outline_color = getGraphicsForNodeBoxWithColorForParentBranch( node ); + if ( to_pdf && ( outline_color == getTreeColorSet().getBranchColor() ) ) { + outline_color = getTreeColorSet().getBranchColorForPdf(); + } + } + 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 ( fill == 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 ); } - if ( type == '?' ) { - if ( SequenceAccessionTools.isProteinDbQuery( query ) ) { - type = 'p'; + else if ( fill == NodeVisualData.NodeFill.SOLID ) { + if ( vis_fill_color != null ) { + g.setColor( vis_fill_color ); } else { - type = 'n'; + g.setColor( outline_color ); } + drawOvalFilled( x - half_box_size, y - half_box_size, box_size, box_size, g ); } - JApplet applet = null; - if ( isApplet() ) { - applet = obtainApplet(); - } - try { - Blast.openNcbiBlastWeb( query, type == 'n', applet, this ); + } + 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 ); } - catch ( final Exception e ) { - e.printStackTrace(); + else if ( fill == 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 ); } - if ( Constants.ALLOW_DDBJ_BLAST ) { - try { - System.out.println( "trying: " + query ); - final Blast s = new Blast(); - s.ddbjBlast( query ); + else if ( fill == NodeVisualData.NodeFill.SOLID ) { + if ( vis_fill_color != null ) { + g.setColor( vis_fill_color ); } - catch ( final Exception e ) { - e.printStackTrace(); + else { + g.setColor( outline_color ); } + drawRectFilled( x - half_box_size, y - half_box_size, box_size, box_size, g ); } } } } - private final int calcDynamicHidingFactor() { - return ( int ) ( 0.5 + ( getFontMetricsForLargeDefaultFont().getHeight() / ( 1.5 * getYdistance() ) ) ); - } - - /** - * Calculate the length of the distance between the given node and its - * parent. - * - * @param node - * @param ext_node_x - * @factor - * @return the distance value - */ - final private float calculateBranchLengthToParent( final PhylogenyNode node, final float factor ) { - if ( getControlPanel().isDrawPhylogram() ) { - if ( node.getDistanceToParent() < 0.0 ) { - return 0.0f; - } - return ( float ) ( getXcorrectionFactor() * node.getDistanceToParent() ); + 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, + final double add ) { + if ( isNodeDataInvisible( node ) && !to_graphics_file && !to_pdf ) { + return 0; } - else { - if ( ( factor == 0 ) || isNonLinedUpCladogram() ) { - return getXdistance(); - } - return getXdistance() * factor; + if ( getControlPanel().isWriteBranchLengthValues() + && ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) + || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) + || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) ) + && ( !node.isRoot() ) && ( node.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) ) { + paintBranchLength( g, node, to_pdf, to_graphics_file ); } - } - - final private Color calculateColorForAnnotation( final SortedSet ann ) { - Color c = getTreeColorSet().getAnnotationColor(); - if ( getControlPanel().isColorAccordingToAnnotation() && ( getControlPanel().getAnnotationColors() != null ) ) { - final StringBuilder sb = new StringBuilder(); - for( final Annotation a : ann ) { - sb.append( !ForesterUtil.isEmpty( a.getRefValue() ) ? a.getRefValue() : a.getDesc() ); - } - final String ann_str = sb.toString(); - if ( !ForesterUtil.isEmpty( ann_str ) ) { - c = getControlPanel().getAnnotationColors().get( ann_str ); - if ( c == null ) { - c = AptxUtil.calculateColorFromString( ann_str, false ); - getControlPanel().getAnnotationColors().put( ann_str, c ); - } - if ( c == null ) { - c = getTreeColorSet().getAnnotationColor(); + if ( !getControlPanel().isShowInternalData() && !node.isExternal() && !node.isCollapse() ) { + return 0; + } + if ( !getControlPanel().isShowExternalData() && ( node.isExternal() || node.isCollapse() ) ) { + return 0; + } + _sb.setLength( 0 ); + int x = 0; + if ( add > 0 ) { + x += add; + } + 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 ); + } + if ( ( getControlPanel().isShowTaxonomyCode() || getControlPanel().isShowTaxonomyScientificNames() + || getControlPanel().isShowTaxonomyCommonNames() || getControlPanel().isShowTaxonomyRank() ) + && node.getNodeData().isHasTaxonomy() ) { + x += paintTaxonomy( g, node, is_in_found_nodes, to_pdf, to_graphics_file, x ); + } + setColor( g, node, to_graphics_file, to_pdf, is_in_found_nodes, getTreeColorSet().getSequenceColor() ); + final boolean saw_species = _sb.length() > 0; + _sb.setLength( 0 ); + nodeDataAsSB( node, _sb ); + if ( node.isCollapse() && ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) ) { + if ( ( _sb.length() == 0 ) && !saw_species ) { + if ( getOptions().isShowAbbreviatedLabelsForCollapsedNodes() + && ( getControlPanel().isShowTaxonomyCode() || getControlPanel().isShowTaxonomyScientificNames() + || getControlPanel().isShowSeqNames() || getControlPanel().isShowNodeNames() ) ) { + final PhylogenyNode first = PhylogenyMethods.getFirstExternalNode( node ); + final PhylogenyNode last = PhylogenyMethods.getLastExternalNode( node ); + if ( getControlPanel().isShowTaxonomyCode() && first.getNodeData().isHasTaxonomy() + && last.getNodeData().isHasTaxonomy() + && !ForesterUtil.isEmpty( first.getNodeData().getTaxonomy().getTaxonomyCode() ) + && !ForesterUtil.isEmpty( last.getNodeData().getTaxonomy().getTaxonomyCode() ) ) { + addLabelForCollapsed( first.getNodeData().getTaxonomy().getTaxonomyCode(), + last.getNodeData().getTaxonomy().getTaxonomyCode(), + node.getAllExternalDescendants().size(), + node ); + } + else if ( getControlPanel().isShowTaxonomyScientificNames() && first.getNodeData().isHasTaxonomy() + && last.getNodeData().isHasTaxonomy() + && !ForesterUtil.isEmpty( first.getNodeData().getTaxonomy().getScientificName() ) + && !ForesterUtil.isEmpty( last.getNodeData().getTaxonomy().getScientificName() ) ) { + addLabelForCollapsed( first.getNodeData().getTaxonomy().getScientificName(), + last.getNodeData().getTaxonomy().getScientificName(), + node.getAllExternalDescendants().size(), + node ); + } + else if ( getControlPanel().isShowSeqNames() && first.getNodeData().isHasSequence() + && last.getNodeData().isHasSequence() + && !ForesterUtil.isEmpty( first.getNodeData().getSequence().getName() ) + && !ForesterUtil.isEmpty( last.getNodeData().getSequence().getName() ) ) { + addLabelForCollapsed( first.getNodeData().getSequence().getName(), + last.getNodeData().getSequence().getName(), + node.getAllExternalDescendants().size(), + node ); + } + else if ( getControlPanel().isShowNodeNames() && !ForesterUtil.isEmpty( first.getName() ) + && !ForesterUtil.isEmpty( last.getName() ) ) { + addLabelForCollapsed( first.getName(), + last.getName(), + node.getAllExternalDescendants().size(), + node ); + } } } - } - return c; - } - - final private float calculateOvBranchLengthToParent( final PhylogenyNode node, final int factor ) { - if ( getControlPanel().isDrawPhylogram() ) { - if ( node.getDistanceToParent() < 0.0 ) { - return 0.0f; + else if ( ( _sb.length() > 0 ) || saw_species ) { + // _sb.setLength( 0 ); + _sb.append( " [" ); + _sb.append( node.getAllExternalDescendants().size() ); + _sb.append( "]" ); + if ( _found_nodes_0 != null || _found_nodes_1 != null ) { + int[] res = calcFoundNodesInSubtree( node ); + if ( res[ 0 ] > 0 ) { + _sb.append( " [" ); + _sb.append( res[ 0 ] ); + _sb.append( "/" ); + _sb.append( res[ 1 ] ); + _sb.append( "]" ); + } + } } - return ( float ) ( getOvXcorrectionFactor() * node.getDistanceToParent() ); } else { - if ( ( factor == 0 ) || isNonLinedUpCladogram() ) { - return getOvXDistance(); - } - return getOvXDistance() * factor; + // _sb.setLength( 0 ); } - } - - final private void cannotOpenBrowserWarningMessage( final String type_type ) { - JOptionPane.showMessageDialog( this, - "Cannot launch web browser for " + type_type + " data of this node", - "Cannot launch web browser", - JOptionPane.WARNING_MESSAGE ); - } - - 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(); + // 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 ( f != null ) { - fc.setFont( f ); + float pos_x; + if ( getControlPanel().getTreeDisplayType() == Options.PHYLOGENY_DISPLAY_TYPE.ALIGNED_PHYLOGRAM + && ( node.isExternal() || node.isCollapse() ) ) { + pos_x = ( float ) ( ( getMaxDistanceToRoot() * getXcorrectionFactor() ) + + ( getOptions().getDefaultNodeShapeSize() / 2 ) + x + ( 2 * TreePanel.MOVE ) + getXdistance() + + 3 ); } else { - fc.setFont( getMainPanel().getTreeFontSet().getLargeFont() ); + pos_x = node.getXcoord() + x + 2 + half_box_size; } - List nodes = new ArrayList(); - if ( ( getFoundNodes0() != null ) || ( getFoundNodes1() != null ) ) { - nodes = getFoundNodesAsListOfPhylogenyNodes(); + float pos_y; + if ( !using_visual_font ) { + pos_y = ( node.getYcoord() + ( getFontMetricsForLargeDefaultFont().getAscent() / down_shift_factor ) ); } - if ( !nodes.contains( node ) ) { - nodes.add( node ); + else { + pos_y = ( node.getYcoord() + ( getFontMetrics( g.getFont() ).getAscent() / down_shift_factor ) ); } - final int count = nodes.size(); - String title = "Change the font for "; - if ( count == 1 ) { - title += "one node"; + if ( getControlPanel().getTreeDisplayType() == Options.PHYLOGENY_DISPLAY_TYPE.ALIGNED_PHYLOGRAM + && ( node.isExternal() || node.isCollapse() ) ) { + drawConnection( node.getXcoord(), pos_x - x, node.getYcoord(), 5, 20, g, to_pdf ); + if ( node.isCollapse() ) { + pos_x -= add; + } } - else { - title += ( count + " nodes" ); + final String sb_str = _sb.toString(); + // GUILHEM_BEG ______________ + if ( _control_panel.isShowSequenceRelations() && node.getNodeData().isHasSequence() + && ( _query_sequence != null ) ) { + x = paintSequenceRelation( g, node, x, half_box_size, pos_x, pos_y, sb_str ); } - fc.showDialog( this, title ); - if ( ( fc.getFont() != null ) && !ForesterUtil.isEmpty( fc.getFont().getFamily().trim() ) ) { - 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; + // GUILHEM_END _____________ + if ( sb_str.length() > 0 ) { + if ( !isAllowAttributedStrings() ) { + TreePanel.drawString( sb_str, pos_x, pos_y, g ); + } + else { + drawStringX( sb_str, pos_x, pos_y, g ); + } + } + 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() ) ) { + final SortedSet ann = node.getNodeData().getSequence().getAnnotations(); + if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) { + g.setColor( Color.BLACK ); + } + else if ( getControlPanel().isColorAccordingToAnnotation() ) { + g.setColor( calculateColorForAnnotation( ann ) ); + } + final String ann_str = TreePanelUtil.createAnnotationString( ann, + getOptions().isShowAnnotationRefSource() ); + TreePanel.drawString( ann_str, + node.getXcoord() + x + 3 + half_box_size, + node.getYcoord() + + ( 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; } - if ( s > Byte.MAX_VALUE ) { - s = Byte.MAX_VALUE; + else { + x += getFontMetrics( g.getFont() ).stringWidth( _sb.toString() ) + 5; } - vd.setFontSize( s ); - vd.setFontStyle( ff.getStyle() ); } - if ( _control_panel.getUseVisualStylesCb() != null ) { - getControlPanel().getUseVisualStylesCb().setSelected( true ); + } + 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 ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) { + g.setColor( Color.BLACK ); + } + else { + g.setColor( getTreeColorSet().getBinaryDomainCombinationsColor() ); + } + if ( getControlPanel().isShowBinaryCharacters() ) { + TreePanel.drawString( node.getNodeData().getBinaryCharacters().getPresentCharactersAsStringBuffer() + .toString(), + node.getXcoord() + x + 1 + half_box_size, + node.getYcoord() + ( 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() + ( getFontMetricsForLargeDefaultFont().getAscent() + / down_shift_factor ), + g ); + paintGainedAndLostCharacters( g, + node, + "+" + node.getNodeData().getBinaryCharacters().getGainedCount(), + "-" + node.getNodeData().getBinaryCharacters().getLostCount() ); + } } } - setEdited( true ); - repaint(); + return x; } - private void colorNodeFont( final PhylogenyNode node ) { - _color_chooser.setPreviewPanel( new JPanel() ); - NodeColorizationActionListener al; - int count = 1; - if ( ( getFoundNodes0() != null ) || ( getFoundNodes1() != null ) ) { - final List additional_nodes = getFoundNodesAsListOfPhylogenyNodes(); - al = new NodeColorizationActionListener( _color_chooser, node, additional_nodes ); - count = additional_nodes.size(); - if ( !additional_nodes.contains( node ) ) { - count++; + private final int paintSequenceRelation( final Graphics2D g, + final PhylogenyNode node, + int x, + final int half_box_size, + final float pos_x, + final float pos_y, + final String sb_str ) { + int nodeTextBoundsWidth = 0; + if ( sb_str.length() > 0 ) { + final Rectangle2D node_text_bounds = new TextLayout( sb_str, g.getFont(), _frc ).getBounds(); //would like to remove this 'new', but how... + nodeTextBoundsWidth = ( int ) node_text_bounds.getWidth(); + } + if ( node.getNodeData().getSequence().equals( _query_sequence ) ) { + if ( nodeTextBoundsWidth > 0 ) { // invert font color and background color to show that this is the query sequence + g.fillRect( ( int ) pos_x - 1, ( int ) pos_y - 8, nodeTextBoundsWidth + 5, 11 ); + g.setColor( getTreeColorSet().getBackgroundColor() ); } } else { - al = new NodeColorizationActionListener( _color_chooser, node ); + final List seqRelations = node.getNodeData().getSequence().getSequenceRelations(); + for( final SequenceRelation seqRelation : seqRelations ) { + final boolean fGotRelationWithQuery = ( seqRelation.getRef0().isEqual( _query_sequence ) + || seqRelation.getRef1().isEqual( _query_sequence ) ) + && 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 String sConfidence = ( !getControlPanel().isShowSequenceRelationConfidence() + || ( seqRelation.getConfidence() == null ) ) ? null + : " (" + seqRelation.getConfidence().getValue() + ")"; + if ( sConfidence != null ) { + float confidenceX = pos_x; + if ( sb_str.length() > 0 ) { + confidenceX += new TextLayout( sb_str, g.getFont(), _frc ).getBounds().getWidth() + + CONFIDENCE_LEFT_MARGIN; + } + if ( confidenceX > linePosX ) { // let's only display confidence value if we are already displaying at least one of Prot/Gene Name and Taxonomy Code + final int confidenceWidth = ( int ) new TextLayout( sConfidence, g.getFont(), _frc ) + .getBounds().getWidth(); + TreePanel.drawString( sConfidence, confidenceX, pos_y, g ); + x += CONFIDENCE_LEFT_MARGIN + confidenceWidth; + } + } + if ( ( x + nodeTextBoundsWidth ) > 0 ) /* we only underline if there is something displayed */ + { + if ( nodeTextBoundsWidth == 0 ) { + nodeTextBoundsWidth -= 3; /* the gap between taxonomy code and node name should not be underlined if nothing comes after it */ + } + else { + nodeTextBoundsWidth += 2; + } + g.drawLine( ( int ) linePosX + 1, + 3 + ( int ) pos_y, + ( int ) linePosX + x + nodeTextBoundsWidth, + 3 + ( int ) pos_y ); + break; + } + } + } } - String title = "Change the (node and font) color for "; - if ( count == 1 ) { - title += "one node"; + return x; + } + + private final void drawConnection( final float x1, + final float x2, + final float y, + final int dist_left, + final int dist_right, + final Graphics2D g, + final boolean pdf ) { + if ( ( ( x1 + dist_left ) < ( x2 - dist_right ) ) ) { + final Stroke strok = g.getStroke(); + Color col = null; + if ( strok == STROKE_005 ) { + g.setStroke( STROKE_001_DASHED ); + } + else if ( strok == STROKE_01 ) { + g.setStroke( STROKE_005_DASHED ); + } + else { + g.setStroke( STROKE_01_DASHED ); + } + if ( pdf ) { + col = g.getColor(); + g.setColor( lighter( col ) ); + } + drawLine( x1 + dist_left, y, x2 - dist_right, y, g ); + g.setStroke( strok ); + if ( pdf ) { + g.setColor( col ); + } + } + } + + public static Color lighter( final Color color ) { + if ( ( color.getRed() == 0 ) && ( color.getGreen() == 0 ) && ( color.getBlue() == 0 ) ) { + return new Color( 200, 200, 200 ); } else { - title += ( count + " nodes" ); + return color; } - final JDialog dialog = JColorChooser.createDialog( this, title, true, _color_chooser, al, null ); - setEdited( true ); - dialog.setVisible( true ); } - final private void colorizeNodes( final Color c, - final PhylogenyNode node, - final List additional_nodes ) { - _control_panel.setColorBranches( true ); - if ( _control_panel.getUseVisualStylesCb() != null ) { - _control_panel.getUseVisualStylesCb().setSelected( true ); - } - if ( node != null ) { - colorizeNodesHelper( c, node ); + private final void addLabelForCollapsed( final String first, + final String last, + final int size, + final PhylogenyNode node ) { + _sb.append( first.length() < AptxConstants.MAX_LENGTH_FOR_COLLAPSED_NAME ? first + : first.substring( 0, AptxConstants.MAX_LENGTH_FOR_COLLAPSED_NAME - 1 ) ); + _sb.append( " ... " ); + _sb.append( last.length() < AptxConstants.MAX_LENGTH_FOR_COLLAPSED_NAME ? last + : last.substring( 0, AptxConstants.MAX_LENGTH_FOR_COLLAPSED_NAME - 1 ) ); + _sb.append( " (" + size + ")" ); + if ( _found_nodes_0 != null || _found_nodes_1 != null ) { + ///// + ///// + int[] res = calcFoundNodesInSubtree( node ); + if ( res[ 0 ] > 0 ) { + _sb.append( " [" ); + _sb.append( res[ 0 ] ); + _sb.append( "/" ); + _sb.append( res[ 1 ] ); + _sb.append( "]" ); + } } - if ( additional_nodes != null ) { - for( final PhylogenyNode n : additional_nodes ) { - colorizeNodesHelper( c, n ); + } + + private final int[] calcFoundNodesInSubtree( final PhylogenyNode node ) { + final List all_descs = PhylogenyMethods.getAllDescendants( node ); + int res[] = new int[ 2 ]; + int found = 0; + int total = 0; + for( final PhylogenyNode desc : all_descs ) { + if ( desc.isHasNodeData() ) { + if ( ( _found_nodes_0 != null && _found_nodes_0.contains( desc.getId() ) ) + || ( _found_nodes_1 != null && _found_nodes_1.contains( desc.getId() ) ) ) { + ++found; + } + ++total; } } - repaint(); + res[ 0 ] = found; + res[ 1 ] = total; + return res; } - final private void colorizeSubtree( final Color c, - final PhylogenyNode node, - final List additional_nodes ) { - _control_panel.setColorBranches( true ); - if ( _control_panel.getUseVisualStylesCb() != null ) { - _control_panel.getUseVisualStylesCb().setSelected( true ); + private final boolean isAllowAttributedStrings() { + return false; + } + + final private void paintNodeDataUnrootedCirc( final Graphics2D g, + final PhylogenyNode node, + final boolean to_pdf, + final boolean to_graphics_file, + final boolean radial_labels, + final double ur_angle, + final boolean is_in_found_nodes ) { + if ( isNodeDataInvisibleUnrootedCirc( node ) && !to_graphics_file && !to_pdf ) { + return; } - if ( node != null ) { - for( final PreorderTreeIterator it = new PreorderTreeIterator( node ); it.hasNext(); ) { - it.next().getBranchData().setBranchColor( new BranchColor( c ) ); + _sb.setLength( 0 ); + _sb.append( " " ); + if ( node.getNodeData().isHasTaxonomy() + && ( getControlPanel().isShowTaxonomyCode() || getControlPanel().isShowTaxonomyScientificNames() + || getControlPanel().isShowTaxonomyCommonNames() ) ) { + final Taxonomy taxonomy = node.getNodeData().getTaxonomy(); + if ( _control_panel.isShowTaxonomyCode() && !ForesterUtil.isEmpty( taxonomy.getTaxonomyCode() ) ) { + _sb.append( taxonomy.getTaxonomyCode() ); + _sb.append( " " ); } - } - if ( additional_nodes != null ) { - for( final PhylogenyNode an : additional_nodes ) { - for( final PreorderTreeIterator it = new PreorderTreeIterator( an ); it.hasNext(); ) { - it.next().getBranchData().setBranchColor( new BranchColor( c ) ); + if ( _control_panel.isShowTaxonomyScientificNames() && _control_panel.isShowTaxonomyCommonNames() ) { + if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) + && !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) { + _sb.append( taxonomy.getScientificName() ); + _sb.append( " (" ); + _sb.append( taxonomy.getCommonName() ); + _sb.append( ") " ); + } + else if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) { + _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() ) ) { + _sb.append( taxonomy.getScientificName() ); + _sb.append( " " ); + } + } + else if ( _control_panel.isShowTaxonomyCommonNames() ) { + if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) { + _sb.append( taxonomy.getCommonName() ); + _sb.append( " " ); } } } - repaint(); - } - - 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; - } - _color_chooser.setPreviewPanel( new JPanel() ); - SubtreeColorizationActionListener al; - if ( ( getFoundNodes0() != null ) || ( getFoundNodes1() != null ) ) { - final List additional_nodes = getFoundNodesAsListOfPhylogenyNodes(); - al = new SubtreeColorizationActionListener( _color_chooser, node, additional_nodes ); + if ( node.isCollapse() && ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) ) { + _sb.append( " [" ); + _sb.append( node.getAllExternalDescendants().size() ); + _sb.append( "]" ); } - else { - al = new SubtreeColorizationActionListener( _color_chooser, node ); + if ( getControlPanel().isShowNodeNames() && ( node.getName().length() > 0 ) ) { + if ( _sb.length() > 0 ) { + _sb.append( " " ); + } + _sb.append( node.getName() ); } - final JDialog dialog = JColorChooser - .createDialog( this, "Subtree colorization", true, _color_chooser, al, null ); - setEdited( true ); - dialog.setVisible( true ); - } - - final private void copySubtree( final PhylogenyNode node ) { - if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) { - errorMessageNoCutCopyPasteInUnrootedDisplay(); - return; + if ( node.getNodeData().isHasSequence() ) { + 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().isShowSeqNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) { + if ( _sb.length() > 0 ) { + _sb.append( " " ); + } + _sb.append( node.getNodeData().getSequence().getName() ); + } } - setNodeInPreorderToNull(); - setCutOrCopiedTree( _phylogeny.copy( node ) ); - final List nodes = PhylogenyMethods.getAllDescendants( node ); - final Set node_ids = new HashSet( nodes.size() ); - for( final PhylogenyNode n : nodes ) { - node_ids.add( n.getId() ); + //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 ) { + m = _urt_nodeid_angle_map.get( node.getId() ) % TWO_PI; + } + else { + m = ( float ) ( ur_angle % TWO_PI ); + } + _at = g.getTransform(); + boolean need_to_reset = false; + final float x_coord = node.getXcoord(); + 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; + if ( ( m > HALF_PI ) && ( m < ONEHALF_PI ) ) { + m -= PI; + left = true; + } + g.rotate( m, x_coord, node.getYcoord() ); + if ( left ) { + 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; + 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 ( need_to_reset ) { + g.setTransform( _at ); + } } - node_ids.add( node.getId() ); - setCopiedAndPastedNodes( node_ids ); - repaint(); } - final private String createASimpleTextRepresentationOfANode( final PhylogenyNode node ) { - final String tax = PhylogenyMethods.getSpecies( node ); - String label = node.getName(); - if ( !ForesterUtil.isEmpty( label ) && !ForesterUtil.isEmpty( tax ) ) { - label = label + " " + tax; - } - else if ( !ForesterUtil.isEmpty( tax ) ) { - label = tax; + final private void paintNodeLite( final Graphics2D g, final PhylogenyNode node ) { + if ( node.isCollapse() ) { + return; } - else { - label = ""; + if ( isInFoundNodes( node ) || isInCurrentExternalNodes( node ) ) { + 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 ); } - if ( !ForesterUtil.isEmpty( label ) ) { - label = " [" + label + "]"; + float new_x = 0; + if ( !node.isExternal() && !node.isCollapse() ) { + boolean first_child = true; + float y2 = 0.0f; + //final int parent_max_branch_to_leaf = getMaxBranchesToLeaf( node ); + for( int i = 0; i < node.getNumberOfDescendants(); ++i ) { + final PhylogenyNode child_node = node.getChildNode( i ); + final int factor_x = node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes(); + if ( first_child ) { + first_child = false; + y2 = node.getYSecondary() - ( getOvYDistance() + * ( node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes() ) ); + } + else { + y2 += getOvYDistance() * child_node.getNumberOfExternalNodes(); + } + final float x2 = calculateOvBranchLengthToParent( child_node, factor_x ); + new_x = x2 + node.getXSecondary(); + final float diff_y = node.getYSecondary() - y2; + final float diff_x = node.getXSecondary() - new_x; + if ( ( diff_y > 2 ) || ( diff_y < -2 ) || ( diff_x > 2 ) || ( diff_x < -2 ) ) { + paintBranchLite( g, node.getXSecondary(), new_x, node.getYSecondary(), y2, child_node ); + } + child_node.setXSecondary( new_x ); + child_node.setYSecondary( y2 ); + y2 += getOvYDistance() * child_node.getNumberOfExternalNodes(); + } } - return label; } - final private void cutSubtree( final PhylogenyNode node ) { - if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) { - errorMessageNoCutCopyPasteInUnrootedDisplay(); + final private void paintNodeRectangular( final Graphics2D g, + final PhylogenyNode node, + final boolean to_pdf, + final boolean dynamically_hide, + final int dynamic_hiding_factor, + final boolean to_graphics_file, + final boolean disallow_shortcutting ) { + final boolean is_in_found_nodes = isInFoundNodes( node ) || isInCurrentExternalNodes( node ); + if ( node.isCollapse() ) { + if ( ( !node.isRoot() && !node.getParent().isCollapse() ) ) { + paintCollapsedNode( g, node, to_graphics_file, to_pdf, is_in_found_nodes ); + } return; } - if ( node.isRoot() ) { - JOptionPane.showMessageDialog( this, - "Cannot cut entire tree as subtree", - "Attempt to cut entire tree", - JOptionPane.ERROR_MESSAGE ); - return; + if ( node.isExternal() ) { + ++_external_node_index; } - final String label = createASimpleTextRepresentationOfANode( node ); - final int r = JOptionPane.showConfirmDialog( null, - "Cut subtree" + label + "?", - "Confirm Cutting of Subtree", - JOptionPane.YES_NO_OPTION ); - if ( r != JOptionPane.OK_OPTION ) { - return; + // Confidence values + if ( getControlPanel().isShowConfidenceValues() && !node.isExternal() && !node.isRoot() + && ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) + || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) + || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) ) + && node.getBranchData().isHasConfidences() ) { + paintConfidenceValues( g, node, to_pdf, to_graphics_file ); } - setNodeInPreorderToNull(); - setCopiedAndPastedNodes( null ); - setCutOrCopiedTree( _phylogeny.copy( node ) ); - _phylogeny.deleteSubtree( node, true ); - _phylogeny.clearHashIdToNodeMap(); - _phylogeny.recalculateNumberOfExternalDescendants( true ); - resetNodeIdToDistToLeafMap(); - setEdited( true ); - repaint(); - } - - final private void cycleColors() { - getMainPanel().getTreeColorSet().cycleColorScheme(); - for( final TreePanel tree_panel : getMainPanel().getTreePanels() ) { - tree_panel.setBackground( getMainPanel().getTreeColorSet().getBackgroundColor() ); + // Draw a line to root: + if ( node.isRoot() && _phylogeny.isRooted() ) { + paintRootBranch( g, node.getXcoord(), node.getYcoord(), node, to_pdf, to_graphics_file ); } - } - - final private void decreaseOvSize() { - if ( ( getOvMaxWidth() > 20 ) && ( getOvMaxHeight() > 20 ) ) { - setOvMaxWidth( getOvMaxWidth() - 5 ); - setOvMaxHeight( getOvMaxHeight() - 5 ); - updateOvSettings(); - getControlPanel().displayedPhylogenyMightHaveChanged( false ); + float new_x = 0; + float new_x_min = Float.MAX_VALUE; + float min_dist = 1.5f; + if ( !disallow_shortcutting ) { + if ( dynamic_hiding_factor > 4000 ) { + min_dist = 4; + } + else if ( dynamic_hiding_factor > 1000 ) { + min_dist = 3; + } + else if ( dynamic_hiding_factor > 100 ) { + min_dist = 2; + } + } + if ( !node.isExternal() && !node.isCollapse() ) { + boolean first_child = true; + float y2 = 0.0f; + for( int i = 0; i < node.getNumberOfDescendants(); ++i ) { + final PhylogenyNode child_node = node.getChildNode( i ); + final int factor_x = node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes(); + if ( first_child ) { + first_child = false; + y2 = node.getYcoord() - ( _y_distance + * ( node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes() ) ); + } + else { + y2 += _y_distance * child_node.getNumberOfExternalNodes(); + } + final float x2 = calculateBranchLengthToParent( child_node, factor_x ); + new_x = x2 + node.getXcoord(); + if ( dynamically_hide && ( x2 < new_x_min ) ) { + new_x_min = x2; + } + final float diff_y = node.getYcoord() - y2; + final float diff_x = node.getXcoord() - new_x; + if ( disallow_shortcutting || ( diff_y > min_dist ) || ( diff_y < -min_dist ) || ( diff_x > min_dist ) + || ( diff_x < -min_dist ) ) { + paintBranchRectangular( g, + node.getXcoord(), + new_x, + node.getYcoord(), + y2, + child_node, + to_pdf, + to_graphics_file ); + } + child_node.setXcoord( new_x ); + child_node.setYcoord( y2 ); + y2 += _y_distance * child_node.getNumberOfExternalNodes(); + } + paintNodeBox( node.getXcoord(), node.getYcoord(), node, g, to_pdf, to_graphics_file ); + } + if ( getControlPanel().isShowMolSequences() && ( node.getNodeData().isHasSequence() ) + && ( node.getNodeData().getSequence().isMolecularSequenceAligned() ) + && ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) ) { + paintMolecularSequences( g, node, to_pdf ); + } + if ( dynamically_hide && ( ( node.isExternal() && ( ( _external_node_index % dynamic_hiding_factor ) != 1 ) ) + || ( !node.isExternal() && ( ( new_x_min < 20 ) + || ( ( _y_distance * node.getNumberOfExternalNodes() ) < getFontMetricsForLargeDefaultFont() + .getHeight() ) ) ) ) ) { + return; } + final int x = paintNodeData( g, node, to_graphics_file, to_pdf, is_in_found_nodes, 0 ); + paintNodeWithRenderableData( x, g, node, to_graphics_file, to_pdf ); } - final private void deleteNodeOrSubtree( final PhylogenyNode node ) { - if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) { - errorMessageNoCutCopyPasteInUnrootedDisplay(); + final private void paintNodeWithRenderableData( final int x, + final Graphics2D g, + final PhylogenyNode node, + final boolean to_graphics_file, + final boolean to_pdf ) { + if ( isNodeDataInvisible( node ) && !( to_graphics_file || to_pdf ) ) { return; } - if ( node.isRoot() && ( node.getNumberOfDescendants() != 1 ) ) { - JOptionPane.showMessageDialog( this, - "Cannot delete entire tree", - "Attempt to delete entire tree", - JOptionPane.ERROR_MESSAGE ); + if ( ( !getControlPanel().isShowInternalData() && !node.isExternal() ) ) { return; } - final String label = createASimpleTextRepresentationOfANode( node ); - final Object[] options = { "Node only", "Entire subtree", "Cancel" }; - final int r = JOptionPane.showOptionDialog( this, - "Delete" + label + "?", - "Delete Node/Subtree", - JOptionPane.CLOSED_OPTION, - JOptionPane.QUESTION_MESSAGE, - null, - options, - options[ 2 ] ); - setNodeInPreorderToNull(); - boolean node_only = true; - if ( r == 1 ) { - node_only = false; - } - else if ( r != 0 ) { + if ( ( !getControlPanel().isShowExternalData() && node.isExternal() ) ) { return; } - if ( node_only ) { - PhylogenyMethods.removeNode( node, _phylogeny ); + if ( getControlPanel().isShowDomainArchitectures() && node.getNodeData().isHasSequence() + && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) && ( node.getNodeData() + .getSequence().getDomainArchitecture() instanceof RenderableDomainArchitecture ) ) { + RenderableDomainArchitecture rds = null; + try { + rds = ( RenderableDomainArchitecture ) node.getNodeData().getSequence().getDomainArchitecture(); + } + catch ( final ClassCastException cce ) { + cce.printStackTrace(); + } + if ( rds != null ) { + final int default_height = 7; + float y = getYdistance(); + if ( getControlPanel().isDynamicallyHideData() ) { + y = getTreeFontSet().getFontMetricsLarge().getHeight(); + } + final int h = y < default_height ? ForesterUtil.roundToInt( y ) : default_height; + rds.setRenderingHeight( h > 1 ? h : 2 ); + if ( getControlPanel().isDrawPhylogram() ) { + if ( getOptions().isLineUpRendarableNodeData() ) { + if ( getOptions().isRightLineUpDomains() ) { + rds.render( ( float ) ( ( getMaxDistanceToRoot() * getXcorrectionFactor() ) + + _length_of_longest_text + 50 //TODO why plus 50? + + ( ( _longest_domain - rds.getTotalLength() ) * rds.getRenderingFactorWidth() ) ), + node.getYcoord() - ( h / 2.0f ), + g, + this, + to_pdf ); + } + else { + rds.render( ( float ) ( ( getMaxDistanceToRoot() * getXcorrectionFactor() ) + + _length_of_longest_text + 50 ), + node.getYcoord() - ( h / 2.0f ), + g, + this, + to_pdf ); + } + } + else { + rds.render( node.getXcoord() + x, node.getYcoord() - ( h / 2.0f ), g, this, to_pdf ); + } + } + else { + if ( getOptions().isRightLineUpDomains() ) { + rds.render( ( ( getPhylogeny().getFirstExternalNode().getXcoord() + _length_of_longest_text ) + - 20 ) + ( ( _longest_domain - rds.getTotalLength() ) * rds.getRenderingFactorWidth() ), + node.getYcoord() - ( h / 2.0f ), + g, + this, + to_pdf ); + } + else { + rds.render( getPhylogeny().getFirstExternalNode().getXcoord() + _length_of_longest_text, + node.getYcoord() - ( h / 2.0f ), + g, + this, + to_pdf ); + } + } + } } - else { - _phylogeny.deleteSubtree( node, true ); + if ( getControlPanel().isShowVectorData() && ( node.getNodeData().getVector() != null ) + && ( node.getNodeData().getVector().size() > 0 ) && ( getStatisticsForExpressionValues() != null ) ) { + final RenderableVector rv = RenderableVector.createInstance( node.getNodeData().getVector(), + getStatisticsForExpressionValues(), + getConfiguration() ); + if ( rv != null ) { + double domain_add = 0; + if ( getControlPanel().isShowDomainArchitectures() && node.getNodeData().isHasSequence() + && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) { + domain_add = _domain_structure_width + 10; + } + if ( getControlPanel().isDrawPhylogram() ) { + rv.render( ( float ) ( node.getXcoord() + x + domain_add ), node.getYcoord() - 3, g, this, to_pdf ); + } + else { + rv.render( ( float ) ( getPhylogeny().getFirstExternalNode().getXcoord() + _length_of_longest_text + + domain_add ), node.getYcoord() - 3, g, this, to_pdf ); + } + } } - _phylogeny.externalNodesHaveChanged(); - _phylogeny.clearHashIdToNodeMap(); - _phylogeny.recalculateNumberOfExternalDescendants( true ); - resetNodeIdToDistToLeafMap(); - setEdited( true ); - repaint(); - } - - final private void displayNodePopupMenu( final PhylogenyNode node, final int x, final int y ) { - makePopupMenus( node ); - _node_popup_menu.putClientProperty( NODE_POPMENU_NODE_CLIENT_PROPERTY, node ); - _node_popup_menu.show( this, x, y ); - } - - final private void drawArc( final double x, - final double y, - final double width, - final double heigth, - final double start_angle, - final double arc_angle, - final Graphics2D g ) { - _arc.setArc( x, y, width, heigth, _180_OVER_PI * start_angle, _180_OVER_PI * arc_angle, Arc2D.OPEN ); - g.draw( _arc ); + //if ( getControlPanel().isShowMolSequences() && ( node.getNodeData().isHasSequence() ) + // && ( node.getNodeData().getSequence().isMolecularSequenceAligned() ) + // && ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) ) { + // paintMolecularSequences( g, node, to_pdf ); + //} } - final private void drawLine( final double x1, final double y1, final double x2, final double y2, final Graphics2D g ) { - if ( ( x1 == x2 ) && ( y1 == y2 ) ) { - return; + final private void paintOvRectangle( final Graphics2D g ) { + final float w_ratio = ( ( float ) getWidth() ) / getVisibleRect().width; + final float h_ratio = ( ( float ) getHeight() ) / getVisibleRect().height; + final float x_ratio = ( ( float ) getWidth() ) / getVisibleRect().x; + final float y_ratio = ( ( float ) getHeight() ) / getVisibleRect().y; + final float width = getOvMaxWidth() / w_ratio; + 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().getFoundColor0() ); + getOvRectangle().setRect( x, y, width, height ); + final Stroke s = g.getStroke(); + g.setStroke( STROKE_1 ); + if ( ( width < 6 ) && ( height < 6 ) ) { + drawRectFilled( x, y, 6, 6, g ); + getOvVirtualRectangle().setRect( x, y, 6, 6 ); } - _line.setLine( x1, y1, x2, y2 ); - g.draw( _line ); + else if ( width < 6 ) { + drawRectFilled( x, y, 6, height, g ); + getOvVirtualRectangle().setRect( x, y, 6, height ); + } + else if ( height < 6 ) { + drawRectFilled( x, y, width, 6, g ); + getOvVirtualRectangle().setRect( x, y, width, 6 ); + } + else { + drawRect( x, y, width, height, g ); + if ( isInOvRect() ) { + drawRect( x + 1, y + 1, width - 2, height - 2, g ); + } + getOvVirtualRectangle().setRect( x, y, width, height ); + } + g.setStroke( s ); } - final private void drawOval( final double x, - final double y, - final double width, - final double heigth, - final Graphics2D g ) { - _ellipse.setFrame( x, y, width, heigth ); - g.draw( _ellipse ); + final private void paintPhylogenyLite( final Graphics2D g ) { + _phylogeny.getRoot().setXSecondary( ( float ) ( getVisibleRect().x + getOvXPosition() + + ( MOVE / ( getVisibleRect().width / getOvRectangle().getWidth() ) ) ) ); + _phylogeny.getRoot().setYSecondary( ( getVisibleRect().y + getOvYStart() ) ); + final Stroke s = g.getStroke(); + g.setStroke( STROKE_05 ); + for( final PhylogenyNode element : _nodes_in_preorder ) { + paintNodeLite( g, element ); + } + g.setStroke( s ); + paintOvRectangle( g ); } - final private void drawOvalFilled( final double x, - final double y, - final double width, - final double heigth, - final Graphics2D g ) { - _ellipse.setFrame( x, y, width, heigth ); - g.fill( _ellipse ); - } - - 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( x, y, color_1, ( x + width ), ( y + heigth ), color_2, false ) ); - g.fill( _ellipse ); - if ( color_border != null ) { - g.setPaint( color_border ); - g.draw( _ellipse ); + /** + * Paint the root branch. (Differs from others because it will always be a + * single horizontal line). + * @param to_graphics_file + * + * @return new x1 value + */ + final private void paintRootBranch( final Graphics2D g, + final float x1, + final float y1, + final PhylogenyNode root, + final boolean to_pdf, + final boolean to_graphics_file ) { + assignGraphicsForBranchWithColorForParentBranch( root, false, g, to_pdf, to_graphics_file ); + float d = getXdistance(); + if ( getControlPanel().isDrawPhylogram() && ( root.getDistanceToParent() > 0.0 ) ) { + d = ( float ) ( getXcorrectionFactor() * root.getDistanceToParent() ); } - } - - final private void drawRect( final float x, final float y, final float width, final float heigth, final Graphics2D g ) { - _rectangle.setFrame( x, y, width, heigth ); - g.draw( _rectangle ); - } - - final private void drawRectFilled( final double x, - final double y, - final double width, - final double heigth, - final Graphics2D g ) { - _rectangle.setFrame( x, y, width, heigth ); - g.fill( _rectangle ); - } - - 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( x, y, color_1, ( x + width ), ( y + heigth ), color_2, false ) ); - g.fill( _rectangle ); - if ( color_border != null ) { - g.setPaint( color_border ); - g.draw( _rectangle ); + if ( d < MIN_ROOT_LENGTH ) { + d = MIN_ROOT_LENGTH; } - } - - private double drawTaxonomyImage( final double x, final double y, final PhylogenyNode node, final Graphics2D g ) { - final List us = new ArrayList(); - for( final Taxonomy t : node.getNodeData().getTaxonomies() ) { - for( final Uri uri : t.getUris() ) { - us.add( uri ); - } + if ( !getControlPanel().isWidthBranches() || ( PhylogenyMethods.getBranchWidthValue( root ) == 1 ) ) { + drawLine( x1 - d, root.getYcoord(), x1, root.getYcoord(), g ); } - double offset = 0; - for( final Uri uri : us ) { - if ( uri != null ) { - final String uri_str = uri.getValue().toString().toLowerCase(); - if ( getImageMap().containsKey( uri_str ) ) { - final BufferedImage bi = getImageMap().get( uri_str ); - if ( ( bi != null ) && ( bi.getHeight() > 5 ) && ( bi.getWidth() > 5 ) ) { - double scaling_factor = 1; - if ( getOptions().isAllowMagnificationOfTaxonomyImages() - || ( bi.getHeight() > ( 1.8 * getYdistance() ) ) ) { - scaling_factor = ( 1.8 * getYdistance() ) / bi.getHeight(); - } - // y = y - ( 0.9 * getYdistance() ); - final double hs = bi.getHeight() * scaling_factor; - double ws = ( bi.getWidth() * scaling_factor ) + offset; - final double my_y = y - ( 0.5 * hs ); - final int x_w = ( int ) ( x + ws + 0.5 ); - final int y_h = ( int ) ( my_y + hs + 0.5 ); - if ( ( ( x_w - x ) > 7 ) && ( ( y_h - my_y ) > 7 ) ) { - g.drawImage( bi, - ( int ) ( x + 0.5 + offset ), - ( int ) ( my_y + 0.5 ), - x_w, - y_h, - 0, - 0, - bi.getWidth(), - bi.getHeight(), - null ); - ws += 8; - } - else { - ws = 0.0; - } - offset = ws; - } - } - } + else { + final double w = PhylogenyMethods.getBranchWidthValue( root ); + drawRectFilled( x1 - d, root.getYcoord() - ( w / 2 ), d, w, g ); } - return offset; - } - - final private void errorMessageNoCutCopyPasteInUnrootedDisplay() { - JOptionPane.showMessageDialog( this, - "Cannot cut, copy, paste, add, or delete subtrees/nodes in unrooted display", - "Attempt to cut/copy/paste/add/delete in unrooted display", - JOptionPane.ERROR_MESSAGE ); + paintNodeBox( x1, root.getYcoord(), root, g, to_pdf, to_graphics_file ); } - 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(); + final private void paintScale( final Graphics2D g, + int x1, + int y1, + final boolean to_pdf, + final boolean to_graphics_file ) { + x1 += MOVE; + final double x2 = x1 + ( getScaleDistance() * getXcorrectionFactor() ); + y1 -= 12; + final int y2 = y1 - 8; + final int y3 = y1 - 4; + g.setFont( getTreeFontSet().getSmallFont() ); + if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) { + g.setColor( Color.BLACK ); } else { - return getTreeColorSet().getFoundColor0and1(); - } - } - - final private Set getCopiedAndPastedNodes() { - return getMainPanel().getCopiedAndPastedNodes(); - } - - final private Set getCurrentExternalNodes() { - return _current_external_nodes; - } - - final private Phylogeny getCutOrCopiedTree() { - return getMainPanel().getCutOrCopiedTree(); - } - - private FontMetrics getFontMetricsForLargeDefaultFont() { - return getTreeFontSet().getFontMetricsLarge(); - } - - List getFoundNodesAsListOfPhylogenyNodes() { - final List additional_nodes = new ArrayList(); - if ( getFoundNodes0() != null ) { - for( final Long id : getFoundNodes0() ) { - final PhylogenyNode n = _phylogeny.getNode( id ); - if ( n != null ) { - additional_nodes.add( n ); - } - } + g.setColor( getTreeColorSet().getBranchLengthColor() ); } - if ( getFoundNodes1() != null ) { - for( final Long id : getFoundNodes1() ) { - if ( ( getFoundNodes0() == null ) || !getFoundNodes0().contains( id ) ) { - final PhylogenyNode n = _phylogeny.getNode( id ); - if ( n != null ) { - additional_nodes.add( n ); - } - } - } + final Stroke s = g.getStroke(); + g.setStroke( STROKE_1 ); + drawLine( x1, y1, x1, y2, g ); + drawLine( x2, y1, x2, y2, g ); + drawLine( x1, y3, x2, y3, g ); + if ( getScaleLabel() != null ) { + g.drawString( getScaleLabel(), ( x1 + 2 ), y3 - 2 ); } - return additional_nodes; - } - - final private float getLastDragPointX() { - return _last_drag_point_x; - } - - final private float getLastDragPointY() { - return _last_drag_point_y; + g.setStroke( s ); } - final private short getMaxBranchesToLeaf( final PhylogenyNode node ) { - if ( !_nodeid_dist_to_leaf.containsKey( node.getId() ) ) { - final short m = PhylogenyMethods.calculateMaxBranchesToLeaf( node ); - _nodeid_dist_to_leaf.put( node.getId(), m ); - return m; + final private int paintTaxonomy( final Graphics2D g, + final PhylogenyNode node, + final boolean is_in_found_nodes, + final boolean to_pdf, + final boolean to_graphics_file, + final float x_shift ) { + final Taxonomy taxonomy = node.getNodeData().getTaxonomy(); + 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() ); + float start_x = node.getXcoord() + 3 + ( getOptions().getDefaultNodeShapeSize() / 2 ) + x_shift; + if ( getControlPanel().getTreeDisplayType() == Options.PHYLOGENY_DISPLAY_TYPE.ALIGNED_PHYLOGRAM + && node.isExternal() ) { + start_x = ( float ) ( ( getMaxDistanceToRoot() * getXcorrectionFactor() ) + + ( getOptions().getDefaultNodeShapeSize() / 2 ) + x_shift + ( 2 * TreePanel.MOVE ) + getXdistance() + + 3 ); + } + float start_y; + if ( !using_visual_font ) { + start_y = node.getYcoord() + ( getFontMetricsForLargeDefaultFont().getAscent() + / ( node.getNumberOfDescendants() == 1 ? 1 : 3.0f ) ); } else { - return _nodeid_dist_to_leaf.get( node.getId() ); + start_y = node.getYcoord() + + ( getFontMetrics( g.getFont() ).getAscent() / ( node.getNumberOfDescendants() == 1 ? 1 : 3.0f ) ); } - } - - final private double getMaxDistanceToRoot() { - if ( _max_distance_to_root < 0 ) { - recalculateMaxDistanceToRoot(); + _sb.setLength( 0 ); + nodeTaxonomyDataAsSB( taxonomy, _sb ); + final String label = _sb.toString(); + /* GUILHEM_BEG */ + if ( _control_panel.isShowSequenceRelations() && ( label.length() > 0 ) + && ( node.getNodeData().isHasSequence() ) + && node.getNodeData().getSequence().equals( _query_sequence ) ) { + // invert font color and background color to show that this is the query sequence + final Rectangle2D nodeTextBounds = new TextLayout( label, + g.getFont(), + new FontRenderContext( null, false, false ) ) + .getBounds(); + g.fillRect( ( int ) start_x - 1, ( int ) start_y - 8, ( int ) nodeTextBounds.getWidth() + 4, 11 ); + g.setColor( getTreeColorSet().getBackgroundColor() ); } - return _max_distance_to_root; - } - - final private float getOvMaxHeight() { - return _ov_max_height; - } - - final private float getOvMaxWidth() { - return _ov_max_width; - } - - final private float getOvXcorrectionFactor() { - return _ov_x_correction_factor; - } - - final private float getOvXDistance() { - return _ov_x_distance; + /* GUILHEM_END */ + TreePanel.drawString( label, start_x, start_y, g ); + if ( !using_visual_font && !is_in_found_nodes ) { + return getFontMetricsForLargeDefaultFont().stringWidth( label ); + } + return getFontMetrics( g.getFont() ).stringWidth( label ); } - final private int getOvXPosition() { - return _ov_x_position; + final private void paintUnrooted( final PhylogenyNode n, + final double low_angle, + final double high_angle, + final boolean radial_labels, + final Graphics2D g, + final boolean to_pdf, + final boolean to_graphics_file ) { + if ( n.isRoot() ) { + n.setXcoord( getWidth() / 2 ); + n.setYcoord( getHeight() / 2 ); + } + if ( n.isExternal() ) { + paintNodeDataUnrootedCirc( g, + n, + to_pdf, + to_graphics_file, + radial_labels, + ( high_angle + low_angle ) / 2, + isInFoundNodes( n ) || isInCurrentExternalNodes( n ) ); + return; + } + final float num_enclosed = n.getNumberOfExternalNodes(); + final float x = n.getXcoord(); + final float y = n.getYcoord(); + double current_angle = low_angle; + // final boolean n_below = n.getYcoord() < getVisibleRect().getMinY() - 20; + // final boolean n_above = n.getYcoord() > getVisibleRect().getMaxY() + 20; + // final boolean n_left = n.getXcoord() < getVisibleRect().getMinX() - 20; + // final boolean n_right = n.getXcoord() > getVisibleRect().getMaxX() + 20; + for( int i = 0; i < n.getNumberOfDescendants(); ++i ) { + final PhylogenyNode desc = n.getChildNode( i ); + /// if ( ( ( n_below ) & ( desc.getYcoord() < getVisibleRect().getMinY() - 20 ) ) + // || ( ( n_above ) & ( desc.getYcoord() > getVisibleRect().getMaxY() + 20 ) ) + // || ( ( n_left ) & ( desc.getXcoord() < getVisibleRect().getMinX() - 20 ) ) + // || ( ( n_right ) & ( desc.getXcoord() > getVisibleRect().getMaxX() + 20 ) ) ) { + // continue; + // } + //if ( ( desc.getYcoord() > n.getYcoord() ) && ( n.getYcoord() > getVisibleRect().getMaxY() - 20 ) ) { + // continue; + //} + //if ( ( desc.getYcoord() < n.getYcoord() ) && ( n.getYcoord() < getVisibleRect().getMinY() + 20 ) ) { + // continue; + // } + final int desc_num_enclosed = desc.getNumberOfExternalNodes(); + final double arc_size = ( desc_num_enclosed / num_enclosed ) * ( high_angle - low_angle ); + float length; + if ( isPhyHasBranchLengths() && getControlPanel().isDrawPhylogram() ) { + if ( desc.getDistanceToParent() < 0 ) { + length = 0; + } + else { + length = ( float ) ( desc.getDistanceToParent() * getUrtFactor() ); + } + } + else { + length = getUrtFactor(); + } + final double mid_angle = current_angle + ( arc_size / 2 ); + final float new_x = ( float ) ( x + ( Math.cos( mid_angle ) * length ) ); + 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 ); + } + if ( n.isRoot() ) { + paintNodeBox( n.getXcoord(), n.getYcoord(), n, g, to_pdf, to_graphics_file ); + } } - final private float getOvYDistance() { - return _ov_y_distance; + final private void paintUnrootedLite( final PhylogenyNode n, + final double low_angle, + final double high_angle, + final Graphics2D g, + final float urt_ov_factor ) { + if ( n.isRoot() ) { + final int x_pos = ( int ) ( getVisibleRect().x + getOvXPosition() + ( getOvMaxWidth() / 2 ) ); + final int y_pos = ( int ) ( getVisibleRect().y + getOvYPosition() + ( getOvMaxHeight() / 2 ) ); + n.setXSecondary( x_pos ); + n.setYSecondary( y_pos ); + } + if ( n.isExternal() ) { + return; + } + final float num_enclosed = n.getNumberOfExternalNodes(); + final float x = n.getXSecondary(); + final float y = n.getYSecondary(); + double current_angle = low_angle; + for( int i = 0; i < n.getNumberOfDescendants(); ++i ) { + final PhylogenyNode desc = n.getChildNode( i ); + final int desc_num_enclosed = desc.getNumberOfExternalNodes(); + final double arc_size = ( desc_num_enclosed / num_enclosed ) * ( high_angle - low_angle ); + float length; + if ( isPhyHasBranchLengths() && getControlPanel().isDrawPhylogram() ) { + if ( desc.getDistanceToParent() < 0 ) { + length = 0; + } + else { + length = ( float ) ( desc.getDistanceToParent() * urt_ov_factor ); + } + } + else { + length = urt_ov_factor; + } + final double mid_angle = current_angle + ( arc_size / 2 ); + final float new_x = ( float ) ( x + ( Math.cos( mid_angle ) * length ) ); + final float new_y = ( float ) ( y + ( Math.sin( mid_angle ) * length ) ); + desc.setXSecondary( new_x ); + desc.setYSecondary( new_y ); + if ( isInFoundNodes( desc ) || isInCurrentExternalNodes( desc ) ) { + 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 ); + current_angle += arc_size; + drawLine( x, y, new_x, new_y, g ); + } } - final private int getOvYPosition() { - return _ov_y_position; + final private void pasteSubtree( final PhylogenyNode node ) { + if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) { + errorMessageNoCutCopyPasteInUnrootedDisplay(); + return; + } + if ( ( getCutOrCopiedTree() == null ) || getCutOrCopiedTree().isEmpty() ) { + JOptionPane.showMessageDialog( this, + "No tree in buffer (need to copy or cut a subtree first)", + "Attempt to paste with empty buffer", + JOptionPane.ERROR_MESSAGE ); + return; + } + final String label = createASimpleTextRepresentationOfANode( getCutOrCopiedTree().getRoot() ); + final Object[] options = { "As sibling", "As descendant", "Cancel" }; + final int r = JOptionPane.showOptionDialog( this, + "How to paste subtree" + label + "?", + "Paste Subtree", + JOptionPane.CLOSED_OPTION, + JOptionPane.QUESTION_MESSAGE, + null, + options, + options[ 2 ] ); + boolean paste_as_sibling = true; + if ( r == 1 ) { + paste_as_sibling = false; + } + else if ( r != 0 ) { + return; + } + final Phylogeny buffer_phy = getCutOrCopiedTree().copy(); + buffer_phy.setAllNodesToNotCollapse(); + PhylogenyMethods.preOrderReId( buffer_phy ); + buffer_phy.setRooted( true ); + boolean need_to_show_whole = false; + if ( paste_as_sibling ) { + if ( node.isRoot() ) { + JOptionPane.showMessageDialog( this, + "Cannot paste sibling to root", + "Attempt to paste sibling to root", + JOptionPane.ERROR_MESSAGE ); + return; + } + buffer_phy.addAsSibling( node ); + } + else { + if ( ( node.getNumberOfExternalNodes() == 1 ) && node.isRoot() ) { + need_to_show_whole = true; + _phylogeny = buffer_phy; + } + else { + buffer_phy.addAsChild( node ); + } + } + if ( getCopiedAndPastedNodes() == null ) { + setCopiedAndPastedNodes( new HashSet() ); + } + final List nodes = PhylogenyMethods.obtainAllNodesAsList( buffer_phy ); + final Set node_ids = new HashSet( nodes.size() ); + for( final PhylogenyNode n : nodes ) { + node_ids.add( n.getId() ); + } + node_ids.add( node.getId() ); + getCopiedAndPastedNodes().addAll( node_ids ); + setNodeInPreorderToNull(); + _phylogeny.externalNodesHaveChanged(); + _phylogeny.clearHashIdToNodeMap(); + _phylogeny.recalculateNumberOfExternalDescendants( true ); + resetNodeIdToDistToLeafMap(); + setEdited( true ); + if ( need_to_show_whole ) { + getControlPanel().showWhole(); + } + repaint(); } - final private int getOvYStart() { - return _ov_y_start; + private final StringBuffer propertiesToString( final PhylogenyNode node ) { + return node.getNodeData().getProperties().asText(); } - final private List getPdbAccs( final PhylogenyNode node ) { - final List pdb_ids = new ArrayList(); - if ( node.getNodeData().isHasSequence() ) { - final Sequence seq = node.getNodeData().getSequence(); - if ( !ForesterUtil.isEmpty( seq.getCrossReferences() ) ) { - final SortedSet cross_refs = seq.getCrossReferences(); - for( final Accession acc : cross_refs ) { - if ( acc.getSource().equalsIgnoreCase( "pdb" ) ) { - pdb_ids.add( acc ); - } - } - } + 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 ); } - return pdb_ids; } - final private double getScaleDistance() { - return _scale_distance; + final private void setCopiedAndPastedNodes( final Set nodeIds ) { + getMainPanel().setCopiedAndPastedNodes( nodeIds ); } - final private String getScaleLabel() { - return _scale_label; + final private void setCutOrCopiedTree( final Phylogeny cut_or_copied_tree ) { + getMainPanel().setCutOrCopiedTree( cut_or_copied_tree ); } - final private TreeFontSet getTreeFontSet() { - return getMainPanel().getTreeFontSet(); + 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 float getUrtFactor() { - return _urt_factor; + final private void setInOv( final boolean in_ov ) { + _in_ov = in_ov; } - final private float getUrtFactorOv() { - return _urt_factor_ov; + final private void setOvMaxHeight( final float ov_max_height ) { + _ov_max_height = ov_max_height; } - final private void handleClickToAction( final NodeClickAction action, final PhylogenyNode node ) { - switch ( action ) { - case SHOW_DATA: - showNodeFrame( node ); - break; - case COLLAPSE: - collapse( node ); - break; - case REROOT: - reRoot( node ); - break; - case SUBTREE: - subTree( node ); - break; - case SWAP: - swap( node ); - break; - 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; - case BLAST: - blast( node ); - break; - case OPEN_TAX_WEB: - openTaxWeb( node ); - break; - case OPEN_PDB_WEB: - openPdbWeb( node ); - break; - case CUT_SUBTREE: - cutSubtree( node ); - break; - case COPY_SUBTREE: - copySubtree( node ); - break; - case PASTE_SUBTREE: - pasteSubtree( node ); - break; - case DELETE_NODE_OR_SUBTREE: - deleteNodeOrSubtree( node ); - break; - case ADD_NEW_NODE: - addEmptyNode( node ); - break; - case EDIT_NODE_DATA: - showNodeEditFrame( node ); - break; - case SELECT_NODES: - selectNode( node ); - break; - case SORT_DESCENDENTS: - sortDescendants( node ); - break; - case GET_EXT_DESC_DATA: - showExtDescNodeData( node ); - break; - default: - throw new IllegalArgumentException( "unknown action: " + action ); - } + final private void setOvMaxWidth( final float ov_max_width ) { + _ov_max_width = ov_max_width; } - final private void increaseCurrentExternalNodesDataBufferChangeCounter() { - _current_external_nodes_data_buffer_change_counter++; + final private void setOvXcorrectionFactor( final float f ) { + _ov_x_correction_factor = f; } - final private void increaseOvSize() { - if ( ( getOvMaxWidth() < ( getMainPanel().getCurrentScrollPane().getViewport().getVisibleRect().getWidth() / 2 ) ) - && ( getOvMaxHeight() < ( getMainPanel().getCurrentScrollPane().getViewport().getVisibleRect() - .getHeight() / 2 ) ) ) { - setOvMaxWidth( getOvMaxWidth() + 5 ); - setOvMaxHeight( getOvMaxHeight() + 5 ); - updateOvSettings(); - getControlPanel().displayedPhylogenyMightHaveChanged( false ); - } + final private void setOvXDistance( final float ov_x_distance ) { + _ov_x_distance = ov_x_distance; } - final private void init() { - _color_chooser = new JColorChooser(); - _rollover_popup = new JTextArea(); - _rollover_popup.setFont( POPUP_FONT ); - resetNodeIdToDistToLeafMap(); - setTextAntialias(); - setTreeFile( null ); - setEdited( false ); - initializeOvSettings(); - setStartingAngle( ( TWO_PI * 3 ) / 4 ); - final ImageLoader il = new ImageLoader( this ); - new Thread( il ).start(); + final private void setOvXPosition( final int ov_x_position ) { + _ov_x_position = ov_x_position; } - final private void initializeOvSettings() { - setOvMaxHeight( getConfiguration().getOvMaxHeight() ); - setOvMaxWidth( getConfiguration().getOvMaxWidth() ); + final private void setOvYDistance( final float ov_y_distance ) { + _ov_y_distance = ov_y_distance; } - final private boolean inOvVirtualRectangle( final int x, final int y ) { - return ( ( x >= ( getOvVirtualRectangle().x - 1 ) ) - && ( x <= ( getOvVirtualRectangle().x + getOvVirtualRectangle().width + 1 ) ) - && ( y >= ( getOvVirtualRectangle().y - 1 ) ) && ( y <= ( getOvVirtualRectangle().y - + getOvVirtualRectangle().height + 1 ) ) ); + final private void setOvYPosition( final int ov_y_position ) { + _ov_y_position = ov_y_position; } - final private boolean inOvVirtualRectangle( final MouseEvent e ) { - return ( inOvVirtualRectangle( e.getX(), e.getY() ) ); + final private void setOvYStart( final int ov_y_start ) { + _ov_y_start = ov_y_start; } - final private boolean isCanBlast( final PhylogenyNode node ) { - if ( !node.getNodeData().isHasSequence() && ForesterUtil.isEmpty( node.getName() ) ) { - return false; - } - return Blast.isContainsQueryForBlast( node ); + final private void setScaleDistance( final double scale_distance ) { + _scale_distance = scale_distance; } - final private String isCanOpenSeqWeb( final PhylogenyNode node ) { - final Accession a = SequenceAccessionTools.obtainAccessorFromDataFields( node ); - if ( a != null ) { - return a.getValue(); - } - return null; + final private void setScaleLabel( final String scale_label ) { + _scale_label = scale_label; } - final private boolean isCanOpenTaxWeb( final PhylogenyNode node ) { - if ( node.getNodeData().isHasTaxonomy() - && ( ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getScientificName() ) ) - || ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getTaxonomyCode() ) ) - || ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getCommonName() ) ) || ( ( node - .getNodeData().getTaxonomy().getIdentifier() != null ) && !ForesterUtil.isEmpty( node - .getNodeData().getTaxonomy().getIdentifier().getValue() ) ) ) ) { - return true; + private final void setupStroke( final Graphics2D g ) { + if ( getYdistance() < 0.0001 ) { + g.setStroke( STROKE_0025 ); + } + if ( getYdistance() < 0.001 ) { + g.setStroke( STROKE_005 ); + } + else if ( getYdistance() < 0.01 ) { + g.setStroke( STROKE_01 ); + } + else if ( getYdistance() < 0.5 ) { + g.setStroke( STROKE_025 ); + } + else if ( getYdistance() < 1 ) { + g.setStroke( STROKE_05 ); + } + else if ( getYdistance() < 2 ) { + g.setStroke( STROKE_075 ); + } + else if ( ( getYdistance() < 20 ) || !getConfiguration().isAllowThickStrokes() ) { + g.setStroke( STROKE_1 ); } else { - return false; + g.setStroke( STROKE_2 ); } } - final private boolean isInCurrentExternalNodes( final PhylogenyNode node ) { - return ( ( getCurrentExternalNodes() != null ) && getCurrentExternalNodes().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() { - return _in_ov; - } - - final private boolean isNodeDataInvisible( final PhylogenyNode node ) { - int y_dist = 40; - if ( getControlPanel().isShowTaxonomyImages() ) { - y_dist = 40 + ( int ) getYdistance(); + final private void setUpUrtFactor() { + final int d = getVisibleRect().width < getVisibleRect().height ? getVisibleRect().width + : getVisibleRect().height; + if ( isPhyHasBranchLengths() && getControlPanel().isDrawPhylogram() ) { + setUrtFactor( ( float ) ( d / ( 2 * getMaxDistanceToRoot() ) ) ); } - return ( ( node.getYcoord() < ( getVisibleRect().getMinY() - y_dist ) ) - || ( node.getYcoord() > ( getVisibleRect().getMaxY() + y_dist ) ) || ( ( node.getParent() != null ) && ( node - .getParent().getXcoord() > getVisibleRect().getMaxX() ) ) ); - } - - final private boolean isNodeDataInvisibleUnrootedCirc( final PhylogenyNode node ) { - return ( ( node.getYcoord() < ( getVisibleRect().getMinY() - 20 ) ) - || ( node.getYcoord() > ( getVisibleRect().getMaxY() + 20 ) ) - || ( node.getXcoord() < ( getVisibleRect().getMinX() - 20 ) ) || ( node.getXcoord() > ( getVisibleRect() - .getMaxX() + 20 ) ) ); + else { + final int max_depth = _circ_max_depth; + if ( max_depth > 0 ) { + setUrtFactor( d / ( 2 * max_depth ) ); + } + else { + setUrtFactor( d / 2 ); + } + } + setUrtFactorOv( getUrtFactor() ); } - final private boolean isNonLinedUpCladogram() { - return getOptions().getCladogramType() == CLADOGRAM_TYPE.NON_LINED_UP; + final private void setUrtFactor( final float urt_factor ) { + _urt_factor = urt_factor; } - final private boolean isUniformBranchLengthsForCladogram() { - return getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP; + final private void setUrtFactorOv( final float urt_factor_ov ) { + _urt_factor_ov = urt_factor_ov; } - final private void keyPressedCalls( final KeyEvent e ) { - if ( isOvOn() && ( getMousePosition() != null ) && ( getMousePosition().getLocation() != null ) ) { - if ( inOvVirtualRectangle( getMousePosition().x, getMousePosition().y ) ) { - if ( !isInOvRect() ) { - setInOvRect( true ); + private void showExtDescNodeData( final PhylogenyNode node, final char separator ) { + final List data = new ArrayList(); + final List nodes = node.getAllExternalDescendants(); + if ( ( getFoundNodes0() != null ) || ( getFoundNodes1() != null ) ) { + for( final PhylogenyNode n : getFoundNodesAsListOfPhylogenyNodes() ) { + if ( !nodes.contains( n ) ) { + nodes.add( n ); } } - else if ( isInOvRect() ) { - setInOvRect( false ); - } - } - if ( e.getModifiersEx() == InputEvent.CTRL_DOWN_MASK ) { - if ( ( e.getKeyCode() == KeyEvent.VK_DELETE ) || ( e.getKeyCode() == KeyEvent.VK_HOME ) - || ( e.getKeyCode() == KeyEvent.VK_F ) ) { - getMainPanel().getTreeFontSet().mediumFonts(); - getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true ); - } - else if ( ( e.getKeyCode() == KeyEvent.VK_SUBTRACT ) || ( e.getKeyCode() == KeyEvent.VK_MINUS ) ) { - getMainPanel().getTreeFontSet().decreaseFontSize( 1, false ); - getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true ); - } - else if ( plusPressed( e.getKeyCode() ) ) { - getMainPanel().getTreeFontSet().increaseFontSize(); - getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true ); - } } - else { - if ( ( e.getKeyCode() == KeyEvent.VK_DELETE ) || ( e.getKeyCode() == KeyEvent.VK_HOME ) - || ( e.getKeyCode() == KeyEvent.VK_F ) ) { - getControlPanel().showWhole(); - } - else if ( ( e.getKeyCode() == KeyEvent.VK_UP ) || ( e.getKeyCode() == KeyEvent.VK_DOWN ) - || ( e.getKeyCode() == KeyEvent.VK_LEFT ) || ( e.getKeyCode() == KeyEvent.VK_RIGHT ) ) { - if ( e.getModifiersEx() == InputEvent.SHIFT_DOWN_MASK ) { - if ( e.getKeyCode() == KeyEvent.VK_UP ) { - getMainPanel().getControlPanel().zoomInY( Constants.WHEEL_ZOOM_IN_FACTOR ); - getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false ); + for( final PhylogenyNode n : nodes ) { + switch ( getOptions().getExtDescNodeDataToReturn() ) { + case NODE_NAME: + if ( !ForesterUtil.isEmpty( n.getName() ) ) { + data.add( n.getName() ); } - else if ( e.getKeyCode() == KeyEvent.VK_DOWN ) { - getMainPanel().getControlPanel().zoomOutY( Constants.WHEEL_ZOOM_OUT_FACTOR ); - getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false ); + break; + case SEQUENCE_NAME: + if ( n.getNodeData().isHasSequence() + && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getName() ) ) { + data.add( n.getNodeData().getSequence().getName() ); } - else if ( e.getKeyCode() == KeyEvent.VK_LEFT ) { - getMainPanel().getControlPanel().zoomOutX( Constants.WHEEL_ZOOM_OUT_FACTOR, - Constants.WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR ); - getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false ); + break; + case GENE_NAME: + if ( n.getNodeData().isHasSequence() + && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getGeneName() ) ) { + data.add( n.getNodeData().getSequence().getGeneName() ); } - else if ( e.getKeyCode() == KeyEvent.VK_RIGHT ) { - getMainPanel().getControlPanel().zoomInX( Constants.WHEEL_ZOOM_IN_FACTOR, - Constants.WHEEL_ZOOM_IN_FACTOR ); - getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false ); + break; + case SEQUENCE_SYMBOL: + if ( n.getNodeData().isHasSequence() + && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getSymbol() ) ) { + data.add( n.getNodeData().getSequence().getSymbol() ); } - } - else { - final int d = 80; - int dx = 0; - int dy = -d; - if ( e.getKeyCode() == KeyEvent.VK_DOWN ) { - dy = d; + break; + case SEQUENCE_MOL_SEQ_FASTA: + final StringBuilder sb = new StringBuilder(); + if ( n.getNodeData().isHasSequence() + && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getMolecularSequence() ) ) { + final StringBuilder ann = new StringBuilder(); + if ( getControlPanel().isShowNodeNames() && !ForesterUtil.isEmpty( n.getName() ) ) { + ann.append( n.getName() ); + ann.append( separator ); + } + if ( n.getNodeData().isHasTaxonomy() ) { + if ( getControlPanel().isShowTaxonomyCode() + && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) { + ann.append( n.getNodeData().getTaxonomy().getTaxonomyCode() ); + ann.append( separator ); + } + if ( getControlPanel().isShowTaxonomyScientificNames() + && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) { + ann.append( n.getNodeData().getTaxonomy().getScientificName() ); + ann.append( separator ); + } + if ( getControlPanel().isShowTaxonomyCommonNames() + && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getCommonName() ) ) { + ann.append( n.getNodeData().getTaxonomy().getCommonName() ); + ann.append( separator ); + } + } + if ( getControlPanel().isShowSeqSymbols() + && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getSymbol() ) ) { + ann.append( n.getNodeData().getSequence().getSymbol() ); + ann.append( separator ); + } + if ( getControlPanel().isShowSeqNames() + && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getName() ) ) { + ann.append( n.getNodeData().getSequence().getName() ); + ann.append( separator ); + } + if ( getControlPanel().isShowGeneNames() + && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getGeneName() ) ) { + ann.append( n.getNodeData().getSequence().getGeneName() ); + ann.append( separator ); + } + if ( getControlPanel().isShowSequenceAcc() + && n.getNodeData().getSequence().getAccession() != null ) { + ann.append( n.getNodeData().getSequence().getAccession().asText() ); + ann.append( separator ); + } + + final String ann_str; + if ( ann.length() > 0 && ann.charAt( ann.length() - 1 ) == separator ) { + ann_str = ann.substring( 0, ann.length() - 1 ); + } + else { + ann_str = ann.toString(); + } + sb.append( SequenceWriter.toFasta( ann_str, + n.getNodeData().getSequence().getMolecularSequence(), + 60 ) ); + data.add( sb.toString() ); } - else if ( e.getKeyCode() == KeyEvent.VK_LEFT ) { - dx = -d; - dy = 0; + break; + case SEQUENCE_ACC: + if ( n.getNodeData().isHasSequence() && ( n.getNodeData().getSequence().getAccession() != null ) + && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getAccession().toString() ) ) { + data.add( n.getNodeData().getSequence().getAccession().toString() ); } - else if ( e.getKeyCode() == KeyEvent.VK_RIGHT ) { - dx = d; - dy = 0; + break; + case TAXONOMY_SCIENTIFIC_NAME: + if ( n.getNodeData().isHasTaxonomy() + && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) { + data.add( n.getNodeData().getTaxonomy().getScientificName() ); } - final Point scroll_position = getMainPanel().getCurrentScrollPane().getViewport().getViewPosition(); - scroll_position.x = scroll_position.x + dx; - scroll_position.y = scroll_position.y + dy; - if ( scroll_position.x <= 0 ) { - scroll_position.x = 0; + break; + case TAXONOMY_CODE: + if ( n.getNodeData().isHasTaxonomy() + && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) { + data.add( n.getNodeData().getTaxonomy().getTaxonomyCode() ); } - else { - final int max_x = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getMaximum() - - getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getVisibleAmount(); - if ( scroll_position.x >= max_x ) { - scroll_position.x = max_x; + break; + case DOMAINS_ALL: + case DOMAINS_COLLAPSED_PER_PROTEIN: + if ( n.getNodeData().isHasSequence() + && ( n.getNodeData().getSequence().getDomainArchitecture() != null ) ) { + final DomainArchitecture da = n.getNodeData().getSequence().getDomainArchitecture(); + final Set s = new HashSet(); + for( int i = 0; i < da.getDomains().size(); ++i ) { + final ProteinDomain d = da.getDomain( i ); + if ( d.getConfidence() <= Math.pow( 10, getDomainStructureEvalueThresholdExp() ) ) { + final String name = d.getName(); + if ( !( s.contains( name ) ) ) { + data.add( name ); + if ( getOptions() + .getExtDescNodeDataToReturn() == NodeDataField.DOMAINS_COLLAPSED_PER_PROTEIN ) { + s.add( name ); + } + } + } } } - if ( scroll_position.y <= 0 ) { - scroll_position.y = 0; + break; + case SEQ_ANNOTATIONS: + if ( n.getNodeData().isHasSequence() ) { + if ( n.getNodeData().isHasSequence() + && ( n.getNodeData().getSequence().getAnnotations() != null ) ) { + final SortedSet a = n.getNodeData().getSequence().getAnnotations(); + for( int i = 0; i < a.size(); ++i ) { + data.add( n.getNodeData().getSequence().getAnnotation( i ).toString() ); + } + } } - else { - final int max_y = getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getMaximum() - - getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getVisibleAmount(); - if ( scroll_position.y >= max_y ) { - scroll_position.y = max_y; + break; + case GO_TERM_IDS: + if ( n.getNodeData().isHasSequence() ) { + if ( n.getNodeData().isHasSequence() + && ( n.getNodeData().getSequence().getAnnotations() != null ) ) { + final SortedSet a = n.getNodeData().getSequence().getAnnotations(); + for( int i = 0; i < a.size(); ++i ) { + final Annotation ann = n.getNodeData().getSequence().getAnnotation( i ); + final String ref = ann.getRef(); + if ( ref.toUpperCase().startsWith( "GO:" ) ) { + data.add( ref ); + } + } } } - repaint(); - getMainPanel().getCurrentScrollPane().getViewport().setViewPosition( scroll_position ); - } + break; + case UNKNOWN: + TreePanelUtil.showExtDescNodeDataUserSelectedHelper( getControlPanel(), n, data ); + break; + default: + throw new IllegalArgumentException( "unknown data element: " + + getOptions().getExtDescNodeDataToReturn() ); } - else if ( ( e.getKeyCode() == KeyEvent.VK_SUBTRACT ) || ( e.getKeyCode() == KeyEvent.VK_MINUS ) ) { - getMainPanel().getControlPanel().zoomOutY( Constants.WHEEL_ZOOM_OUT_FACTOR ); - getMainPanel().getControlPanel().zoomOutX( Constants.WHEEL_ZOOM_OUT_FACTOR, - Constants.WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR ); - getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false ); + } // for loop + final StringBuilder sb = new StringBuilder(); + final int size = TreePanelUtil.nodeDataIntoStringBuffer( data, getOptions(), sb ); + if ( ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.CONSOLE ) + || ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.BUFFER_ONLY ) ) { + if ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.CONSOLE ) { + System.out.println( sb ); } - else if ( plusPressed( e.getKeyCode() ) ) { - getMainPanel().getControlPanel().zoomInX( Constants.WHEEL_ZOOM_IN_FACTOR, - Constants.WHEEL_ZOOM_IN_FACTOR ); - getMainPanel().getControlPanel().zoomInY( Constants.WHEEL_ZOOM_IN_FACTOR ); - getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false ); + if ( sb.length() < 1 ) { + clearCurrentExternalNodesDataBuffer(); } - else if ( e.getKeyCode() == KeyEvent.VK_S ) { - if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) - || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) { - setStartingAngle( ( getStartingAngle() % TWO_PI ) + ANGLE_ROTATION_UNIT ); - getControlPanel().displayedPhylogenyMightHaveChanged( false ); - } + else { + setCurrentExternalNodesDataBuffer( sb ); } - else if ( e.getKeyCode() == KeyEvent.VK_A ) { - if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) - || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) { - setStartingAngle( ( getStartingAngle() % TWO_PI ) - ANGLE_ROTATION_UNIT ); - if ( getStartingAngle() < 0 ) { - setStartingAngle( TWO_PI + getStartingAngle() ); - } - getControlPanel().displayedPhylogenyMightHaveChanged( false ); - } + } + else if ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.WINODW ) { + if ( sb.length() < 1 ) { + TreePanelUtil.showInformationMessage( this, + "No Appropriate Data (" + obtainTitleForExtDescNodeData() + ")", + "Descendants of selected node do not contain selected data" ); + clearCurrentExternalNodesDataBuffer(); } - else if ( e.getKeyCode() == KeyEvent.VK_D ) { - boolean selected = false; - if ( getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.HORIZONTAL ) { - getOptions().setNodeLabelDirection( NODE_LABEL_DIRECTION.RADIAL ); - selected = true; - } - else { - getOptions().setNodeLabelDirection( NODE_LABEL_DIRECTION.HORIZONTAL ); - } - if ( getMainPanel().getMainFrame() == null ) { - // Must be "E" applet version. - final ArchaeopteryxE ae = ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet(); - if ( ae.getlabelDirectionCbmi() != null ) { - ae.getlabelDirectionCbmi().setSelected( selected ); - } + else { + setCurrentExternalNodesDataBuffer( sb ); + String title; + if ( ( getFoundNodes0() != null ) && !getFoundNodes0().isEmpty() ) { + title = ( getOptions().getExtDescNodeDataToReturn() == NodeDataField.UNKNOWN ? "Data" + : obtainTitleForExtDescNodeData() ) + " for " + data.size() + " nodes, unique entries: " + + size; } else { - getMainPanel().getMainFrame().getlabelDirectionCbmi().setSelected( selected ); + title = ( getOptions().getExtDescNodeDataToReturn() == NodeDataField.UNKNOWN ? "Data" + : obtainTitleForExtDescNodeData() ) + " for " + data.size() + "/" + + node.getNumberOfExternalNodes() + " external descendats of node " + node + + ", unique entries: " + size; } - repaint(); - } - else if ( e.getKeyCode() == KeyEvent.VK_X ) { - switchDisplaygetPhylogenyGraphicsType(); - repaint(); - } - else if ( e.getKeyCode() == KeyEvent.VK_C ) { - cycleColors(); - repaint(); - } - else if ( getOptions().isShowOverview() && isOvOn() && ( e.getKeyCode() == KeyEvent.VK_O ) ) { - MainFrame.cycleOverview( getOptions(), this ); - repaint(); - } - else if ( getOptions().isShowOverview() && isOvOn() && ( e.getKeyCode() == KeyEvent.VK_I ) ) { - increaseOvSize(); - } - else if ( getOptions().isShowOverview() && isOvOn() && ( e.getKeyCode() == KeyEvent.VK_U ) ) { - decreaseOvSize(); + final String s = sb.toString().trim(); + getMainPanel().getMainFrame().showTextFrame( s, title ); } - e.consume(); } } - final private void makePopupMenus( final PhylogenyNode node ) { - _node_popup_menu = new JPopupMenu(); - final List clickto_names = _main_panel.getControlPanel().getSingleClickToNames(); - _node_popup_menu_items = new JMenuItem[ clickto_names.size() ]; - for( int i = 0; i < clickto_names.size(); i++ ) { - final String title = clickto_names.get( i ); - _node_popup_menu_items[ i ] = new JMenuItem( title ); - if ( title.equals( Configuration.clickto_options[ Configuration.open_seq_web ][ 0 ] ) ) { - final String id = isCanOpenSeqWeb( node ); - if ( !ForesterUtil.isEmpty( id ) ) { - _node_popup_menu_items[ i ].setText( _node_popup_menu_items[ i ].getText() + " [" + id + "]" ); - _node_popup_menu_items[ i ].setEnabled( true ); - } - else { - _node_popup_menu_items[ i ].setEnabled( false ); + final private void showNodeDataPopup( final MouseEvent e, final PhylogenyNode node ) { + try { + if ( ( node.getName().length() > 0 ) + || ( node.getNodeData().isHasTaxonomy() + && !TreePanelUtil.isTaxonomyEmpty( node.getNodeData().getTaxonomy() ) ) + || ( node.getNodeData().isHasSequence() + && !TreePanelUtil.isSequenceEmpty( node.getNodeData().getSequence() ) ) + || ( node.getNodeData().isHasDate() ) || ( node.getNodeData().isHasDistribution() ) + || node.getBranchData().isHasConfidences() ) { + _popup_buffer.setLength( 0 ); + short lines = 0; + if ( node.getName().length() > 0 ) { + lines++; + _popup_buffer.append( node.getName() ); } - } - else if ( title.equals( Configuration.clickto_options[ Configuration.open_pdb_web ][ 0 ] ) ) { - final List accs = getPdbAccs( node ); - _node_popup_menu_items[ i ] = new JMenuItem( title ); - if ( !ForesterUtil.isEmpty( accs ) ) { - if ( accs.size() == 1 ) { - _node_popup_menu_items[ i ].setText( _node_popup_menu_items[ i ].getText() + " [" - + TreePanelUtil.pdbAccToString( accs, 0 ) + "]" ); - _node_popup_menu_items[ i ].setEnabled( true ); + if ( node.getNodeData().isHasTaxonomy() + && !TreePanelUtil.isTaxonomyEmpty( node.getNodeData().getTaxonomy() ) ) { + lines++; + boolean enc_data = false; + final Taxonomy tax = node.getNodeData().getTaxonomy(); + if ( _popup_buffer.length() > 0 ) { + _popup_buffer.append( "\n" ); } - else if ( accs.size() == 2 ) { - _node_popup_menu_items[ i ].setText( _node_popup_menu_items[ i ].getText() + " [" - + TreePanelUtil.pdbAccToString( accs, 0 ) + ", " - + TreePanelUtil.pdbAccToString( accs, 1 ) + "]" ); - _node_popup_menu_items[ i ].setEnabled( true ); + if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) { + _popup_buffer.append( "[" ); + _popup_buffer.append( tax.getTaxonomyCode() ); + _popup_buffer.append( "]" ); + enc_data = true; } - else if ( accs.size() == 3 ) { - _node_popup_menu_items[ i ].setText( _node_popup_menu_items[ i ].getText() + " [" - + TreePanelUtil.pdbAccToString( accs, 0 ) + ", " - + TreePanelUtil.pdbAccToString( accs, 1 ) + ", " - + TreePanelUtil.pdbAccToString( accs, 2 ) + "]" ); - _node_popup_menu_items[ i ].setEnabled( true ); + if ( !ForesterUtil.isEmpty( tax.getScientificName() ) ) { + if ( enc_data ) { + _popup_buffer.append( " " ); + } + _popup_buffer.append( tax.getScientificName() ); + enc_data = true; } - else { - _node_popup_menu_items[ i ].setText( _node_popup_menu_items[ i ].getText() + " [" - + TreePanelUtil.pdbAccToString( accs, 0 ) + ", " - + TreePanelUtil.pdbAccToString( accs, 1 ) + ", " - + TreePanelUtil.pdbAccToString( accs, 2 ) + ", + " + ( accs.size() - 3 ) + " more]" ); - _node_popup_menu_items[ i ].setEnabled( true ); + if ( !ForesterUtil.isEmpty( tax.getCommonName() ) ) { + if ( enc_data ) { + _popup_buffer.append( " (" ); + } + else { + _popup_buffer.append( "(" ); + } + _popup_buffer.append( tax.getCommonName() ); + _popup_buffer.append( ")" ); + enc_data = true; + } + if ( !ForesterUtil.isEmpty( tax.getAuthority() ) ) { + if ( enc_data ) { + _popup_buffer.append( " (" ); + } + else { + _popup_buffer.append( "(" ); + } + _popup_buffer.append( tax.getAuthority() ); + _popup_buffer.append( ")" ); + enc_data = true; + } + if ( !ForesterUtil.isEmpty( tax.getRank() ) ) { + if ( enc_data ) { + _popup_buffer.append( " [" ); + } + else { + _popup_buffer.append( "[" ); + } + _popup_buffer.append( tax.getRank() ); + _popup_buffer.append( "]" ); + enc_data = true; + } + if ( tax.getSynonyms().size() > 0 ) { + if ( enc_data ) { + _popup_buffer.append( " " ); + } + _popup_buffer.append( "[" ); + int counter = 1; + for( final String syn : tax.getSynonyms() ) { + if ( !ForesterUtil.isEmpty( syn ) ) { + enc_data = true; + _popup_buffer.append( syn ); + if ( counter < tax.getSynonyms().size() ) { + _popup_buffer.append( ", " ); + } + } + counter++; + } + _popup_buffer.append( "]" ); + } + if ( !enc_data ) { + if ( ( tax.getIdentifier() != null ) + && !ForesterUtil.isEmpty( tax.getIdentifier().getValue() ) ) { + if ( !ForesterUtil.isEmpty( tax.getIdentifier().getProvider() ) ) { + _popup_buffer.append( "[" ); + _popup_buffer.append( tax.getIdentifier().getProvider() ); + _popup_buffer.append( "] " ); + } + _popup_buffer.append( tax.getIdentifier().getValue() ); + } } } - else { - _node_popup_menu_items[ i ].setEnabled( false ); - } - // - } - else if ( title.equals( Configuration.clickto_options[ Configuration.open_tax_web ][ 0 ] ) ) { - _node_popup_menu_items[ i ].setEnabled( isCanOpenTaxWeb( node ) ); - } - else if ( title.equals( Configuration.clickto_options[ Configuration.blast ][ 0 ] ) ) { - _node_popup_menu_items[ i ].setEnabled( isCanBlast( node ) ); - } - else if ( title.equals( Configuration.clickto_options[ Configuration.delete_subtree_or_node ][ 0 ] ) ) { - if ( !getOptions().isEditable() ) { - continue; - } - _node_popup_menu_items[ i ].setEnabled( isCanDelete() ); - } - else if ( title.equals( Configuration.clickto_options[ Configuration.cut_subtree ][ 0 ] ) ) { - if ( !getOptions().isEditable() ) { - continue; - } - _node_popup_menu_items[ i ].setEnabled( isCanCut( node ) ); - } - else if ( title.equals( Configuration.clickto_options[ Configuration.copy_subtree ][ 0 ] ) ) { - if ( !getOptions().isEditable() ) { - continue; - } - _node_popup_menu_items[ i ].setEnabled( isCanCopy() ); - } - else if ( title.equals( Configuration.clickto_options[ Configuration.paste_subtree ][ 0 ] ) ) { - if ( !getOptions().isEditable() ) { - continue; - } - _node_popup_menu_items[ i ].setEnabled( isCanPaste() ); - } - else if ( title.equals( Configuration.clickto_options[ Configuration.edit_node_data ][ 0 ] ) ) { - if ( !getOptions().isEditable() ) { - continue; - } - } - else if ( title.equals( Configuration.clickto_options[ Configuration.add_new_node ][ 0 ] ) ) { - if ( !getOptions().isEditable() ) { - continue; + if ( node.getNodeData().isHasSequence() + && !TreePanelUtil.isSequenceEmpty( node.getNodeData().getSequence() ) ) { + lines++; + boolean enc_data = false; + if ( _popup_buffer.length() > 0 ) { + _popup_buffer.append( "\n" ); + } + final Sequence seq = node.getNodeData().getSequence(); + if ( seq.getAccession() != null ) { + _popup_buffer.append( "[" ); + if ( !ForesterUtil.isEmpty( seq.getAccession().getSource() ) ) { + _popup_buffer.append( seq.getAccession().getSource() ); + _popup_buffer.append( ":" ); + } + _popup_buffer.append( seq.getAccession().getValue() ); + _popup_buffer.append( "]" ); + enc_data = true; + } + if ( !ForesterUtil.isEmpty( seq.getSymbol() ) ) { + if ( enc_data ) { + _popup_buffer.append( " [" ); + } + else { + _popup_buffer.append( "[" ); + } + _popup_buffer.append( seq.getSymbol() ); + _popup_buffer.append( "]" ); + enc_data = true; + } + if ( !ForesterUtil.isEmpty( seq.getGeneName() ) ) { + if ( enc_data ) { + _popup_buffer.append( " [" ); + } + else { + _popup_buffer.append( "[" ); + } + _popup_buffer.append( seq.getGeneName() ); + _popup_buffer.append( "]" ); + enc_data = true; + } + if ( !ForesterUtil.isEmpty( seq.getName() ) ) { + if ( enc_data ) { + _popup_buffer.append( " " ); + } + _popup_buffer.append( seq.getName() ); + } } - } - else if ( title.equals( Configuration.clickto_options[ Configuration.reroot ][ 0 ] ) ) { - _node_popup_menu_items[ i ].setEnabled( isCanReroot() ); - } - else if ( title.equals( Configuration.clickto_options[ Configuration.collapse_uncollapse ][ 0 ] ) ) { - _node_popup_menu_items[ i ].setEnabled( ( isCanCollapse() && !node.isExternal() ) ); - } - else if ( title.equals( Configuration.clickto_options[ Configuration.color_subtree ][ 0 ] ) ) { - _node_popup_menu_items[ i ].setEnabled( isCanColorSubtree() ); - } - else if ( title.equals( Configuration.clickto_options[ Configuration.subtree ][ 0 ] ) ) { - _node_popup_menu_items[ i ].setEnabled( isCanSubtree( node ) ); - } - else if ( title.equals( Configuration.clickto_options[ Configuration.swap ][ 0 ] ) ) { - _node_popup_menu_items[ i ].setEnabled( node.getNumberOfDescendants() == 2 ); - } - else if ( title.equals( Configuration.clickto_options[ Configuration.sort_descendents ][ 0 ] ) ) { - _node_popup_menu_items[ i ].setEnabled( node.getNumberOfDescendants() > 1 ); - } - _node_popup_menu_items[ i ].addActionListener( this ); - _node_popup_menu.add( _node_popup_menu_items[ i ] ); - } - } - - private final void nodeDataAsSB( final PhylogenyNode node, final StringBuilder sb ) { - if ( node != null ) { - if ( getControlPanel().isShowNodeNames() && ( !ForesterUtil.isEmpty( node.getName() ) ) ) { - if ( sb.length() > 0 ) { - sb.append( " " ); + if ( node.getNodeData().isHasDate() ) { + lines++; + if ( _popup_buffer.length() > 0 ) { + _popup_buffer.append( "\n" ); + } + _popup_buffer.append( node.getNodeData().getDate().asSimpleText() ); } - sb.append( node.getName() ); - } - if ( node.getNodeData().isHasSequence() ) { - if ( getControlPanel().isShowSeqSymbols() - && ( node.getNodeData().getSequence().getSymbol().length() > 0 ) ) { - if ( sb.length() > 0 ) { - sb.append( " " ); + if ( node.getNodeData().isHasDistribution() ) { + lines++; + if ( _popup_buffer.length() > 0 ) { + _popup_buffer.append( "\n" ); } - sb.append( node.getNodeData().getSequence().getSymbol() ); + _popup_buffer.append( node.getNodeData().getDistribution().asSimpleText() ); } - if ( getControlPanel().isShowGeneNames() - && ( node.getNodeData().getSequence().getGeneName().length() > 0 ) ) { - if ( sb.length() > 0 ) { - sb.append( " " ); + if ( node.getBranchData().isHasConfidences() ) { + final List confs = node.getBranchData().getConfidences(); + for( final Confidence confidence : confs ) { + lines++; + if ( _popup_buffer.length() > 0 ) { + _popup_buffer.append( "\n" ); + } + if ( !ForesterUtil.isEmpty( confidence.getType() ) ) { + _popup_buffer.append( "[" ); + _popup_buffer.append( confidence.getType() ); + _popup_buffer.append( "] " ); + } + _popup_buffer.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence.getValue(), + getOptions() + .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) ); + if ( confidence.getStandardDeviation() != Confidence.CONFIDENCE_DEFAULT_VALUE ) { + _popup_buffer.append( " (sd=" ); + _popup_buffer.append( FORMATTER_CONFIDENCE + .format( ForesterUtil.round( confidence.getStandardDeviation(), + getOptions() + .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) ); + _popup_buffer.append( ")" ); + } } - sb.append( node.getNodeData().getSequence().getGeneName() ); } - if ( getControlPanel().isShowSeqNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) { - if ( sb.length() > 0 ) { - sb.append( " " ); + if ( node.getNodeData().isHasProperties() ) { + if ( _popup_buffer.length() > 0 ) { + _popup_buffer.append( "\n" ); } - sb.append( node.getNodeData().getSequence().getName() ); + _popup_buffer.append( node.getNodeData().getProperties().asText() ); } - if ( getControlPanel().isShowSequenceAcc() - && ( node.getNodeData().getSequence().getAccession() != null ) ) { - if ( sb.length() > 0 ) { - sb.append( " " ); + if ( _popup_buffer.length() > 0 ) { + if ( !getConfiguration().isUseNativeUI() ) { + _rollover_popup + .setBorder( BorderFactory.createLineBorder( getTreeColorSet().getBranchColor() ) ); + _rollover_popup.setBackground( getTreeColorSet().getBackgroundColor() ); + 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 { + _rollover_popup.setForeground( getTreeColorSet().getSequenceColor() ); + } } - if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() ) ) { - sb.append( node.getNodeData().getSequence().getAccession().getSource() ); - sb.append( ":" ); + else { + _rollover_popup.setBorder( BorderFactory.createLineBorder( Color.BLACK ) ); } - sb.append( node.getNodeData().getSequence().getAccession().getValue() ); - } - } - if ( getControlPanel().isShowProperties() && node.getNodeData().isHasProperties() ) { - if ( sb.length() > 0 ) { - sb.append( " " ); + _rollover_popup.setText( _popup_buffer.toString() ); + _node_desc_popup = PopupFactory.getSharedInstance() + .getPopup( null, + _rollover_popup, + e.getLocationOnScreen().x + 10, + e.getLocationOnScreen().y - ( lines * 20 ) ); + _node_desc_popup.show(); } - sb.append( propertiesToString( node ) ); } } + catch ( final Exception ex ) { + // Do nothing. + } } - private final void nodeTaxonomyDataAsSB( final Taxonomy taxonomy, final StringBuilder sb ) { - if ( _control_panel.isShowTaxonomyCode() && !ForesterUtil.isEmpty( taxonomy.getTaxonomyCode() ) ) { - sb.append( taxonomy.getTaxonomyCode() ); - sb.append( " " ); + final private void showNodeEditFrame( final PhylogenyNode n ) { + if ( _node_frame_index < TreePanel.MAX_NODE_FRAMES ) { + // pop up edit box for single node + _node_frames[ _node_frame_index ] = new NodeFrame( n, _phylogeny, this, _node_frame_index, "" ); + _node_frame_index++; } - 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: - return "Node Names"; - case GENE_NAME: - return "Gene Names"; - case SEQUENCE_NAME: - return "Sequence Names"; - case SEQUENCE_SYMBOL: - return "Sequence Symbols"; - case SEQUENCE_MOL_SEQ: - return "Molecular Sequences"; - case SEQUENCE_MOL_SEQ_FASTA: - return "Molecular Sequences (Fasta)"; - case SEQUENCE_ACC: - return "Sequence Accessors"; - case TAXONOMY_SCIENTIFIC_NAME: - return "Scientific Names"; - case TAXONOMY_CODE: - return "Taxonomy Codes"; - case TAXONOMY_COMM0N_NAME: - return "Taxonomy Common Names"; - case UNKNOWN: - return "User Selected Data"; - default: - throw new IllegalArgumentException( "unknown data element: " - + getOptions().getExtDescNodeDataToReturn() ); + else { + JOptionPane.showMessageDialog( this, "too many node windows are open" ); } } - final private void openPdbWeb( final PhylogenyNode node ) { - final List pdb_ids = getPdbAccs( node ); - if ( ForesterUtil.isEmpty( pdb_ids ) ) { - cannotOpenBrowserWarningMessage( "PDB" ); - return; - } - final List uri_strs = TreePanelUtil.createUrisForPdbWeb( node, pdb_ids, getConfiguration(), this ); - if ( !ForesterUtil.isEmpty( uri_strs ) ) { - for( final String uri_str : uri_strs ) { - 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(); - } - } + final private void showNodeFrame( final PhylogenyNode n ) { + if ( _node_frame_index < TreePanel.MAX_NODE_FRAMES ) { + // pop up edit box for single node + _node_frames[ _node_frame_index ] = new NodeFrame( n, _phylogeny, this, _node_frame_index ); + _node_frame_index++; } else { - cannotOpenBrowserWarningMessage( "PDB" ); + JOptionPane.showMessageDialog( this, "too many node windows are open" ); } } - final private void openSeqWeb( final PhylogenyNode node ) { - if ( ForesterUtil.isEmpty( isCanOpenSeqWeb( node ) ) ) { - cannotOpenBrowserWarningMessage( "sequence" ); - return; + final private void switchDisplaygetPhylogenyGraphicsType() { + switch ( getPhylogenyGraphicsType() ) { + case RECTANGULAR: + setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ); + getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ); + break; + case EURO_STYLE: + setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED ); + getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED ); + break; + case ROUNDED: + setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED ); + getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED ); + break; + case CURVED: + setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR ); + getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR ); + break; + case TRIANGULAR: + setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX ); + getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX ); + break; + case CONVEX: + setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED ); + getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED ); + break; + case UNROOTED: + setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ); + getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ); + break; + case CIRCULAR: + setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ); + getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ); + break; + default: + throw new RuntimeException( "unkwnown display type: " + getPhylogenyGraphicsType() ); } - 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(); + if ( getControlPanel().getDynamicallyHideData() != null ) { + if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) { + getControlPanel().getDynamicallyHideData().setEnabled( false ); } - catch ( final URISyntaxException e ) { - AptxUtil.showErrorMessage( this, e.toString() ); - e.printStackTrace(); + else { + getControlPanel().getDynamicallyHideData().setEnabled( true ); } } + if ( isPhyHasBranchLengths() && ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) { + getControlPanel().setDrawPhylogramEnabled( true ); + } else { - cannotOpenBrowserWarningMessage( "sequence" ); + getControlPanel().setDrawPhylogramEnabled( false ); } + getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( getPhylogenyGraphicsType() ); } - final private void openTaxWeb( final PhylogenyNode node ) { - if ( !isCanOpenTaxWeb( node ) ) { - cannotOpenBrowserWarningMessage( "taxonomic" ); - return; - } - String uri_str = null; - final Taxonomy tax = node.getNodeData().getTaxonomy(); - if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getValue() ) - && tax.getIdentifier().getValue().startsWith( "http://" ) ) { - try { - uri_str = new URI( tax.getIdentifier().getValue() ).toString(); - } - catch ( final URISyntaxException e ) { - AptxUtil.showErrorMessage( this, e.toString() ); - uri_str = null; - e.printStackTrace(); - } + final void calcMaxDepth() { + if ( _phylogeny != null ) { + _circ_max_depth = PhylogenyMethods.calculateMaxDepth( _phylogeny ); } - else if ( ( tax.getIdentifier() != null ) - && !ForesterUtil.isEmpty( tax.getIdentifier().getValue() ) - && !ForesterUtil.isEmpty( tax.getIdentifier().getProvider() ) - && ( tax.getIdentifier().getProvider().equalsIgnoreCase( "ncbi" ) || tax.getIdentifier().getProvider() - .equalsIgnoreCase( "uniprot" ) ) ) { - try { - uri_str = "http://www.uniprot.org/taxonomy/" - + URLEncoder.encode( tax.getIdentifier().getValue(), ForesterConstants.UTF8 ); + } + + /** + * Set parameters for printing the displayed tree + * + */ + final void calcParametersForPainting( final int x, final int y ) { + // updateStyle(); not needed? + if ( ( _phylogeny != null ) && !_phylogeny.isEmpty() ) { + initNodeData(); + calculateLongestExtNodeInfo(); + if ( ( getLongestExtNodeInfo() > ( x * 0.6 ) ) + && ( getTreeFontSet().getLargeFont().getSize() > ( 2 + TreeFontSet.FONT_SIZE_CHANGE_STEP ) ) ) { + while ( ( getLongestExtNodeInfo() > ( x * 0.7 ) ) + && ( getTreeFontSet().getLargeFont().getSize() > 2 ) ) { + getMainPanel().getTreeFontSet().decreaseFontSize( getConfiguration().getMinBaseFontSize(), true ); + calculateLongestExtNodeInfo(); + } } - catch ( final UnsupportedEncodingException e ) { - AptxUtil.showErrorMessage( this, e.toString() ); - e.printStackTrace(); + else { + while ( ( getLongestExtNodeInfo() < ( x * 0.6 ) ) && ( getTreeFontSet().getLargeFont() + .getSize() <= ( getTreeFontSet().getLargeFontMemory().getSize() + - TreeFontSet.FONT_SIZE_CHANGE_STEP ) ) ) { + getMainPanel().getTreeFontSet().increaseFontSize(); + calculateLongestExtNodeInfo(); + } } - } - else if ( !ForesterUtil.isEmpty( tax.getScientificName() ) ) { - try { - uri_str = "http://www.uniprot.org/taxonomy/?query=" - + URLEncoder.encode( tax.getScientificName(), ForesterConstants.UTF8 ); + //_length_of_longest_text = calcLengthOfLongestText(); + int ext_nodes = _phylogeny.getRoot().getNumberOfExternalNodes(); + final int max_depth = PhylogenyMethods.calculateMaxDepthConsiderCollapsed( _phylogeny ) + 1; + if ( ext_nodes == 1 ) { + ext_nodes = max_depth; + if ( ext_nodes < 1 ) { + ext_nodes = 1; + } } - catch ( final UnsupportedEncodingException e ) { - AptxUtil.showErrorMessage( this, e.toString() ); - e.printStackTrace(); + updateOvSizes(); + float xdist = 0; + float ov_xdist = 0; + if ( !isNonLinedUpCladogram() ) { + xdist = ( float ) ( ( x - getLongestExtNodeInfo() - TreePanel.MOVE ) / ( ext_nodes + 3.0 ) ); + ov_xdist = ( float ) ( getOvMaxWidth() / ( ext_nodes + 3.0 ) ); } - } - else if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) { - try { - uri_str = "http://www.uniprot.org/taxonomy/?query=" - + URLEncoder.encode( tax.getTaxonomyCode(), ForesterConstants.UTF8 ); + else { + xdist = ( ( x - getLongestExtNodeInfo() - TreePanel.MOVE ) / ( max_depth + 1 ) ); + ov_xdist = ( getOvMaxWidth() / ( max_depth + 1 ) ); } - catch ( final UnsupportedEncodingException e ) { - AptxUtil.showErrorMessage( this, e.toString() ); - e.printStackTrace(); + float ydist = ( float ) ( ( y - TreePanel.MOVE ) / ( ext_nodes * 2.0 ) ); + if ( xdist < 0.0 ) { + xdist = 0.0f; } - } - else if ( !ForesterUtil.isEmpty( tax.getCommonName() ) ) { - try { - uri_str = "http://www.uniprot.org/taxonomy/?query=" - + URLEncoder.encode( tax.getCommonName(), ForesterConstants.UTF8 ); + if ( ov_xdist < 0.0 ) { + ov_xdist = 0.0f; } - catch ( final UnsupportedEncodingException e ) { - AptxUtil.showErrorMessage( this, e.toString() ); - e.printStackTrace(); + if ( ydist < 0.0 ) { + ydist = 0.0f; } - } - if ( !ForesterUtil.isEmpty( uri_str ) ) { - try { - AptxUtil.launchWebBrowser( new URI( uri_str ), - isApplet(), - isApplet() ? obtainApplet() : null, - "_aptx_tax" ); + setXdistance( xdist ); + setYdistance( ydist ); + setOvXDistance( ov_xdist ); + final double height = _phylogeny.calculateHeight( !_options.isCollapsedWithAverageHeigh() ); + //final double height = PhylogenyMethods.calculateMaxDepth( _phylogeny ); + if ( height > 0 ) { + final float corr = ( float ) ( ( x - ( 2.0 * TreePanel.MOVE ) - getLongestExtNodeInfo() + - getXdistance() ) / height ); + setXcorrectionFactor( corr > 0 ? corr : 0 ); + final float ov_corr = ( float ) ( ( getOvMaxWidth() - getOvXDistance() ) / height ); + setOvXcorrectionFactor( ov_corr > 0 ? ov_corr : 0 ); } - catch ( final IOException e ) { - AptxUtil.showErrorMessage( this, e.toString() ); - e.printStackTrace(); + else { + setXcorrectionFactor( 0 ); + setOvXcorrectionFactor( 0 ); } - catch ( final URISyntaxException e ) { - AptxUtil.showErrorMessage( this, e.toString() ); - e.printStackTrace(); + _circ_max_depth = max_depth; + setUpUrtFactor(); + // + if ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) + && ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) { + // int dynamic_hiding_factor = calcDynamicHidingFactor(); + // if ( dynamic_hiding_factor > 1 ) { + // while ( dynamic_hiding_factor > 1 + // && getTreeFontSet()._fm_large.getHeight() > TreeFontSet.SMALL_FONTS_BASE ) { + // getTreeFontSet().decreaseFontSize( 1, true ); + // dynamic_hiding_factor = calcDynamicHidingFactor(); + // } + // } + // else if ( getTreeFontSet().isDecreasedSizeBySystem() ) { + // while ( dynamic_hiding_factor < 1 && getTreeFontSet()._fm_large.getHeight() < 12 ) { + // getTreeFontSet().increaseFontSize(); + // dynamic_hiding_factor = calcDynamicHidingFactor(); + // } + // } } - } - else { - cannotOpenBrowserWarningMessage( "taxonomic" ); + // } } - final private void paintBranchLength( final Graphics2D g, - final PhylogenyNode node, - final boolean to_pdf, - final boolean to_graphics_file ) { - g.setFont( getTreeFontSet().getSmallFont() ); - if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) { - g.setColor( Color.BLACK ); + final void calculateLongestExtNodeInfo() { + if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) { + return; } - else { - g.setColor( getTreeColorSet().getBranchLengthColor() ); + int max_possible_length = ForesterUtil + .roundToInt( ( getSize().getWidth() - ( 2 * MOVE ) ) * AptxConstants.EXT_NODE_INFO_LENGTH_MAX_RATIO ); + if ( max_possible_length < 20 ) { + max_possible_length = 20; } - 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().getSmallMaxDescent(), g ); + int longest = 30; + int longest_txt = 0; + _longest_domain = 0; + PhylogenyNode longest_txt_node = _phylogeny.getFirstExternalNode(); + for( final PhylogenyNode node : _phylogeny.getExternalNodes() ) { + int sum = 0; + if ( node.isCollapse() ) { + continue; } - else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) { - TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), node.getParent() - .getXcoord() + ROUNDED_D, node.getYcoord() - getTreeFontSet().getSmallMaxDescent(), g ); + final StringBuilder sb = new StringBuilder(); + nodeDataAsSB( node, sb ); + if ( node.getNodeData().isHasTaxonomy() ) { + nodeTaxonomyDataAsSB( node.getNodeData().getTaxonomy(), sb ); + } + final int txt = sb.length(); + if ( txt > longest_txt ) { + longest_txt = txt; + longest_txt_node = node; + } + boolean use_vis = false; + final Graphics2D g = ( Graphics2D ) getGraphics(); + if ( g != null && getControlPanel().isUseVisualStyles() ) { + use_vis = setFont( g, node, false ); + } + if ( !use_vis ) { + sum = getFontMetricsForLargeDefaultFont().stringWidth( sb.toString() ); } else { - TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), node.getParent() - .getXcoord() + 3, node.getYcoord() - getTreeFontSet().getSmallMaxDescent(), g ); + sum = getFontMetrics( g.getFont() ).stringWidth( sb.toString() ); + } + if ( getControlPanel().isShowBinaryCharacters() && node.getNodeData().isHasBinaryCharacters() ) { + sum += getFontMetricsForLargeDefaultFont().stringWidth( node.getNodeData().getBinaryCharacters() + .getGainedCharactersAsStringBuffer().toString() ); + } + if ( getControlPanel().isShowVectorData() && ( node.getNodeData().getVector() != null ) + && ( node.getNodeData().getVector().size() > 0 ) ) { + if ( getConfiguration() != null ) { + sum += getConfiguration().getVectorDataWidth() + 10; + } + else { + sum += RenderableVector.VECTOR_DEFAULT_WIDTH + 10; + } + } + if ( getControlPanel().isShowDomainArchitectures() && node.getNodeData().isHasSequence() + && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) { + // FIXME + // TODO this might need some clean up + final DomainArchitecture d = node.getNodeData().getSequence().getDomainArchitecture(); + sum += ( ( _domain_structure_width + / ( ( RenderableDomainArchitecture ) d ).getOriginalSize().getWidth() ) * d.getTotalLength() ) + + 10; + if ( d.getTotalLength() > _longest_domain ) { + _longest_domain = d.getTotalLength(); + } + } + if ( getControlPanel().isShowMolSequences() && ( node.getNodeData().isHasSequence() ) + && ( node.getNodeData().getSequence().isMolecularSequenceAligned() ) + && ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) ) { + // FIXME + sum += RenderableMsaSequence.DEFAULT_WIDTH + 30; + } + if ( sum >= max_possible_length ) { + _longest_ext_node_info = max_possible_length; + // return; //FIXME why? } + if ( sum > longest ) { + longest = sum; + } + } + _ext_node_with_longest_txt_info = longest_txt_node; + if ( longest >= max_possible_length ) { + _longest_ext_node_info = max_possible_length; } else { - TreePanel.drawString( FORMATTER_BRANCH_LENGTH.format( node.getDistanceToParent() ), 3, node.getYcoord() - - getTreeFontSet().getSmallMaxDescent(), g ); + _longest_ext_node_info = longest; } + _length_of_longest_text = calcLengthOfLongestText(); } - final private void paintBranchLite( final Graphics2D g, - final float x1, - final float x2, - final float y1, - final float y2, - final PhylogenyNode node ) { - g.setColor( getTreeColorSet().getOvColor() ); - if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR ) { - drawLine( x1, y1, x2, y2, g ); - } - else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CONVEX ) { - _quad_curve.setCurve( x1, y1, x1, y2, x2, y2 ); - ( g ).draw( _quad_curve ); + final void calculateScaleDistance() { + if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) { + return; } - else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CURVED ) { - final float dx = x2 - x1; - final float dy = y2 - y1; - _cubic_curve.setCurve( x1, y1, x1 + ( dx * 0.4f ), y1 + ( dy * 0.2f ), x1 + ( dx * 0.6f ), y1 - + ( dy * 0.8f ), x2, y2 ); - ( g ).draw( _cubic_curve ); + final double height = getMaxDistanceToRoot(); + if ( height > 0 ) { + if ( ( height <= 0.5 ) ) { + setScaleDistance( 0.01 ); + } + else if ( height <= 5.0 ) { + setScaleDistance( 0.1 ); + } + else if ( height <= 50.0 ) { + setScaleDistance( 1 ); + } + else if ( height <= 500.0 ) { + setScaleDistance( 10 ); + } + else { + setScaleDistance( 100 ); + } } else { - final float x2a = x2; - final float x1a = x1; - // draw the vertical line - if ( node.isFirstChildNode() || node.isLastChildNode() ) { - drawLine( x1, y1, x1, y2, g ); - } - // draw the horizontal line - drawLine( x1a, y2, x2a, y2, g ); + setScaleDistance( 0.0 ); + } + String scale_label = String.valueOf( getScaleDistance() ); + if ( !ForesterUtil.isEmpty( _phylogeny.getDistanceUnit() ) ) { + scale_label += " [" + _phylogeny.getDistanceUnit() + "]"; } + setScaleLabel( scale_label ); } - /** - * Paint a branch which consists of a vertical and a horizontal bar - * @param is_ind_found_nodes - */ - final private void paintBranchRectangular( final Graphics2D g, - final float x1, - final float x2, - final float y1, - final float y2, - final PhylogenyNode node, - final boolean to_pdf, - final boolean to_graphics_file ) { - assignGraphicsForBranchWithColorForParentBranch( node, false, g, to_pdf, to_graphics_file ); - if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR ) { - drawLine( x1, y1, x2, y2, g ); - } - else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CONVEX ) { - _quad_curve.setCurve( x1, y1, x1, y2, x2, y2 ); - g.draw( _quad_curve ); + final Color calculateSequenceBasedColor( final Sequence seq ) { + if ( ForesterUtil.isEmpty( seq.getName() ) ) { + return getTreeColorSet().getSequenceColor(); } - else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CURVED ) { - final float dx = x2 - x1; - final float dy = y2 - y1; - _cubic_curve.setCurve( x1, y1, x1 + ( dx * 0.4f ), y1 + ( dy * 0.2f ), x1 + ( dx * 0.6f ), y1 - + ( dy * 0.8f ), x2, y2 ); - g.draw( _cubic_curve ); + Color c = null; + final String seq_name = seq.getName(); + c = getControlPanel().getSequenceColors().get( seq_name ); + if ( c == null ) { + c = AptxUtil.calculateColorFromString( seq_name, false ); + getControlPanel().getSequenceColors().put( seq_name, c ); } - else { - 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 ) ) { - if ( !to_graphics_file - && !to_pdf - && ( ( ( y2 < ( getVisibleRect().getMinY() - 20 ) ) && ( y1 < ( getVisibleRect().getMinY() - 20 ) ) ) || ( ( y2 > ( getVisibleRect() - .getMaxY() + 20 ) ) && ( y1 > ( getVisibleRect().getMaxY() + 20 ) ) ) ) ) { - // Do nothing. + return c; + } + + final Color calculateTaxonomyBasedColor( final Taxonomy tax ) { + if ( getOptions().isColorByTaxonomicGroup() ) { + if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) { + boolean ex = false; + String group = null; + try { + group = TaxonomyUtil.getTaxGroupByTaxCode( tax.getTaxonomyCode() ); } - 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.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 ); - } - } - else { - drawLine( x1, y1, x1, y2, g ); + catch ( final Exception e ) { + ex = true; + } + if ( !ex && !ForesterUtil.isEmpty( group ) ) { + final Color c = ForesterUtil.obtainColorDependingOnTaxonomyGroup( group ); + if ( c != null ) { + return c; } } } - // draw the horizontal line - if ( !to_graphics_file && !to_pdf - && ( ( y2 < ( getVisibleRect().getMinY() - 20 ) ) || ( y2 > ( getVisibleRect().getMaxY() + 20 ) ) ) ) { - return; + return getTreeColorSet().getTaxonomyColor(); + } + else { + if ( ForesterUtil.isEmpty( tax.getTaxonomyCode() ) && ForesterUtil.isEmpty( tax.getScientificName() ) ) { + return getTreeColorSet().getTaxonomyColor(); } - float x1_r = 0; - 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 ); - } + Color c = null; + if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) { + c = getControlPanel().getSpeciesColors().get( tax.getTaxonomyCode() ); } - 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 ); - } - } - else { - drawRectFilled( x1a, y2 - ( w / 2 ), x2a - x1a, w, g ); - } + if ( ( c == null ) && !ForesterUtil.isEmpty( tax.getScientificName() ) ) { + c = getControlPanel().getSpeciesColors().get( tax.getScientificName() ); } - if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) { - if ( x1_r > x2a ) { - x1_r = x2a; - } - if ( y2 > y2_r ) { - final double diff = y2 - y2_r; - _arc.setArc( x1, y2_r - diff, 2 * ( x1_r - x1 ), 2 * diff, 180, 90, Arc2D.OPEN ); + if ( c == null ) { + if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) { + c = AptxUtil.calculateColorFromString( tax.getTaxonomyCode(), true ); + getControlPanel().getSpeciesColors().put( tax.getTaxonomyCode(), c ); } else { - _arc.setArc( x1, y2, 2 * ( x1_r - x1 ), 2 * ( y2_r - y2 ), 90, 90, Arc2D.OPEN ); + c = AptxUtil.calculateColorFromString( tax.getScientificName(), true ); + getControlPanel().getSpeciesColors().put( tax.getScientificName(), c ); } - g.draw( _arc ); } - } - if ( node.isExternal() ) { - paintNodeBox( x2, y2, node, g, to_pdf, to_graphics_file ); + return c; } } - final private double paintCirculars( final PhylogenyNode n, - final Phylogeny phy, - final float center_x, - final float center_y, - final double radius, - final boolean radial_labels, - final Graphics2D g, - final boolean to_pdf, - final boolean to_graphics_file ) { - if ( n.isExternal() || n.isCollapse() ) { //~~circ collapse - if ( !_urt_nodeid_angle_map.containsKey( n.getId() ) ) { - System.out.println( "no " + n + " =====>>>>>>> ERROR!" );//TODO - } - return _urt_nodeid_angle_map.get( n.getId() ); - } - else { - final List descs = n.getDescendants(); - double sum = 0; - for( final PhylogenyNode desc : descs ) { - sum += paintCirculars( desc, - phy, - center_x, - center_y, - radius, - radial_labels, - g, - to_pdf, - to_graphics_file ); - } - double r = 0; - if ( !n.isRoot() ) { - r = 1 - ( ( ( double ) _circ_max_depth - n.calculateDepth() ) / _circ_max_depth ); - } - final double theta = sum / descs.size(); - n.setXcoord( ( float ) ( center_x + ( r * radius * Math.cos( theta ) ) ) ); - n.setYcoord( ( float ) ( center_y + ( r * radius * Math.sin( theta ) ) ) ); - _urt_nodeid_angle_map.put( n.getId(), theta ); - for( final PhylogenyNode desc : descs ) { - paintBranchCircular( n, desc, g, radial_labels, to_pdf, to_graphics_file ); - } - return theta; - } + void clearCurrentExternalNodesDataBuffer() { + setCurrentExternalNodesDataBuffer( new StringBuilder() ); } - final private void paintCircularsLite( final PhylogenyNode n, - final Phylogeny phy, - final int center_x, - final int center_y, - final int radius, - final Graphics2D g ) { - if ( n.isExternal() ) { + /** + * Collapse the tree from the given node + * + * @param node + * a PhylogenyNode + */ + final void collapse( final PhylogenyNode node ) { + if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) { + JOptionPane.showMessageDialog( this, + "Cannot collapse in unrooted display type", + "Attempt to collapse in unrooted display", + JOptionPane.WARNING_MESSAGE ); return; } - else { - final List descs = n.getDescendants(); - for( final PhylogenyNode desc : descs ) { - paintCircularsLite( desc, phy, center_x, center_y, radius, g ); - } - float r = 0; - if ( !n.isRoot() ) { - r = 1 - ( ( ( float ) _circ_max_depth - n.calculateDepth() ) / _circ_max_depth ); - } - final double theta = _urt_nodeid_angle_map.get( n.getId() ); - n.setXSecondary( ( float ) ( center_x + ( radius * r * Math.cos( theta ) ) ) ); - n.setYSecondary( ( float ) ( center_y + ( radius * r * Math.sin( theta ) ) ) ); - for( final PhylogenyNode desc : descs ) { - paintBranchCircularLite( n, desc, g ); - } + if ( !node.isExternal() && !node.isRoot() ) { + final boolean collapse = !node.isCollapse(); + TreePanelUtil.collapseSubtree( node, collapse ); + updateSetOfCollapsedExternalNodes(); + _phylogeny.recalculateNumberOfExternalDescendants( true ); + resetNodeIdToDistToLeafMap(); + calculateLongestExtNodeInfo(); + setNodeInPreorderToNull(); + _control_panel.displayedPhylogenyMightHaveChanged( true ); + resetPreferredSize(); + updateOvSizes(); + _main_panel.adjustJScrollPane(); + repaint(); } } - final private void paintCollapsedNode( final Graphics2D g, - final PhylogenyNode node, - 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() ) { - c = Color.BLACK; - } - else if ( is_in_found_nodes ) { - c = getColorForFoundNode( node ); - } - else if ( getControlPanel().isColorAccordingToSequence() ) { - c = getSequenceBasedColor( node ); - } - else if ( getControlPanel().isColorAccordingToTaxonomy() ) { - c = getTaxonomyBasedColor( node ); - } - else if ( getOptions().isColorLabelsSameAsParentBranch() && getControlPanel().isUseVisualStyles() - && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) { - c = PhylogenyMethods.getBranchColorValue( node ); - } - else { - c = getTreeColorSet().getCollapseFillColor(); - } - double d = node.getAllExternalDescendants().size(); - if ( d > 1000 ) { - d = ( 3 * _y_distance ) / 3; - } - else { - d = ( Math.log10( d ) * _y_distance ) / 2.5; - } - final int box_size = getOptions().getDefaultNodeShapeSize() + 1; - if ( d < box_size ) { - d = box_size; - } - final float xx = node.getXcoord() - ( 2 * box_size ); - final float xxx = xx > ( node.getParent().getXcoord() + 1 ) ? xx : node.getParent().getXcoord() + 1; - _polygon.reset(); - _polygon.moveTo( xxx, node.getYcoord() ); - _polygon.lineTo( node.getXcoord() + 1, node.getYcoord() - d ); - _polygon.lineTo( node.getXcoord() + 1, node.getYcoord() + d ); - _polygon.closePath(); - if ( getOptions().getDefaultNodeFill() == NodeVisualData.NodeFill.SOLID ) { - g.setColor( c ); - g.fill( _polygon ); + final void uncollapseAll( final PhylogenyNode node ) { + if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) { + JOptionPane.showMessageDialog( this, + "Cannot uncollapse in unrooted display type", + "Attempt to uncollapse in unrooted display", + JOptionPane.WARNING_MESSAGE ); + return; } - else if ( getOptions().getDefaultNodeFill() == NodeVisualData.NodeFill.NONE ) { - g.setColor( getBackground() ); - g.fill( _polygon ); - g.setColor( c ); - g.draw( _polygon ); + if ( !node.isExternal() ) { + TreePanelUtil.uncollapseSubtree( node ); + updateSetOfCollapsedExternalNodes(); + _phylogeny.recalculateNumberOfExternalDescendants( true ); + resetNodeIdToDistToLeafMap(); + calculateLongestExtNodeInfo(); + setNodeInPreorderToNull(); + _control_panel.displayedPhylogenyMightHaveChanged( true ); + resetPreferredSize(); + updateOvSizes(); + _main_panel.adjustJScrollPane(); + repaint(); } - else if ( getOptions().getDefaultNodeFill() == NodeFill.GRADIENT ) { - g.setPaint( new GradientPaint( xxx, node.getYcoord(), getBackground(), node.getXcoord(), ( float ) ( node - .getYcoord() - d ), c, false ) ); - g.fill( _polygon ); - g.setPaint( c ); - g.draw( _polygon ); + } + + final void collapseSpeciesSpecificSubtrees() { + if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) { + return; } - paintNodeData( g, node, to_graphics_file, to_pdf, is_in_found_nodes ); + setWaitCursor(); + TreePanelUtil.collapseSpeciesSpecificSubtrees( _phylogeny ); + updateSetOfCollapsedExternalNodes(); + _phylogeny.recalculateNumberOfExternalDescendants( true ); + resetNodeIdToDistToLeafMap(); + calculateLongestExtNodeInfo(); + setNodeInPreorderToNull(); + resetPreferredSize(); + resetDepthCollapseDepthValue(); + resetRankCollapseRankValue(); + _main_panel.adjustJScrollPane(); + getControlPanel().showWhole(); + setArrowCursor(); } - final private void paintConfidenceValues( final Graphics2D g, - final PhylogenyNode node, - final boolean to_pdf, - final boolean to_graphics_file ) { - final List confidences = node.getBranchData().getConfidences(); - boolean not_first = false; - Collections.sort( confidences ); - final StringBuilder sb = new StringBuilder(); - for( final Confidence confidence : confidences ) { - if ( ForesterUtil.isEmpty( SHOW_ONLY_THIS_CONF_TYPE ) - || ( !ForesterUtil.isEmpty( confidence.getType() ) && confidence.getType() - .equalsIgnoreCase( SHOW_ONLY_THIS_CONF_TYPE ) ) ) { - final double value = confidence.getValue(); - if ( value != Confidence.CONFIDENCE_DEFAULT_VALUE ) { - if ( value < getOptions().getMinConfidenceValue() ) { - return; - } - if ( not_first ) { - sb.append( "/" ); - } - else { - not_first = true; - } - sb.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( value, getOptions() - .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) ); - if ( getOptions().isShowConfidenceStddev() ) { - if ( confidence.getStandardDeviation() != Confidence.CONFIDENCE_DEFAULT_VALUE ) { - sb.append( "(" ); - sb.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence - .getStandardDeviation(), getOptions() - .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) ); - sb.append( ")" ); - } - } - } - } + final void colorRank( final String rank ) { + if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) { + return; } - if ( sb.length() > 0 ) { - 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; + setWaitCursor(); + AptxUtil.removeBranchColors( _phylogeny ); + final int colorizations = TreePanelUtil.colorPhylogenyAccordingToRanks( _phylogeny, rank, this ); + if ( colorizations > 0 ) { + _control_panel.setColorBranches( true ); + if ( _control_panel.getUseVisualStylesCb() != null ) { + _control_panel.getUseVisualStylesCb().setSelected( true ); } - else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) { - x += ROUNDED_D; + if ( _control_panel.getColorAccSpeciesCb() != null ) { + _control_panel.getColorAccSpeciesCb().setSelected( false ); } - if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) { - g.setColor( Color.BLACK ); + _options.setColorLabelsSameAsParentBranch( true ); + if ( getMainPanel().getMainFrame()._color_labels_same_as_parent_branch != null ) { + getMainPanel().getMainFrame()._color_labels_same_as_parent_branch.setSelected( true ); + } + _control_panel.repaint(); + } + setArrowCursor(); + repaint(); + if ( colorizations > 0 ) { + String msg = "Taxonomy colorization via " + rank + " completed:\n"; + if ( colorizations > 1 ) { + msg += "colorized " + colorizations + " subtrees"; } else { - g.setColor( getTreeColorSet().getConfidenceColor() ); + msg += "colorized one subtree"; } - final String conf_str = sb.toString(); - TreePanel.drawString( conf_str, - parent_x - + ( ( x - parent_x - getTreeFontSet().getFontMetricsSmall() - .stringWidth( conf_str ) ) / 2 ), - ( node.getYcoord() + getTreeFontSet().getSmallMaxAscent() ) - 1, - g ); + setEdited( true ); + JOptionPane.showMessageDialog( this, + msg, + "Taxonomy Rank-Colorization Completed (" + rank + ")", + JOptionPane.INFORMATION_MESSAGE ); + } + else { + String msg = "Could not taxonomy rank-colorize any subtree via " + rank + ".\n"; + msg += "Possible solutions (given that suitable taxonomic information is present):\n"; + msg += "select a different rank (e.g. phylum, genus, ...)\n"; + msg += " and/or\n"; + msg += "execute:\n"; + msg += "1. \"" + MainFrame.OBTAIN_DETAILED_TAXONOMIC_INFORMATION + "\" (Tools)\n"; + msg += "2. \"" + MainFrame.INFER_ANCESTOR_TAXONOMIES + "\" (Analysis)"; + JOptionPane.showMessageDialog( this, + msg, + "Taxonomy Rank-Colorization Failed", + JOptionPane.WARNING_MESSAGE ); } } - final private void paintGainedAndLostCharacters( final Graphics2D g, - final PhylogenyNode node, - final String gained, - final String lost ) { - if ( node.getParent() != null ) { - final float parent_x = node.getParent().getXcoord(); - final float x = node.getXcoord(); - g.setFont( getTreeFontSet().getLargeFont() ); - g.setColor( getTreeColorSet().getGainedCharactersColor() ); - if ( Constants.SPECIAL_CUSTOM ) { - g.setColor( Color.BLUE ); - } - TreePanel - .drawString( gained, - 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 - getFontMetricsForLargeDefaultFont().stringWidth( lost ) ) / 2 ), - ( node.getYcoord() + getFontMetricsForLargeDefaultFont().getMaxAscent() ), - g ); + final void confColor() { + if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) { + return; + } + setWaitCursor(); + AptxUtil.removeBranchColors( _phylogeny ); + TreePanelUtil.colorPhylogenyAccordingToConfidenceValues( _phylogeny, this ); + _control_panel.setColorBranches( true ); + if ( _control_panel.getUseVisualStylesCb() != null ) { + _control_panel.getUseVisualStylesCb().setSelected( true ); + } + setArrowCursor(); + repaint(); + } + + final void decreaseDomainStructureEvalueThresholdExp() { + if ( _domain_structure_e_value_thr_exp > -20 ) { + _domain_structure_e_value_thr_exp -= 1; } } /** - * Draw a box at the indicated node. - * + * Find the node, if any, at the given location + * * @param x * @param y - * @param node - * @param g + * @return pointer to the node at x,y, null if not found */ - final private void paintNodeBox( final float x, - final float y, - final PhylogenyNode node, - final Graphics2D g, - final boolean to_pdf, - 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().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 ); + public final PhylogenyNode findNode( final int x, final int y ) { + if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) { + return null; } - if ( ( isInFoundNodes( node ) || isInCurrentExternalNodes( node ) ) - || ( getOptions().isShowDefaultNodeShapesExternal() && node.isExternal() ) - || ( getOptions().isShowDefaultNodeShapesInternal() && node.isInternal() ) - || ( getOptions().isShowDefaultNodeShapesForMarkedNodes() - && ( node.getNodeData().getNodeVisualData() != null ) && ( !node.getNodeData() - .getNodeVisualData().isEmpty() ) ) - || ( 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() ) ) ) { - 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().getDuplicationBoxColor(); - } - else if ( event.isSpeciation() ) { - outline_color = getTreeColorSet().getSpecBoxColor(); - } - else if ( event.isSpeciationOrDuplication() ) { - outline_color = getTreeColorSet().getDuplicationOrSpeciationColor(); - } - } - if ( outline_color == null ) { - outline_color = getGraphicsForNodeBoxWithColorForParentBranch( node ); - if ( to_pdf && ( outline_color == getTreeColorSet().getBranchColor() ) ) { - outline_color = getTreeColorSet().getBranchColorForPdf(); - } - } - 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(); + 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 ) ) { + return node; } - 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 ( fill == 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 ( 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 ); + } + return null; + } + + final Configuration getConfiguration() { + return _configuration; + } + + final ControlPanel getControlPanel() { + return _control_panel; + } + + String getCurrentExternalNodesDataBufferAsString() { + return _current_external_nodes_data_buffer.toString(); + } + + int getCurrentExternalNodesDataBufferChangeCounter() { + return _current_external_nodes_data_buffer_change_counter; + } + + final int getDomainStructureEvalueThresholdExp() { + return _domain_structure_e_value_thr_exp; + } + + public final Set getFoundNodes0() { + return _found_nodes_0; + } + + public final Set getFoundNodes1() { + return _found_nodes_1; + } + + public List getFoundNodesAsListOfPhylogenyNodes() { + final List additional_nodes = new ArrayList(); + if ( getFoundNodes0() != null ) { + for( final Long id : getFoundNodes0() ) { + final PhylogenyNode n = _phylogeny.getNode( id ); + if ( n != null ) { + additional_nodes.add( n ); } } - 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 ( fill == 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 ( fill == NodeVisualData.NodeFill.SOLID ) { - if ( vis_fill_color != null ) { - g.setColor( vis_fill_color ); - } - else { - g.setColor( outline_color ); + } + if ( getFoundNodes1() != null ) { + for( final Long id : getFoundNodes1() ) { + if ( ( getFoundNodes0() == null ) || !getFoundNodes0().contains( id ) ) { + final PhylogenyNode n = _phylogeny.getNode( id ); + if ( n != null ) { + additional_nodes.add( n ); } - drawRectFilled( x - half_box_size, y - half_box_size, box_size, box_size, g ); } } } + return additional_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 0; - } - if ( getControlPanel().isWriteBranchLengthValues() - && ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) - || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) ) - && ( !node.isRoot() ) && ( node.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) ) { - paintBranchLength( g, node, to_pdf, to_graphics_file ); - } - if ( !getControlPanel().isShowInternalData() && !node.isExternal() && !node.isCollapse() ) { - return 0; - } - _sb.setLength( 0 ); - 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 ); - } - if ( ( getControlPanel().isShowTaxonomyCode() || getControlPanel().isShowTaxonomyScientificNames() || getControlPanel() - .isShowTaxonomyCommonNames() ) && node.getNodeData().isHasTaxonomy() ) { - x += paintTaxonomy( g, node, is_in_found_nodes, to_pdf, to_graphics_file, x ); - } - 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( node.getAllExternalDescendants().size() ); - _sb.append( ")" ); - } + final Color getGraphicsForNodeBoxWithColorForParentBranch( final PhylogenyNode node ) { + if ( getControlPanel().isUseVisualStyles() && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) { + return ( PhylogenyMethods.getBranchColorValue( node ) ); } else { - _sb.setLength( 0 ); - } - 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; + return ( getTreeColorSet().getBranchColor() ); } - 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 { - pos_y = ( node.getYcoord() + ( getFontMetrics( g.getFont() ).getAscent() / down_shift_factor ) ); - } - final String sb_str = _sb.toString(); - // GUILHEM_BEG ______________ - if ( _control_panel.isShowSequenceRelations() && node.getNodeData().isHasSequence() - && ( _query_sequence != null ) ) { - int nodeTextBoundsWidth = 0; - if ( sb_str.length() > 0 ) { - final Rectangle2D node_text_bounds = new TextLayout( sb_str, g.getFont(), _frc ).getBounds(); //would like to remove this 'new', but how... - nodeTextBoundsWidth = ( int ) node_text_bounds.getWidth(); - } - if ( node.getNodeData().getSequence().equals( _query_sequence ) ) { - if ( nodeTextBoundsWidth > 0 ) { // invert font color and background color to show that this is the query sequence - g.fillRect( ( int ) pos_x - 1, ( int ) pos_y - 8, nodeTextBoundsWidth + 5, 11 ); - g.setColor( getTreeColorSet().getBackgroundColor() ); - } - } - else { - final List seqRelations = node.getNodeData().getSequence().getSequenceRelations(); - for( final SequenceRelation seqRelation : seqRelations ) { - final boolean fGotRelationWithQuery = ( seqRelation.getRef0().isEqual( _query_sequence ) || seqRelation - .getRef1().isEqual( _query_sequence ) ) - && 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 String sConfidence = ( !getControlPanel().isShowSequenceRelationConfidence() || ( seqRelation - .getConfidence() == null ) ) ? null : " (" + seqRelation.getConfidence().getValue() - + ")"; - if ( sConfidence != null ) { - float confidenceX = pos_x; - if ( sb_str.length() > 0 ) { - confidenceX += new TextLayout( sb_str, g.getFont(), _frc ).getBounds().getWidth() - + CONFIDENCE_LEFT_MARGIN; - } - if ( confidenceX > linePosX ) { // let's only display confidence value if we are already displaying at least one of Prot/Gene Name and Taxonomy Code - final int confidenceWidth = ( int ) new TextLayout( sConfidence, g.getFont(), _frc ) - .getBounds().getWidth(); - TreePanel.drawString( sConfidence, confidenceX, pos_y, g ); - x += CONFIDENCE_LEFT_MARGIN + confidenceWidth; - } - } - if ( ( x + nodeTextBoundsWidth ) > 0 ) /* we only underline if there is something displayed */ - { - if ( nodeTextBoundsWidth == 0 ) { - nodeTextBoundsWidth -= 3; /* the gap between taxonomy code and node name should not be underlined if nothing comes after it */ - } - else { - nodeTextBoundsWidth += 2; - } - g.drawLine( ( int ) linePosX + 1, 3 + ( int ) pos_y, ( int ) linePosX + x - + nodeTextBoundsWidth, 3 + ( int ) pos_y ); - break; - } - } - } - } - } - if ( sb_str.length() > 0 ) { - TreePanel.drawString( sb_str, pos_x, pos_y, g ); + } + + final int getLongestExtNodeInfo() { + return _longest_ext_node_info; + } + + final Options getOptions() { + if ( _options == null ) { + _options = getControlPanel().getOptions(); } - // 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; - } + return _options; + } + + final Rectangle2D getOvRectangle() { + return _ov_rectangle; + } + + final Rectangle getOvVirtualRectangle() { + return _ov_virtual_rectangle; + } + + final PHYLOGENY_GRAPHICS_TYPE getPhylogenyGraphicsType() { + return _graphics_type; + } + + final Color getSequenceBasedColor( final PhylogenyNode node ) { + if ( node.getNodeData().isHasSequence() ) { + return calculateSequenceBasedColor( node.getNodeData().getSequence() ); } - if ( getControlPanel().isShowAnnotation() && node.getNodeData().isHasSequence() - && ( node.getNodeData().getSequence().getAnnotations() != null ) - && ( !node.getNodeData().getSequence().getAnnotations().isEmpty() ) ) { - final SortedSet ann = node.getNodeData().getSequence().getAnnotations(); - if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) { - g.setColor( Color.BLACK ); - } - else if ( getControlPanel().isColorAccordingToAnnotation() ) { - g.setColor( calculateColorForAnnotation( ann ) ); - } - final String ann_str = TreePanelUtil.createAnnotationString( ann, getOptions().isShowAnnotationRefSource() ); - TreePanel.drawString( ann_str, node.getXcoord() + x + 3 + half_box_size, node.getYcoord() - + ( 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; - } - } + // return non-colorized color + return getTreeColorSet().getSequenceColor(); + } + + final double getStartingAngle() { + return _urt_starting_angle; + } + + DescriptiveStatistics getStatisticsForExpressionValues() { + return _statistics_for_vector_data; + } + + final Color getTaxonomyBasedColor( final PhylogenyNode node ) { + if ( node.isExternal() && node.getNodeData().isHasTaxonomy() ) { + return calculateTaxonomyBasedColor( node.getNodeData().getTaxonomy() ); } - 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 ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) { - g.setColor( Color.BLACK ); - } - else { - g.setColor( getTreeColorSet().getBinaryDomainCombinationsColor() ); - } - if ( getControlPanel().isShowBinaryCharacters() ) { - TreePanel.drawString( node.getNodeData().getBinaryCharacters().getPresentCharactersAsStringBuffer() - .toString(), node.getXcoord() + x + 1 + half_box_size, node.getYcoord() - + ( 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() - + ( getFontMetricsForLargeDefaultFont().getAscent() / down_shift_factor ), - g ); - paintGainedAndLostCharacters( g, node, "+" - + node.getNodeData().getBinaryCharacters().getGainedCount(), "-" - + node.getNodeData().getBinaryCharacters().getLostCount() ); - } - } + // return non-colorized color + return getTreeColorSet().getTaxonomyColor(); + } + + public final File getTreeFile() { + return _treefile; + } + + final float getXcorrectionFactor() { + return _x_correction_factor; + } + + final float getXdistance() { + return _x_distance; + } + + final float getYdistance() { + return _y_distance; + } + + final void increaseDomainStructureEvalueThresholdExp() { + if ( _domain_structure_e_value_thr_exp < 3 ) { + _domain_structure_e_value_thr_exp += 1; } - return x; } - final private void paintNodeDataUnrootedCirc( final Graphics2D g, - final PhylogenyNode node, - final boolean to_pdf, - final boolean to_graphics_file, - final boolean radial_labels, - final double ur_angle, - final boolean is_in_found_nodes ) { - if ( isNodeDataInvisibleUnrootedCirc( node ) && !to_graphics_file && !to_pdf ) { + final void initNodeData() { + if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) { return; } - _sb.setLength( 0 ); - _sb.append( " " ); - if ( node.getNodeData().isHasTaxonomy() - && ( getControlPanel().isShowTaxonomyCode() || getControlPanel().isShowTaxonomyScientificNames() || getControlPanel() - .isShowTaxonomyCommonNames() ) ) { - final Taxonomy taxonomy = node.getNodeData().getTaxonomy(); - 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() ) ) { - _sb.append( taxonomy.getScientificName() ); - _sb.append( " (" ); - _sb.append( taxonomy.getCommonName() ); - _sb.append( ") " ); - } - else if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) { - _sb.append( taxonomy.getScientificName() ); - _sb.append( " " ); + double _max_original_domain_structure_width = 0.0; + for( final PhylogenyNode node : _phylogeny.getExternalNodes() ) { + if ( node.getNodeData().isHasSequence() + && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) { + RenderableDomainArchitecture rds = null; + if ( !( node.getNodeData().getSequence() + .getDomainArchitecture() instanceof RenderableDomainArchitecture ) ) { + if ( SPECIAL_DOMAIN_COLORING ) { + rds = new RenderableDomainArchitecture( node.getNodeData().getSequence() + .getDomainArchitecture(), node.getName() ); + } + else { + rds = new RenderableDomainArchitecture( node.getNodeData().getSequence() + .getDomainArchitecture() ); + } + node.getNodeData().getSequence().setDomainArchitecture( rds ); } - else if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) { - _sb.append( taxonomy.getCommonName() ); - _sb.append( " " ); + else { + rds = ( RenderableDomainArchitecture ) node.getNodeData().getSequence().getDomainArchitecture(); } - } - else if ( _control_panel.isShowTaxonomyScientificNames() ) { - if ( !ForesterUtil.isEmpty( taxonomy.getScientificName() ) ) { - _sb.append( taxonomy.getScientificName() ); - _sb.append( " " ); + if ( getControlPanel().isShowDomainArchitectures() ) { + final double dsw = rds.getOriginalSize().getWidth(); + if ( dsw > _max_original_domain_structure_width ) { + _max_original_domain_structure_width = dsw; + } } } - else if ( _control_panel.isShowTaxonomyCommonNames() ) { - if ( !ForesterUtil.isEmpty( taxonomy.getCommonName() ) ) { - _sb.append( taxonomy.getCommonName() ); - _sb.append( " " ); + } + if ( getControlPanel().isShowDomainArchitectures() ) { + final float ds_factor_width = ( float ) ( _domain_structure_width / _max_original_domain_structure_width ); + for( final PhylogenyNode node : _phylogeny.getExternalNodes() ) { + if ( node.getNodeData().isHasSequence() + && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) { + final RenderableDomainArchitecture rds = ( RenderableDomainArchitecture ) node.getNodeData() + .getSequence().getDomainArchitecture(); + rds.setRenderingFactorWidth( ds_factor_width ); + rds.setParameter( _domain_structure_e_value_thr_exp ); } } } - if ( node.isCollapse() && ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) ) { - _sb.append( " [" ); - _sb.append( node.getAllExternalDescendants().size() ); - _sb.append( "]" ); + } + + final boolean inOv( final MouseEvent e ) { + return ( ( e.getX() > ( getVisibleRect().x + getOvXPosition() + 1 ) ) + && ( e.getX() < ( ( getVisibleRect().x + getOvXPosition() + getOvMaxWidth() ) - 1 ) ) + && ( e.getY() > ( getVisibleRect().y + getOvYPosition() + 1 ) ) + && ( e.getY() < ( ( getVisibleRect().y + getOvYPosition() + getOvMaxHeight() ) - 1 ) ) ); + } + + final boolean inOvRectangle( final MouseEvent e ) { + return ( ( e.getX() >= ( getOvRectangle().getX() - 1 ) ) + && ( e.getX() <= ( getOvRectangle().getX() + getOvRectangle().getWidth() + 1 ) ) + && ( e.getY() >= ( getOvRectangle().getY() - 1 ) ) + && ( e.getY() <= ( getOvRectangle().getY() + getOvRectangle().getHeight() + 1 ) ) ); + } + + final boolean isCanCollapse() { + return ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ); + } + + final boolean isCanUncollapseAll( final PhylogenyNode node ) { + if ( node.isExternal() || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) ) { + return false; } - if ( getControlPanel().isShowNodeNames() && ( node.getName().length() > 0 ) ) { - if ( _sb.length() > 0 ) { - _sb.append( " " ); - } - _sb.append( node.getName() ); + if ( node.isCollapse() ) { + return true; } - if ( node.getNodeData().isHasSequence() ) { - 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().isShowSeqNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) { - if ( _sb.length() > 0 ) { - _sb.append( " " ); - } - _sb.append( node.getNodeData().getSequence().getName() ); + final PhylogenyNodeIterator it = new PreorderTreeIterator( node ); + while ( it.hasNext() ) { + if ( it.next().isCollapse() ) { + return true; } } - //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 ) { - m = _urt_nodeid_angle_map.get( node.getId() ) % TWO_PI; + return false; + } + + final boolean isCanColorSubtree() { + return ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ); + } + + final boolean isCanCopy() { + return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable() ); + } + + final boolean isCanCut( final PhylogenyNode node ) { + return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable() + && !node.isRoot() ); + } + + final boolean isCanDelete() { + return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable() ); + } + + final boolean isCanPaste() { + return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable() + && ( getCutOrCopiedTree() != null ) && !getCutOrCopiedTree().isEmpty() ); + } + + final boolean isCanReroot() { + return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && ( _subtree_index < 1 ) ); + } + + final boolean isCanSubtree( final PhylogenyNode node ) { + return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && !node.isExternal() + && ( !node.isRoot() || ( _subtree_index > 0 ) ) ); + } + + final boolean isCurrentTreeIsSubtree() { + return ( _subtree_index > 0 ); + } + + final boolean isEdited() { + return _edited; + } + + final boolean isInOvRect() { + return _in_ov_rect; + } + + final boolean isOvOn() { + return _ov_on; + } + + final boolean isPhyHasBranchLengths() { + return _phy_has_branch_lengths; + } + + final void midpointRoot() { + if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) { + return; + } + if ( !_phylogeny.isRerootable() ) { + JOptionPane.showMessageDialog( this, + "This is not rerootable", + "Not rerootable", + JOptionPane.WARNING_MESSAGE ); + return; + } + setNodeInPreorderToNull(); + setWaitCursor(); + PhylogenyMethods.midpointRoot( _phylogeny ); + resetNodeIdToDistToLeafMap(); + setArrowCursor(); + setEdited( true ); + repaint(); + } + + final void mouseClicked( final MouseEvent e ) { + if ( getOptions().isShowOverview() && isOvOn() && isInOv() ) { + final double w_ratio = getVisibleRect().width / getOvRectangle().getWidth(); + final double h_ratio = getVisibleRect().height / getOvRectangle().getHeight(); + double x = ( e.getX() - getVisibleRect().x - getOvXPosition() - ( getOvRectangle().getWidth() / 2.0 ) ) + * w_ratio; + double y = ( e.getY() - getVisibleRect().y - getOvYPosition() - ( getOvRectangle().getHeight() / 2.0 ) ) + * h_ratio; + if ( x < 0 ) { + x = 0; } - else { - m = ( float ) ( ur_angle % TWO_PI ); + if ( y < 0 ) { + y = 0; } - _at = g.getTransform(); - boolean need_to_reset = false; - final float x_coord = node.getXcoord(); - float y_coord; - if ( !using_visual_font ) { - y_coord = node.getYcoord() + ( getFontMetricsForLargeDefaultFont().getAscent() / 3.0f ); + final double max_x = getWidth() - getVisibleRect().width; + final double max_y = getHeight() - getVisibleRect().height; + if ( x > max_x ) { + x = max_x; } - else { - y_coord = node.getYcoord() + ( getFontMetrics( g.getFont() ).getAscent() / 3.0f ); + if ( y > max_y ) { + y = max_y; } - if ( radial_labels ) { - need_to_reset = true; - boolean left = false; - if ( ( m > HALF_PI ) && ( m < ONEHALF_PI ) ) { - m -= PI; - left = true; + getMainPanel().getCurrentScrollPane().getViewport() + .setViewPosition( new Point( ForesterUtil.roundToInt( x ), ForesterUtil.roundToInt( y ) ) ); + setInOvRect( true ); + repaint(); + } + else { + final PhylogenyNode node = findNode( e.getX(), e.getY() ); + if ( node != null ) { + if ( !node.isRoot() && node.getParent().isCollapse() ) { + return; } - g.rotate( m, x_coord, node.getYcoord() ); - if ( left ) { - 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 ); + _highlight_node = node; + // Check if shift key is down + if ( ( e.getModifiers() & InputEvent.SHIFT_MASK ) != 0 ) { + // Yes, so add to _found_nodes + if ( getFoundNodes0() == null ) { + setFoundNodes0( new HashSet() ); } + getFoundNodes0().add( node.getId() ); + // Check if control key is down } - } - else { - if ( ( m > HALF_PI ) && ( m < ONEHALF_PI ) ) { - need_to_reset = true; - if ( !using_visual_font ) { - g.translate( -getFontMetricsForLargeDefaultFont().getStringBounds( sb_str, g ).getWidth(), 0 ); + else if ( ( e.getModifiers() & InputEvent.CTRL_MASK ) != 0 ) { + // Yes, so pop-up menu + displayNodePopupMenu( node, e.getX(), e.getY() ); + // Handle unadorned click + } + else { + // Check for right mouse button + if ( e.getModifiers() == 4 ) { + displayNodePopupMenu( node, e.getX(), e.getY() ); } else { - g.translate( -getFontMetrics( g.getFont() ).getStringBounds( sb_str, g ).getWidth(), 0 ); + // if not in _found_nodes, clear _found_nodes + handleClickToAction( _control_panel.getActionWhenNodeClicked(), node ); } } } - TreePanel.drawString( sb_str, x_coord, y_coord, g ); - if ( need_to_reset ) { - g.setTransform( _at ); - } + else { + // no node was clicked so partition tree instead + _highlight_node = null; + + _clicked_x = e.getX(); + if (!getPhylogeny().isEmpty()) { + // should be calculated on each partition as the tree can theoretically + // change in the meantime + PhylogenyNode furthestNode = PhylogenyMethods.calculateNodeWithMaxDistanceToRoot( _phylogeny ); + _furthest_node_x = furthestNode.getXcoord(); + _root_x = _phylogeny.getRoot().getXcoord(); + + // don't bother if 0 distance tree or clicked x lies outside of tree + if (_furthest_node_x != _root_x && !(_clicked_x < _root_x || _clicked_x > _furthest_node_x)) + { + _partition_tree = true; + + } + + } + } + } + repaint(); } - final private void paintNodeLite( final Graphics2D g, final PhylogenyNode node ) { - if ( node.isCollapse() ) { - if ( !node.isRoot() && !node.getParent().isCollapse() ) { - paintCollapsedNode( g, node, false, false, false ); + final void mouseDragInBrowserPanel( final MouseEvent e ) { + setCursor( MOVE_CURSOR ); + final Point scroll_position = getMainPanel().getCurrentScrollPane().getViewport().getViewPosition(); + scroll_position.x -= ( e.getX() - getLastDragPointX() ); + scroll_position.y -= ( e.getY() - getLastDragPointY() ); + if ( scroll_position.x < 0 ) { + scroll_position.x = 0; + } + else { + final int max_x = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getMaximum() + - getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getVisibleAmount(); + if ( scroll_position.x > max_x ) { + scroll_position.x = max_x; } - return; } - if ( isInFoundNodes( node ) || isInCurrentExternalNodes( node ) ) { - 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 ); + if ( scroll_position.y < 0 ) { + scroll_position.y = 0; } - float new_x = 0; - if ( !node.isExternal() && !node.isCollapse() ) { - boolean first_child = true; - float y2 = 0.0f; - final int parent_max_branch_to_leaf = getMaxBranchesToLeaf( node ); - for( int i = 0; i < node.getNumberOfDescendants(); ++i ) { - final PhylogenyNode child_node = node.getChildNode( i ); - int factor_x; - if ( !isUniformBranchLengthsForCladogram() ) { - factor_x = node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes(); - } - else { - factor_x = parent_max_branch_to_leaf - getMaxBranchesToLeaf( child_node ); - } - if ( first_child ) { - first_child = false; - y2 = node.getYSecondary() - - ( getOvYDistance() * ( node.getNumberOfExternalNodes() - child_node - .getNumberOfExternalNodes() ) ); - } - else { - y2 += getOvYDistance() * child_node.getNumberOfExternalNodes(); - } - final float x2 = calculateOvBranchLengthToParent( child_node, factor_x ); - new_x = x2 + node.getXSecondary(); - final float diff_y = node.getYSecondary() - y2; - final float diff_x = node.getXSecondary() - new_x; - if ( ( diff_y > 2 ) || ( diff_y < -2 ) || ( diff_x > 2 ) || ( diff_x < -2 ) ) { - paintBranchLite( g, node.getXSecondary(), new_x, node.getYSecondary(), y2, child_node ); - } - child_node.setXSecondary( new_x ); - child_node.setYSecondary( y2 ); - y2 += getOvYDistance() * child_node.getNumberOfExternalNodes(); + else { + final int max_y = getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getMaximum() + - getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getVisibleAmount(); + if ( scroll_position.y > max_y ) { + scroll_position.y = max_y; } } + if ( isOvOn() || getOptions().isShowScale() ) { + repaint(); + } + getMainPanel().getCurrentScrollPane().getViewport().setViewPosition( scroll_position ); } - final private void paintNodeRectangular( final Graphics2D g, - final PhylogenyNode node, - final boolean to_pdf, - final boolean dynamically_hide, - final int dynamic_hiding_factor, - final boolean to_graphics_file, - final boolean disallow_shortcutting ) { - final boolean is_in_found_nodes = isInFoundNodes( node ) || isInCurrentExternalNodes( node ); - if ( node.isCollapse() ) { - if ( ( !node.isRoot() && !node.getParent().isCollapse() ) ) { - paintCollapsedNode( g, node, to_graphics_file, to_pdf, is_in_found_nodes ); + final void mouseDragInOvRectangle( final MouseEvent e ) { + setCursor( HAND_CURSOR ); + final double w_ratio = getVisibleRect().width / getOvRectangle().getWidth(); + final double h_ratio = getVisibleRect().height / getOvRectangle().getHeight(); + final Point scroll_position = getMainPanel().getCurrentScrollPane().getViewport().getViewPosition(); + double dx = ( ( w_ratio * e.getX() ) - ( w_ratio * getLastDragPointX() ) ); + double dy = ( ( h_ratio * e.getY() ) - ( h_ratio * getLastDragPointY() ) ); + scroll_position.x = ForesterUtil.roundToInt( scroll_position.x + dx ); + scroll_position.y = ForesterUtil.roundToInt( scroll_position.y + dy ); + if ( scroll_position.x <= 0 ) { + scroll_position.x = 0; + dx = 0; + } + else { + final int max_x = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getMaximum() + - getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getVisibleAmount(); + if ( scroll_position.x >= max_x ) { + dx = 0; + scroll_position.x = max_x; } - return; } - if ( node.isExternal() ) { - ++_external_node_index; + if ( scroll_position.y <= 0 ) { + dy = 0; + scroll_position.y = 0; } - // Confidence values - if ( getControlPanel().isShowConfidenceValues() - && !node.isExternal() - && !node.isRoot() - && ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) - || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) ) - && node.getBranchData().isHasConfidences() ) { - paintConfidenceValues( g, node, to_pdf, to_graphics_file ); - } - // Draw a line to root: - if ( node.isRoot() && _phylogeny.isRooted() ) { - paintRootBranch( g, node.getXcoord(), node.getYcoord(), node, to_pdf, to_graphics_file ); - } - float new_x = 0; - float new_x_min = Float.MAX_VALUE; - float min_dist = 1.5f; - if ( !disallow_shortcutting ) { - if ( dynamic_hiding_factor > 4000 ) { - min_dist = 4; - } - else if ( dynamic_hiding_factor > 1000 ) { - min_dist = 3; - } - else if ( dynamic_hiding_factor > 100 ) { - min_dist = 2; - } - } - if ( !node.isExternal() && !node.isCollapse() ) { - boolean first_child = true; - float y2 = 0.0f; - final int parent_max_branch_to_leaf = getMaxBranchesToLeaf( node ); - for( int i = 0; i < node.getNumberOfDescendants(); ++i ) { - final PhylogenyNode child_node = node.getChildNode( i ); - int factor_x; - if ( !isUniformBranchLengthsForCladogram() ) { - factor_x = node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes(); - } - else { - factor_x = parent_max_branch_to_leaf - getMaxBranchesToLeaf( child_node ); - } - if ( first_child ) { - first_child = false; - y2 = node.getYcoord() - - ( _y_distance * ( node.getNumberOfExternalNodes() - child_node.getNumberOfExternalNodes() ) ); - } - else { - y2 += _y_distance * child_node.getNumberOfExternalNodes(); - } - final float x2 = calculateBranchLengthToParent( child_node, factor_x ); - new_x = x2 + node.getXcoord(); - if ( dynamically_hide && ( x2 < new_x_min ) ) { - new_x_min = x2; - } - final float diff_y = node.getYcoord() - y2; - final float diff_x = node.getXcoord() - new_x; - if ( disallow_shortcutting || ( diff_y > min_dist ) || ( diff_y < -min_dist ) || ( diff_x > min_dist ) - || ( diff_x < -min_dist ) ) { - paintBranchRectangular( g, - node.getXcoord(), - new_x, - node.getYcoord(), - y2, - child_node, - to_pdf, - to_graphics_file ); - } - child_node.setXcoord( new_x ); - child_node.setYcoord( y2 ); - y2 += _y_distance * child_node.getNumberOfExternalNodes(); + else { + final int max_y = getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getMaximum() + - getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getVisibleAmount(); + if ( scroll_position.y >= max_y ) { + dy = 0; + scroll_position.y = max_y; } - paintNodeBox( node.getXcoord(), node.getYcoord(), node, g, to_pdf, to_graphics_file ); - } - 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() ) < getFontMetricsForLargeDefaultFont() - .getHeight() ) ) ) ) ) { - return; } - final int x = paintNodeData( g, node, to_graphics_file, to_pdf, is_in_found_nodes ); - paintNodeWithRenderableData( x, g, node, to_graphics_file, to_pdf ); + repaint(); + getMainPanel().getCurrentScrollPane().getViewport().setViewPosition( scroll_position ); + setLastMouseDragPointX( ( float ) ( e.getX() + dx ) ); + setLastMouseDragPointY( ( float ) ( e.getY() + dy ) ); } - final private void paintNodeWithRenderableData( final int x, - final Graphics2D g, - final PhylogenyNode node, - final boolean to_graphics_file, - final boolean to_pdf ) { - if ( isNodeDataInvisible( node ) && !( to_graphics_file || to_pdf ) ) { - return; - } - if ( ( !getControlPanel().isShowInternalData() && !node.isExternal() ) ) { - return; + final void mouseMoved( final MouseEvent e ) { + requestFocusInWindow(); + if ( _current_external_nodes != null ) { + _current_external_nodes = null; + repaint(); } - if ( getControlPanel().isShowDomainArchitectures() && node.getNodeData().isHasSequence() - && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) - && ( node.getNodeData().getSequence().getDomainArchitecture() instanceof RenderableDomainArchitecture ) ) { - RenderableDomainArchitecture rds = null; - try { - rds = ( RenderableDomainArchitecture ) node.getNodeData().getSequence().getDomainArchitecture(); - } - catch ( final ClassCastException cce ) { - cce.printStackTrace(); + if ( getControlPanel().isNodeDescPopup() ) { + if ( _node_desc_popup != null ) { + _node_desc_popup.hide(); + _node_desc_popup = null; } - if ( rds != null ) { - final int default_height = 7; - float y = getYdistance(); - if ( getControlPanel().isDynamicallyHideData() ) { - y = getTreeFontSet().getFontMetricsLarge().getHeight(); - } - final int h = y < default_height ? ForesterUtil.roundToInt( y ) : default_height; - rds.setRenderingHeight( h > 1 ? h : 2 ); - if ( getControlPanel().isDrawPhylogram() ) { - if ( getOptions().isLineUpRendarableNodeData() ) { - if ( getOptions().isRightLineUpDomains() ) { - rds.render( ( float ) ( ( getMaxDistanceToRoot() * getXcorrectionFactor() ) - + _length_of_longest_text + ( ( _longest_domain - rds.getTotalLength() ) * rds - .getRenderingFactorWidth() ) ), node.getYcoord() - ( h / 2.0f ), g, this, to_pdf ); - } - else { - rds.render( ( float ) ( ( getMaxDistanceToRoot() * getXcorrectionFactor() ) + _length_of_longest_text ), - node.getYcoord() - ( h / 2.0f ), - g, - this, - to_pdf ); - } - } - else { - rds.render( node.getXcoord() + x, node.getYcoord() - ( h / 2.0f ), g, this, to_pdf ); - } + } + if ( getOptions().isShowOverview() && isOvOn() ) { + if ( inOvVirtualRectangle( e ) ) { + if ( !isInOvRect() ) { + setInOvRect( true ); + repaint(); } - else { - if ( getOptions().isRightLineUpDomains() ) { - rds.render( ( ( getPhylogeny().getFirstExternalNode().getXcoord() + _length_of_longest_text ) - 20 ) - + ( ( _longest_domain - rds.getTotalLength() ) * rds - .getRenderingFactorWidth() ), - node.getYcoord() - ( h / 2.0f ), - g, - this, - to_pdf ); - } - else { - rds.render( getPhylogeny().getFirstExternalNode().getXcoord() + _length_of_longest_text, - node.getYcoord() - ( h / 2.0f ), - g, - this, - to_pdf ); - } + } + else { + if ( isInOvRect() ) { + setInOvRect( false ); + repaint(); } } } - if ( getControlPanel().isShowVectorData() && ( node.getNodeData().getVector() != null ) - && ( node.getNodeData().getVector().size() > 0 ) && ( getStatisticsForExpressionValues() != null ) ) { - final RenderableVector rv = RenderableVector.createInstance( node.getNodeData().getVector(), - getStatisticsForExpressionValues(), - getConfiguration() ); - if ( rv != null ) { - double domain_add = 0; - if ( getControlPanel().isShowDomainArchitectures() && node.getNodeData().isHasSequence() - && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) { - domain_add = _domain_structure_width + 10; - } - if ( getControlPanel().isDrawPhylogram() ) { - rv.render( ( float ) ( node.getXcoord() + x + domain_add ), node.getYcoord() - 3, g, this, to_pdf ); - } - else { - rv.render( ( float ) ( getPhylogeny().getFirstExternalNode().getXcoord() + _length_of_longest_text + domain_add ), - node.getYcoord() - 3, - g, - this, - to_pdf ); - } + if ( inOv( e ) && getOptions().isShowOverview() && isOvOn() ) { + if ( !isInOv() ) { + setInOv( true ); } } - if ( getControlPanel().isShowMolSequences() && ( node.getNodeData().isHasSequence() ) - && ( node.getNodeData().getSequence().isMolecularSequenceAligned() ) - && ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) ) { - final RenderableMsaSequence rs = RenderableMsaSequence.createInstance( node.getNodeData().getSequence() - .getMolecularSequence(), node.getNodeData().getSequence().getType(), getConfiguration() ); - if ( rs != null ) { - final int default_height = 7; - float y = getYdistance(); - if ( getControlPanel().isDynamicallyHideData() ) { - y = getTreeFontSet().getFontMetricsLarge().getHeight(); + else { + if ( isInOv() ) { + setInOv( false ); + } + final PhylogenyNode node = findNode( e.getX(), e.getY() ); + if ( ( node != null ) && ( node.isRoot() || !node.getParent().isCollapse() ) ) { + if ( ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.GET_EXT_DESC_DATA ) ) { + for( final PhylogenyNode n : node.getAllExternalDescendants() ) { + addToCurrentExternalNodes( n.getId() ); + } + setCursor( HAND_CURSOR ); + repaint(); } - final int h = y < default_height ? ForesterUtil.roundToInt( y ) : default_height; - rs.setRenderingHeight( h > 1 ? h : 2 ); - if ( getControlPanel().isDrawPhylogram() ) { - rs.render( ( float ) ( ( getMaxDistanceToRoot() * getXcorrectionFactor() ) + _length_of_longest_text ), - node.getYcoord() - ( h / 2.0f ), - g, - this, - to_pdf ); + else if ( ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.CUT_SUBTREE ) + || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.COPY_SUBTREE ) + || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.PASTE_SUBTREE ) + || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.DELETE_NODE_OR_SUBTREE ) + || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.REROOT ) + || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.ADD_NEW_NODE ) ) { + setCursor( CUT_CURSOR ); } else { - rs.render( getPhylogeny().getFirstExternalNode().getXcoord() + _length_of_longest_text, - node.getYcoord() - ( h / 2.0f ), - g, - this, - to_pdf ); + setCursor( HAND_CURSOR ); + if ( getControlPanel().isNodeDescPopup() ) { + showNodeDataPopup( e, node ); + } } } - } - } - - final private int calcLengthOfLongestText() { - final StringBuilder sb = new StringBuilder(); - if ( _ext_node_with_longest_txt_info != null ) { - nodeDataAsSB( _ext_node_with_longest_txt_info, sb ); - if ( _ext_node_with_longest_txt_info.getNodeData().isHasTaxonomy() ) { - nodeTaxonomyDataAsSB( _ext_node_with_longest_txt_info.getNodeData().getTaxonomy(), sb ); + else { + setCursor( ARROW_CURSOR ); } } - return getFontMetricsForLargeDefaultFont().stringWidth( sb.toString() ); } - final private void paintOvRectangle( final Graphics2D g ) { - final float w_ratio = ( ( float ) getWidth() ) / getVisibleRect().width; - final float h_ratio = ( ( float ) getHeight() ) / getVisibleRect().height; - final float x_ratio = ( ( float ) getWidth() ) / getVisibleRect().x; - final float y_ratio = ( ( float ) getHeight() ) / getVisibleRect().y; - final float width = getOvMaxWidth() / w_ratio; - 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().getFoundColor0() ); - getOvRectangle().setRect( x, y, width, height ); - final Stroke s = g.getStroke(); - g.setStroke( STROKE_1 ); - if ( ( width < 6 ) && ( height < 6 ) ) { - drawRectFilled( x, y, 6, 6, g ); - getOvVirtualRectangle().setRect( x, y, 6, 6 ); - } - else if ( width < 6 ) { - drawRectFilled( x, y, 6, height, g ); - getOvVirtualRectangle().setRect( x, y, 6, height ); - } - else if ( height < 6 ) { - drawRectFilled( x, y, width, 6, g ); - getOvVirtualRectangle().setRect( x, y, width, 6 ); - } - else { - drawRect( x, y, width, height, g ); - if ( isInOvRect() ) { - drawRect( x + 1, y + 1, width - 2, height - 2, g ); - } - getOvVirtualRectangle().setRect( x, y, width, height ); - } - g.setStroke( s ); + final void mouseReleasedInBrowserPanel( final MouseEvent e ) { + setCursor( ARROW_CURSOR ); } - final private void paintPhylogenyLite( final Graphics2D g ) { - _phylogeny - .getRoot() - .setXSecondary( ( float ) ( getVisibleRect().x + getOvXPosition() + ( MOVE / ( getVisibleRect().width / getOvRectangle() - .getWidth() ) ) ) ); - _phylogeny.getRoot().setYSecondary( ( getVisibleRect().y + getOvYStart() ) ); - final Stroke s = g.getStroke(); - g.setStroke( STROKE_05 ); - for( final PhylogenyNode element : _nodes_in_preorder ) { - paintNodeLite( g, element ); - } - g.setStroke( s ); - paintOvRectangle( g ); + final void multiplyUrtFactor( final float f ) { + _urt_factor *= f; } - /** - * Paint the root branch. (Differs from others because it will always be a - * single horizontal line). - * @param to_graphics_file - * - * @return new x1 value - */ - final private void paintRootBranch( final Graphics2D g, - final float x1, - final float y1, - final PhylogenyNode root, - final boolean to_pdf, - final boolean to_graphics_file ) { - assignGraphicsForBranchWithColorForParentBranch( root, false, g, to_pdf, to_graphics_file ); - float d = getXdistance(); - if ( getControlPanel().isDrawPhylogram() && ( root.getDistanceToParent() > 0.0 ) ) { - d = ( float ) ( getXcorrectionFactor() * root.getDistanceToParent() ); - } - if ( d < MIN_ROOT_LENGTH ) { - d = MIN_ROOT_LENGTH; - } - if ( !getControlPanel().isWidthBranches() || ( PhylogenyMethods.getBranchWidthValue( root ) == 1 ) ) { - drawLine( x1 - d, root.getYcoord(), x1, root.getYcoord(), g ); + final void paintBranchCircular( final PhylogenyNode p, + final PhylogenyNode c, + final Graphics2D g, + final boolean radial_labels, + final boolean to_pdf, + final boolean to_graphics_file ) { + final double angle = _urt_nodeid_angle_map.get( c.getId() ); + final double root_x = _root.getXcoord(); + final double root_y = _root.getYcoord(); + final double dx = root_x - p.getXcoord(); + final double dy = root_y - p.getYcoord(); + final double parent_radius = Math.sqrt( ( dx * dx ) + ( dy * dy ) ); + final double arc = ( _urt_nodeid_angle_map.get( p.getId() ) ) - angle; + assignGraphicsForBranchWithColorForParentBranch( c, false, g, to_pdf, to_graphics_file ); + if ( ( c.isFirstChildNode() || c.isLastChildNode() ) + && ( ( Math.abs( parent_radius * arc ) > 1.5 ) || to_pdf || to_graphics_file ) ) { + final double r2 = 2.0 * parent_radius; + drawArc( root_x - parent_radius, root_y - parent_radius, r2, r2, ( -angle - arc ), arc, g ); } - else { - final double w = PhylogenyMethods.getBranchWidthValue( root ); - drawRectFilled( x1 - d, root.getYcoord() - ( w / 2 ), d, w, g ); + drawLine( c.getXcoord(), + c.getYcoord(), + 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 ); + if ( c.isExternal() ) { + 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; + } + paintNodeDataUnrootedCirc( g, c, to_pdf, to_graphics_file, radial_labels, 0, is_in_found_nodes ); } - paintNodeBox( x1, root.getYcoord(), root, g, to_pdf, to_graphics_file ); } - final private void paintScale( final Graphics2D g, - int x1, - int y1, - final boolean to_pdf, - final boolean to_graphics_file ) { - x1 += MOVE; - final double x2 = x1 + ( getScaleDistance() * getXcorrectionFactor() ); - y1 -= 12; - final int y2 = y1 - 8; - final int y3 = y1 - 4; - g.setFont( getTreeFontSet().getSmallFont() ); - if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) { - g.setColor( Color.BLACK ); - } - else { - g.setColor( getTreeColorSet().getBranchLengthColor() ); + final void paintBranchCircularLite( final PhylogenyNode p, final PhylogenyNode c, final Graphics2D g ) { + final double angle = _urt_nodeid_angle_map.get( c.getId() ); + final double root_x = _root.getXSecondary(); + final double root_y = _root.getYSecondary(); + final double dx = root_x - p.getXSecondary(); + final double dy = root_y - p.getYSecondary(); + final double arc = ( _urt_nodeid_angle_map.get( p.getId() ) ) - angle; + final double parent_radius = Math.sqrt( ( dx * dx ) + ( dy * dy ) ); + g.setColor( getTreeColorSet().getOvColor() ); + if ( ( c.isFirstChildNode() || c.isLastChildNode() ) && ( Math.abs( arc ) > 0.02 ) ) { + final double r2 = 2.0 * parent_radius; + drawArc( root_x - parent_radius, root_y - parent_radius, r2, r2, ( -angle - arc ), arc, g ); } - final Stroke s = g.getStroke(); - g.setStroke( STROKE_1 ); - drawLine( x1, y1, x1, y2, g ); - drawLine( x2, y1, x2, y2, g ); - drawLine( x1, y3, x2, y3, g ); - if ( getScaleLabel() != null ) { - g.drawString( getScaleLabel(), ( x1 + 2 ), y3 - 2 ); + drawLine( c.getXSecondary(), + c.getYSecondary(), + root_x + ( Math.cos( angle ) * parent_radius ), + root_y + ( Math.sin( angle ) * parent_radius ), + 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 ); } - g.setStroke( s ); } - final private int paintTaxonomy( final Graphics2D g, - final PhylogenyNode node, - final boolean is_in_found_nodes, - final boolean to_pdf, - final boolean to_graphics_file, - final float x_shift ) { - final Taxonomy taxonomy = node.getNodeData().getTaxonomy(); - 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 { - start_y = node.getYcoord() - + ( getFontMetrics( g.getFont() ).getAscent() / ( node.getNumberOfDescendants() == 1 ? 1 : 3.0f ) ); - } - _sb.setLength( 0 ); - nodeTaxonomyDataAsSB( taxonomy, _sb ); - final String label = _sb.toString(); - /* GUILHEM_BEG */ - if ( _control_panel.isShowSequenceRelations() && ( label.length() > 0 ) - && ( node.getNodeData().isHasSequence() ) && node.getNodeData().getSequence().equals( _query_sequence ) ) { - // invert font color and background color to show that this is the query sequence - final Rectangle2D nodeTextBounds = new TextLayout( label, g.getFont(), new FontRenderContext( null, - false, - false ) ) - .getBounds(); - g.fillRect( ( int ) start_x - 1, ( int ) start_y - 8, ( int ) nodeTextBounds.getWidth() + 4, 11 ); - g.setColor( getTreeColorSet().getBackgroundColor() ); + final void paintCircular( final Phylogeny phy, + final double starting_angle, + final int center_x, + final int center_y, + final int radius, + final Graphics2D g, + final boolean to_pdf, + final boolean to_graphics_file ) { + 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; + double current_angle = starting_angle; + int i = 0; + for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) { + final PhylogenyNode n = it.next(); + 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() ); + } } - /* GUILHEM_END */ - TreePanel.drawString( label, start_x, start_y, g ); - if ( !using_visual_font && !is_in_found_nodes ) { - return getFontMetricsForLargeDefaultFont().stringWidth( label ); + 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 ); + } + + final void paintCircularLite( final Phylogeny phy, + final double starting_angle, + final int center_x, + final int center_y, + final int radius, + final Graphics2D g ) { + final int circ_num_ext_nodes = phy.getNumberOfExternalNodes(); + _root = phy.getRoot(); + _root.setXSecondary( center_x ); + _root.setYSecondary( center_y ); + double current_angle = starting_angle; + for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) { + final PhylogenyNode n = it.next(); + 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 ); } - return getFontMetrics( g.getFont() ).stringWidth( label ); + paintCircularsLite( phy.getRoot(), phy, center_x, center_y, radius, g ); } - final private void paintUnrooted( final PhylogenyNode n, - final double low_angle, - final double high_angle, - final boolean radial_labels, - final Graphics2D g, - final boolean to_pdf, - final boolean to_graphics_file ) { - if ( n.isRoot() ) { - n.setXcoord( getWidth() / 2 ); - n.setYcoord( getHeight() / 2 ); + final void paintPhylogeny( final Graphics2D g, + final boolean to_pdf, + final boolean to_graphics_file, + final int graphics_file_width, + final int graphics_file_height, + final int graphics_file_x, + final int graphics_file_y ) { + if (_partition_tree) { +// float threshold = (_clicked_x - _root_x) / (_furthest_node_x - _root_x); +// drawLine( _clicked_x, 0, _clicked_x, getHeight(),g); + + _partition_tree = false; } - if ( n.isExternal() ) { - paintNodeDataUnrootedCirc( g, - n, - to_pdf, - to_graphics_file, - radial_labels, - ( high_angle + low_angle ) / 2, - isInFoundNodes( n ) || isInCurrentExternalNodes( n ) ); + + if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) { return; } - final float num_enclosed = n.getNumberOfExternalNodes(); - final float x = n.getXcoord(); - final float y = n.getYcoord(); - double current_angle = low_angle; - // final boolean n_below = n.getYcoord() < getVisibleRect().getMinY() - 20; - // final boolean n_above = n.getYcoord() > getVisibleRect().getMaxY() + 20; - // final boolean n_left = n.getXcoord() < getVisibleRect().getMinX() - 20; - // final boolean n_right = n.getXcoord() > getVisibleRect().getMaxX() + 20; - for( int i = 0; i < n.getNumberOfDescendants(); ++i ) { - final PhylogenyNode desc = n.getChildNode( i ); - /// if ( ( ( n_below ) & ( desc.getYcoord() < getVisibleRect().getMinY() - 20 ) ) - // || ( ( n_above ) & ( desc.getYcoord() > getVisibleRect().getMaxY() + 20 ) ) - // || ( ( n_left ) & ( desc.getXcoord() < getVisibleRect().getMinX() - 20 ) ) - // || ( ( n_right ) & ( desc.getXcoord() > getVisibleRect().getMaxX() + 20 ) ) ) { - // continue; - // } - //if ( ( desc.getYcoord() > n.getYcoord() ) && ( n.getYcoord() > getVisibleRect().getMaxY() - 20 ) ) { - // continue; - //} - //if ( ( desc.getYcoord() < n.getYcoord() ) && ( n.getYcoord() < getVisibleRect().getMinY() + 20 ) ) { - // continue; - // } - final int desc_num_enclosed = desc.getNumberOfExternalNodes(); - final double arc_size = ( desc_num_enclosed / num_enclosed ) * ( high_angle - low_angle ); - float length; - if ( isPhyHasBranchLengths() && getControlPanel().isDrawPhylogram() ) { - if ( desc.getDistanceToParent() < 0 ) { - length = 0; + if ( _control_panel.isShowSequenceRelations() ) { + _query_sequence = _control_panel.getSelectedQuerySequence(); + } + // Color the background + if ( !to_pdf ) { + final Rectangle r = getVisibleRect(); + if ( !getOptions().isBackgroundColorGradient() || getOptions().isPrintBlackAndWhite() ) { + g.setColor( getTreeColorSet().getBackgroundColor() ); + if ( !to_graphics_file ) { + g.fill( r ); } else { - length = ( float ) ( desc.getDistanceToParent() * getUrtFactor() ); + if ( getOptions().isPrintBlackAndWhite() ) { + g.setColor( Color.WHITE ); + } + g.fillRect( graphics_file_x, graphics_file_y, graphics_file_width, graphics_file_height ); } } else { - length = getUrtFactor(); - } - final double mid_angle = current_angle + ( arc_size / 2 ); - final float new_x = ( float ) ( x + ( Math.cos( mid_angle ) * length ) ); - 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 ); - } - if ( n.isRoot() ) { - paintNodeBox( n.getXcoord(), n.getYcoord(), n, g, to_pdf, to_graphics_file ); + if ( !to_graphics_file ) { + g.setPaint( new GradientPaint( r.x, + r.y, + getTreeColorSet().getBackgroundColor(), + r.x, + r.y + r.height, + getTreeColorSet().getBackgroundColorGradientBottom() ) ); + g.fill( r ); + } + else { + g.setPaint( new GradientPaint( graphics_file_x, + graphics_file_y, + getTreeColorSet().getBackgroundColor(), + graphics_file_x, + graphics_file_y + graphics_file_height, + getTreeColorSet().getBackgroundColorGradientBottom() ) ); + g.fillRect( graphics_file_x, graphics_file_y, graphics_file_width, graphics_file_height ); + } + } + setupStroke( g ); } - } - - final private void paintUnrootedLite( final PhylogenyNode n, - final double low_angle, - final double high_angle, - final Graphics2D g, - final float urt_ov_factor ) { - if ( n.isRoot() ) { - final int x_pos = ( int ) ( getVisibleRect().x + getOvXPosition() + ( getOvMaxWidth() / 2 ) ); - final int y_pos = ( int ) ( getVisibleRect().y + getOvYPosition() + ( getOvMaxHeight() / 2 ) ); - n.setXSecondary( x_pos ); - n.setYSecondary( y_pos ); + else { + g.setStroke( new BasicStroke( getOptions().getPrintLineWidth() ) ); } - if ( n.isExternal() ) { - return; + if ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) + && ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) { + _external_node_index = 0; + // Position starting X of tree + if ( !_phylogeny.isRooted() /*|| ( _subtree_index > 0 )*/ ) { + _phylogeny.getRoot().setXcoord( TreePanel.MOVE ); + } + else if ( ( _phylogeny.getRoot().getDistanceToParent() > 0.0 ) && getControlPanel().isDrawPhylogram() ) { + _phylogeny.getRoot().setXcoord( ( float ) ( TreePanel.MOVE + + ( _phylogeny.getRoot().getDistanceToParent() * getXcorrectionFactor() ) ) ); + } + else { + _phylogeny.getRoot().setXcoord( TreePanel.MOVE + getXdistance() ); + } + // Position starting Y of tree + _phylogeny.getRoot().setYcoord( ( getYdistance() * _phylogeny.getRoot().getNumberOfExternalNodes() ) + + ( TreePanel.MOVE / 2.0f ) ); + final int dynamic_hiding_factor = calcDynamicHidingFactor(); + if ( getControlPanel().isDynamicallyHideData() ) { + if ( dynamic_hiding_factor > 1 ) { + getControlPanel().setDynamicHidingIsOn( true ); + } + else { + getControlPanel().setDynamicHidingIsOn( false ); + } + } + if ( _nodes_in_preorder == null ) { + _nodes_in_preorder = new PhylogenyNode[ _phylogeny.getNodeCount() ]; + int i = 0; + for( final PhylogenyNodeIterator it = _phylogeny.iteratorPreorder(); it.hasNext(); ) { + _nodes_in_preorder[ i++ ] = it.next(); + } + } + final boolean disallow_shortcutting = ( dynamic_hiding_factor < 40 ) + /* || getControlPanel().isUseVisualStyles() || getOptions().isShowDefaultNodeShapesForMarkedNodes()*/ //TODO check if this is really not needed. + || to_graphics_file || to_pdf; + for( final PhylogenyNode element : _nodes_in_preorder ) { + paintNodeRectangular( g, + element, + to_pdf, + getControlPanel().isDynamicallyHideData() && ( dynamic_hiding_factor > 1 ), + dynamic_hiding_factor, + to_graphics_file, + disallow_shortcutting ); + } + if ( getOptions().isShowScale() && getControlPanel().isDrawPhylogram() && ( getScaleDistance() > 0.0 ) ) { + if ( !( to_graphics_file || to_pdf ) ) { + paintScale( g, + getVisibleRect().x, + getVisibleRect().y + getVisibleRect().height, + to_pdf, + to_graphics_file ); + } + else { + paintScale( g, graphics_file_x, graphics_file_y + graphics_file_height, to_pdf, to_graphics_file ); + } + } + if ( getOptions().isShowOverview() && isOvOn() && !to_graphics_file && !to_pdf ) { + paintPhylogenyLite( g ); + } } - final float num_enclosed = n.getNumberOfExternalNodes(); - final float x = n.getXSecondary(); - final float y = n.getYSecondary(); - double current_angle = low_angle; - for( int i = 0; i < n.getNumberOfDescendants(); ++i ) { - final PhylogenyNode desc = n.getChildNode( i ); - final int desc_num_enclosed = desc.getNumberOfExternalNodes(); - final double arc_size = ( desc_num_enclosed / num_enclosed ) * ( high_angle - low_angle ); - float length; - if ( isPhyHasBranchLengths() && getControlPanel().isDrawPhylogram() ) { - if ( desc.getDistanceToParent() < 0 ) { - length = 0; + else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) { + if ( getControlPanel().getDynamicallyHideData() != null ) { + getControlPanel().setDynamicHidingIsOn( false ); + } + final double angle = getStartingAngle(); + final boolean radial_labels = getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL; + _dynamic_hiding_factor = 0; + if ( getControlPanel().isDynamicallyHideData() ) { + _dynamic_hiding_factor = ( int ) ( ( getFontMetricsForLargeDefaultFont().getHeight() * 1.5 + * getPhylogeny().getNumberOfExternalNodes() ) / ( TWO_PI * 10 ) ); + } + if ( getControlPanel().getDynamicallyHideData() != null ) { + if ( _dynamic_hiding_factor > 1 ) { + getControlPanel().setDynamicHidingIsOn( true ); } else { - length = ( float ) ( desc.getDistanceToParent() * urt_ov_factor ); + getControlPanel().setDynamicHidingIsOn( false ); } } - else { - length = urt_ov_factor; + paintUnrooted( _phylogeny.getRoot(), + angle, + ( float ) ( angle + ( 2 * Math.PI ) ), + radial_labels, + g, + to_pdf, + to_graphics_file ); + if ( getOptions().isShowScale() ) { + if ( !( to_graphics_file || to_pdf ) ) { + paintScale( g, + getVisibleRect().x, + getVisibleRect().y + getVisibleRect().height, + to_pdf, + to_graphics_file ); + } + else { + paintScale( g, graphics_file_x, graphics_file_y + graphics_file_height, to_pdf, to_graphics_file ); + } } - final double mid_angle = current_angle + ( arc_size / 2 ); - final float new_x = ( float ) ( x + ( Math.cos( mid_angle ) * length ) ); - final float new_y = ( float ) ( y + ( Math.sin( mid_angle ) * length ) ); - desc.setXSecondary( new_x ); - desc.setYSecondary( new_y ); - if ( isInFoundNodes( desc ) || isInCurrentExternalNodes( desc ) ) { - 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 ); + if ( getOptions().isShowOverview() && isOvOn() && !to_graphics_file && !to_pdf ) { g.setColor( getTreeColorSet().getOvColor() ); + paintUnrootedLite( _phylogeny.getRoot(), + angle, + angle + ( 2 * Math.PI ), + g, + ( getUrtFactorOv() / ( getVisibleRect().width / getOvMaxWidth() ) ) ); + paintOvRectangle( g ); + } + } + else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) { + final int radius = ( int ) ( ( Math.min( getPreferredSize().getWidth(), getPreferredSize().getHeight() ) + / 2 ) - ( MOVE + getLongestExtNodeInfo() ) ); + final int d = radius + MOVE + getLongestExtNodeInfo(); + _dynamic_hiding_factor = 0; + if ( getControlPanel().isDynamicallyHideData() && ( radius > 0 ) ) { + _dynamic_hiding_factor = ( int ) ( ( getFontMetricsForLargeDefaultFont().getHeight() * 1.5 + * getPhylogeny().getNumberOfExternalNodes() ) / ( TWO_PI * radius ) ); + } + if ( getControlPanel().getDynamicallyHideData() != null ) { + if ( _dynamic_hiding_factor > 1 ) { + getControlPanel().setDynamicHidingIsOn( true ); + } + else { + getControlPanel().setDynamicHidingIsOn( false ); + } + } + paintCircular( _phylogeny, getStartingAngle(), d, d, radius > 0 ? radius : 0, g, to_pdf, to_graphics_file ); + if ( getOptions().isShowOverview() && isOvOn() && !to_graphics_file && !to_pdf ) { + final int radius_ov = ( int ) ( getOvMaxHeight() < getOvMaxWidth() ? getOvMaxHeight() / 2 + : getOvMaxWidth() / 2 ); + double x_scale = 1.0; + double y_scale = 1.0; + int x_pos = getVisibleRect().x + getOvXPosition(); + int y_pos = getVisibleRect().y + getOvYPosition(); + if ( getWidth() > getHeight() ) { + x_scale = ( double ) getHeight() / getWidth(); + x_pos = ForesterUtil.roundToInt( x_pos / x_scale ); + } + else { + y_scale = ( double ) getWidth() / getHeight(); + y_pos = ForesterUtil.roundToInt( y_pos / y_scale ); + } + _at = g.getTransform(); + g.scale( x_scale, y_scale ); + paintCircularLite( _phylogeny, + getStartingAngle(), + x_pos + radius_ov, + y_pos + radius_ov, + ( int ) ( radius_ov - ( getLongestExtNodeInfo() + / ( getVisibleRect().width / getOvRectangle().getWidth() ) ) ), + g ); + g.setTransform( _at ); + paintOvRectangle( g ); } - paintUnrootedLite( desc, current_angle, current_angle + arc_size, g, urt_ov_factor ); - current_angle += arc_size; - drawLine( x, y, new_x, new_y, g ); } } - final private void pasteSubtree( final PhylogenyNode node ) { - if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) { - errorMessageNoCutCopyPasteInUnrootedDisplay(); + final void recalculateMaxDistanceToRoot() { + _max_distance_to_root = PhylogenyMethods.calculateMaxDistanceToRoot( getPhylogeny() ); + if ( getPhylogeny().getRoot().getDistanceToParent() > 0 ) { + _max_distance_to_root += getPhylogeny().getRoot().getDistanceToParent(); + } + } + + /** + * Remove all edit-node frames + */ + final void removeAllEditNodeJFrames() { + for( int i = 0; i <= ( TreePanel.MAX_NODE_FRAMES - 1 ); i++ ) { + if ( _node_frames[ i ] != null ) { + _node_frames[ i ].dispose(); + _node_frames[ i ] = null; + } + } + _node_frame_index = 0; + } + + /** + * Remove a node-edit frame. + */ + final void removeEditNodeFrame( final int i ) { + _node_frame_index--; + _node_frames[ i ] = null; + if ( i < _node_frame_index ) { + for( int j = 0; j < ( _node_frame_index - 1 ); j++ ) { + _node_frames[ j ] = _node_frames[ j + 1 ]; + } + _node_frames[ _node_frame_index ] = null; + } + } + + final void reRoot( final PhylogenyNode node ) { + if ( !getPhylogeny().isRerootable() ) { + JOptionPane.showMessageDialog( this, + "This is not rerootable", + "Not rerootable", + JOptionPane.WARNING_MESSAGE ); return; } - if ( ( getCutOrCopiedTree() == null ) || getCutOrCopiedTree().isEmpty() ) { + if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) { JOptionPane.showMessageDialog( this, - "No tree in buffer (need to copy or cut a subtree first)", - "Attempt to paste with empty buffer", - JOptionPane.ERROR_MESSAGE ); + "Cannot reroot in unrooted display type", + "Attempt to reroot tree in unrooted display", + JOptionPane.WARNING_MESSAGE ); return; } - final String label = createASimpleTextRepresentationOfANode( getCutOrCopiedTree().getRoot() ); - final Object[] options = { "As sibling", "As descendant", "Cancel" }; - final int r = JOptionPane.showOptionDialog( this, - "How to paste subtree" + label + "?", - "Paste Subtree", - JOptionPane.CLOSED_OPTION, - JOptionPane.QUESTION_MESSAGE, - null, - options, - options[ 2 ] ); - boolean paste_as_sibling = true; - if ( r == 1 ) { - paste_as_sibling = false; + getPhylogeny().reRoot( node ); + getPhylogeny().recalculateNumberOfExternalDescendants( true ); + resetNodeIdToDistToLeafMap(); + setNodeInPreorderToNull(); + resetPreferredSize(); + getMainPanel().adjustJScrollPane(); + setEdited( true ); + repaint(); + if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) { + getControlPanel().showWhole(); } - else if ( r != 0 ) { + } + + final void resetNodeIdToDistToLeafMap() { + _nodeid_dist_to_leaf = new HashMap(); + } + + final void resetPreferredSize() { + if ( ( getPhylogeny() == null ) || getPhylogeny().isEmpty() ) { return; } - final Phylogeny buffer_phy = getCutOrCopiedTree().copy(); - buffer_phy.setAllNodesToNotCollapse(); - PhylogenyMethods.preOrderReId( buffer_phy ); - buffer_phy.setRooted( true ); - boolean need_to_show_whole = false; - if ( paste_as_sibling ) { - if ( node.isRoot() ) { - JOptionPane.showMessageDialog( this, - "Cannot paste sibling to root", - "Attempt to paste sibling to root", - JOptionPane.ERROR_MESSAGE ); - return; - } - buffer_phy.addAsSibling( node ); + int x = 0; + int y = 0; + y = TreePanel.MOVE + + ForesterUtil.roundToInt( getYdistance() * getPhylogeny().getRoot().getNumberOfExternalNodes() * 2 ); + if ( getControlPanel().isDrawPhylogram() ) { + x = TreePanel.MOVE + getLongestExtNodeInfo() + + ForesterUtil.roundToInt( ( getXcorrectionFactor() + * getPhylogeny().calculateHeight( !_options.isCollapsedWithAverageHeigh() ) ) + + getXdistance() ); } else { - if ( ( node.getNumberOfExternalNodes() == 1 ) && node.isRoot() ) { - need_to_show_whole = true; - _phylogeny = buffer_phy; + if ( !isNonLinedUpCladogram() ) { + x = TreePanel.MOVE + getLongestExtNodeInfo() + ForesterUtil + .roundToInt( getXdistance() * ( getPhylogeny().getRoot().getNumberOfExternalNodes() + 2 ) ); } else { - buffer_phy.addAsChild( node ); + x = TreePanel.MOVE + getLongestExtNodeInfo() + ForesterUtil + .roundToInt( getXdistance() * ( PhylogenyMethods.calculateMaxDepth( getPhylogeny() ) + 1 ) ); } } - if ( getCopiedAndPastedNodes() == null ) { - setCopiedAndPastedNodes( new HashSet() ); - } - final List nodes = PhylogenyMethods.obtainAllNodesAsList( buffer_phy ); - final Set node_ids = new HashSet( nodes.size() ); - for( final PhylogenyNode n : nodes ) { - node_ids.add( n.getId() ); - } - node_ids.add( node.getId() ); - getCopiedAndPastedNodes().addAll( node_ids ); - setNodeInPreorderToNull(); - _phylogeny.externalNodesHaveChanged(); - _phylogeny.clearHashIdToNodeMap(); - _phylogeny.recalculateNumberOfExternalDescendants( true ); - resetNodeIdToDistToLeafMap(); - setEdited( true ); - if ( need_to_show_whole ) { - getControlPanel().showWhole(); - } - repaint(); + setPreferredSize( new Dimension( x, y ) ); } - private final StringBuffer propertiesToString( final PhylogenyNode node ) { - final PropertiesMap properties = node.getNodeData().getProperties(); - final StringBuffer sb = new StringBuffer(); - boolean first = true; - for( final String ref : properties.getPropertyRefs() ) { - if ( first ) { - first = false; - } - else { - sb.append( " " ); + final void selectNode( final PhylogenyNode node ) { + if ( ( getFoundNodes0() != null ) && getFoundNodes0().contains( node.getId() ) ) { + getFoundNodes0().remove( node.getId() ); + getControlPanel().setSearchFoundCountsOnLabel0( getFoundNodes0().size() ); + if ( getFoundNodes0().size() < 1 ) { + getControlPanel().searchReset0(); } - final Property p = properties.getProperty( ref ); - sb.append( TreePanelUtil.getPartAfterColon( p.getRef() ) ); - sb.append( "=" ); - sb.append( p.getValue() ); - if ( !ForesterUtil.isEmpty( p.getUnit() ) ) { - sb.append( TreePanelUtil.getPartAfterColon( p.getUnit() ) ); + } + else { + getControlPanel().getSearchFoundCountsLabel0().setVisible( true ); + getControlPanel().getSearchResetButton0().setEnabled( true ); + getControlPanel().getSearchResetButton0().setVisible( true ); + if ( getFoundNodes0() == null ) { + setFoundNodes0( new HashSet() ); } + getFoundNodes0().add( node.getId() ); + getControlPanel().setSearchFoundCountsOnLabel0( getFoundNodes0().size() ); } - 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 void setArrowCursor() { + setCursor( ARROW_CURSOR ); + repaint(); } - final private void setCopiedAndPastedNodes( final Set nodeIds ) { - getMainPanel().setCopiedAndPastedNodes( nodeIds ); + final void setControlPanel( final ControlPanel atv_control ) { + _control_panel = atv_control; } - final private void setCutOrCopiedTree( final Phylogeny cut_or_copied_tree ) { - getMainPanel().setCutOrCopiedTree( cut_or_copied_tree ); + void setCurrentExternalNodesDataBuffer( final StringBuilder sb ) { + increaseCurrentExternalNodesDataBufferChangeCounter(); + _current_external_nodes_data_buffer = sb; } - 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; + public final void setFoundNodes0( final Set found_nodes ) { + _found_nodes_0 = found_nodes; } - final private void setInOv( final boolean in_ov ) { - _in_ov = in_ov; + public final void setFoundNodes1( final Set found_nodes ) { + _found_nodes_1 = found_nodes; } - final private void setOvMaxHeight( final float ov_max_height ) { - _ov_max_height = ov_max_height; + final void setInOvRect( final boolean in_ov_rect ) { + _in_ov_rect = in_ov_rect; } - final private void setOvMaxWidth( final float ov_max_width ) { - _ov_max_width = ov_max_width; + final void setLargeFonts() { + getTreeFontSet().largeFonts(); } - final private void setOvXcorrectionFactor( final float f ) { - _ov_x_correction_factor = f; + final void setLastMouseDragPointX( final float x ) { + _last_drag_point_x = x; } - final private void setOvXDistance( final float ov_x_distance ) { - _ov_x_distance = ov_x_distance; + final void setLastMouseDragPointY( final float y ) { + _last_drag_point_y = y; } - final private void setOvXPosition( final int ov_x_position ) { - _ov_x_position = ov_x_position; + final void setMediumFonts() { + getTreeFontSet().mediumFonts(); } - final private void setOvYDistance( final float ov_y_distance ) { - _ov_y_distance = ov_y_distance; + final void setNodeInPreorderToNull() { + _nodes_in_preorder = null; } - final private void setOvYPosition( final int ov_y_position ) { - _ov_y_position = ov_y_position; + final void setOvOn( final boolean ov_on ) { + _ov_on = ov_on; } - final private void setOvYStart( final int ov_y_start ) { - _ov_y_start = ov_y_start; + final void setPhylogenyGraphicsType( final PHYLOGENY_GRAPHICS_TYPE graphics_type ) { + _graphics_type = graphics_type; + setTextAntialias(); } - final private void setScaleDistance( final double scale_distance ) { - _scale_distance = scale_distance; + final void setSmallFonts() { + getTreeFontSet().smallFonts(); } - final private void setScaleLabel( final String scale_label ) { - _scale_label = scale_label; + final void setStartingAngle( final double starting_angle ) { + _urt_starting_angle = starting_angle; } - private final void setupStroke( final Graphics2D g ) { - if ( getYdistance() < 0.0001 ) { - g.setStroke( STROKE_0025 ); - } - if ( getYdistance() < 0.001 ) { - g.setStroke( STROKE_005 ); - } - else if ( getYdistance() < 0.01 ) { - g.setStroke( STROKE_01 ); - } - else if ( getYdistance() < 0.5 ) { - g.setStroke( STROKE_025 ); - } - else if ( getYdistance() < 1 ) { - g.setStroke( STROKE_05 ); - } - else if ( getYdistance() < 2 ) { - g.setStroke( STROKE_075 ); - } - else if ( ( getYdistance() < 20 ) || !getConfiguration().isAllowThickStrokes() ) { - g.setStroke( STROKE_1 ); - } - else { - g.setStroke( STROKE_2 ); - } + void setStatisticsForExpressionValues( final DescriptiveStatistics statistics_for_expression_values ) { + _statistics_for_vector_data = statistics_for_expression_values; } - final private void setUpUrtFactor() { - final int d = getVisibleRect().width < getVisibleRect().height ? getVisibleRect().width - : getVisibleRect().height; - if ( isPhyHasBranchLengths() && getControlPanel().isDrawPhylogram() ) { - setUrtFactor( ( float ) ( d / ( 2 * getMaxDistanceToRoot() ) ) ); - } - else { - final int max_depth = _circ_max_depth; - if ( max_depth > 0 ) { - setUrtFactor( d / ( 2 * max_depth ) ); + final void setSuperTinyFonts() { + getTreeFontSet().superTinyFonts(); + } + + final void setTextAntialias() { + if ( ( _phylogeny != null ) && !_phylogeny.isEmpty() ) { + if ( _phylogeny.getNumberOfExternalNodes() <= LIMIT_FOR_HQ_RENDERING ) { + _rendering_hints.put( RenderingHints.KEY_RENDERING, RenderingHints.VALUE_RENDER_QUALITY ); } else { - setUrtFactor( d / 2 ); + _rendering_hints.put( RenderingHints.KEY_RENDERING, RenderingHints.VALUE_RENDER_SPEED ); } } - setUrtFactorOv( getUrtFactor() ); - } - - final private void setUrtFactor( final float urt_factor ) { - _urt_factor = urt_factor; - } - - final private void setUrtFactorOv( final float urt_factor_ov ) { - _urt_factor_ov = urt_factor_ov; - } - - private void showExtDescNodeData( final PhylogenyNode node ) { - final List data = new ArrayList(); - final List nodes = node.getAllExternalDescendants(); - if ( ( getFoundNodes0() != null ) || ( getFoundNodes1() != null ) ) { - for( final PhylogenyNode n : getFoundNodesAsListOfPhylogenyNodes() ) { - if ( !nodes.contains( n ) ) { - nodes.add( n ); - } - } + if ( getMainPanel().getOptions().isAntialiasScreen() ) { + _rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON ); + // try { + _rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_LCD_HRGB ); + // } + // catch ( final Throwable e ) { + // _rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_ON ); + //} } - for( final PhylogenyNode n : nodes ) { - switch ( getOptions().getExtDescNodeDataToReturn() ) { - case NODE_NAME: - if ( !ForesterUtil.isEmpty( n.getName() ) ) { - data.add( n.getName() ); - } - break; - case SEQUENCE_NAME: - if ( n.getNodeData().isHasSequence() - && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getName() ) ) { - data.add( n.getNodeData().getSequence().getName() ); - } - break; - case GENE_NAME: - if ( n.getNodeData().isHasSequence() - && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getGeneName() ) ) { - data.add( n.getNodeData().getSequence().getGeneName() ); - } - break; - case SEQUENCE_SYMBOL: - if ( n.getNodeData().isHasSequence() - && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getSymbol() ) ) { - data.add( n.getNodeData().getSequence().getSymbol() ); - } - break; - case SEQUENCE_MOL_SEQ: - if ( n.getNodeData().isHasSequence() - && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getMolecularSequence() ) ) { - data.add( n.getNodeData().getSequence().getMolecularSequence() ); - } - break; - case SEQUENCE_MOL_SEQ_FASTA: - final StringBuilder sb = new StringBuilder(); - if ( n.getNodeData().isHasSequence() - && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getMolecularSequence() ) ) { - final StringBuilder ann = new StringBuilder(); - if ( !ForesterUtil.isEmpty( n.getName() ) ) { - ann.append( n.getName() ); - ann.append( "|" ); - } - if ( !ForesterUtil.isEmpty( n.getNodeData().getSequence().getSymbol() ) ) { - ann.append( "SYM=" ); - ann.append( n.getNodeData().getSequence().getSymbol() ); - ann.append( "|" ); - } - if ( !ForesterUtil.isEmpty( n.getNodeData().getSequence().getName() ) ) { - ann.append( "NAME=" ); - ann.append( n.getNodeData().getSequence().getName() ); - ann.append( "|" ); - } - if ( !ForesterUtil.isEmpty( n.getNodeData().getSequence().getGeneName() ) ) { - ann.append( "GN=" ); - ann.append( n.getNodeData().getSequence().getGeneName() ); - ann.append( "|" ); - } - if ( n.getNodeData().getSequence().getAccession() != null ) { - ann.append( "ACC=" ); - ann.append( n.getNodeData().getSequence().getAccession().asText() ); - ann.append( "|" ); - } - if ( n.getNodeData().isHasTaxonomy() ) { - if ( !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) { - ann.append( "TAXID=" ); - ann.append( n.getNodeData().getTaxonomy().getTaxonomyCode() ); - ann.append( "|" ); - } - if ( !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) { - ann.append( "SN=" ); - ann.append( n.getNodeData().getTaxonomy().getScientificName() ); - ann.append( "|" ); - } - } - String ann_str; - if ( ann.charAt( ann.length() - 1 ) == '|' ) { - ann_str = ann.substring( 0, ann.length() - 1 ); - } - else { - ann_str = ann.toString(); - } - sb.append( SequenceWriter.toFasta( ann_str, n.getNodeData().getSequence() - .getMolecularSequence(), 60 ) ); - data.add( sb.toString() ); - } - break; - case SEQUENCE_ACC: - if ( n.getNodeData().isHasSequence() && ( n.getNodeData().getSequence().getAccession() != null ) - && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getAccession().toString() ) ) { - data.add( n.getNodeData().getSequence().getAccession().toString() ); - } - break; - case TAXONOMY_SCIENTIFIC_NAME: - if ( n.getNodeData().isHasTaxonomy() - && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) { - data.add( n.getNodeData().getTaxonomy().getScientificName() ); - } - break; - case TAXONOMY_COMM0N_NAME: - if ( n.getNodeData().isHasTaxonomy() - && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getCommonName() ) ) { - data.add( n.getNodeData().getTaxonomy().getCommonName() ); - } - break; - case TAXONOMY_CODE: - if ( n.getNodeData().isHasTaxonomy() - && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) { - data.add( n.getNodeData().getTaxonomy().getTaxonomyCode() ); - } - break; - case UNKNOWN: - TreePanelUtil.showExtDescNodeDataUserSelectedHelper( getControlPanel(), n, data ); - break; - default: - throw new IllegalArgumentException( "unknown data element: " - + getOptions().getExtDescNodeDataToReturn() ); - } - } // for loop - final StringBuilder sb = new StringBuilder(); - final int size = TreePanelUtil.makeSB( data, getOptions(), sb ); - if ( ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.CONSOLE ) - || ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.BUFFER_ONLY ) ) { - if ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.CONSOLE ) { - System.out.println( sb ); - } - if ( sb.length() < 1 ) { - clearCurrentExternalNodesDataBuffer(); - } - else { - setCurrentExternalNodesDataBuffer( sb ); - } + else { + _rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_OFF ); + _rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_OFF ); } - else if ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.WINODW ) { - if ( sb.length() < 1 ) { - TreePanelUtil.showInformationMessage( this, "No Appropriate Data (" + obtainTitleForExtDescNodeData() - + ")", "Descendants of selected node do not contain selected data" ); - clearCurrentExternalNodesDataBuffer(); + } + + final void setTinyFonts() { + getTreeFontSet().tinyFonts(); + } + + public final void setTreeFile( final File treefile ) { + _treefile = treefile; + } + + final void setXcorrectionFactor( final float f ) { + _x_correction_factor = f; + } + + final void setXdistance( final float x ) { + _x_distance = x; + } + + final void setYdistance( final float y ) { + _y_distance = y; + } + + final void sortDescendants( final PhylogenyNode node ) { + if ( !node.isExternal() ) { + DESCENDANT_SORT_PRIORITY pri = DESCENDANT_SORT_PRIORITY.NODE_NAME; + if ( getControlPanel().isShowTaxonomyScientificNames() || getControlPanel().isShowTaxonomyCode() ) { + pri = DESCENDANT_SORT_PRIORITY.TAXONOMY; } - else { - setCurrentExternalNodesDataBuffer( sb ); - String title; - if ( ( getFoundNodes0() != null ) && !getFoundNodes0().isEmpty() ) { - title = ( getOptions().getExtDescNodeDataToReturn() == NODE_DATA.UNKNOWN ? "Data" - : obtainTitleForExtDescNodeData() ) - + " for " - + data.size() - + " nodes, unique entries: " - + size; - } - else { - title = ( getOptions().getExtDescNodeDataToReturn() == NODE_DATA.UNKNOWN ? "Data" - : obtainTitleForExtDescNodeData() ) - + " for " - + data.size() - + "/" - + node.getNumberOfExternalNodes() - + " external descendats of node " - + node - + ", unique entries: " + size; - } - final String s = sb.toString().trim(); - if ( getMainPanel().getMainFrame() == null ) { - // Must be "E" applet version. - final ArchaeopteryxE ae = ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet(); - ae.showTextFrame( s, title ); - } - else { - getMainPanel().getMainFrame().showTextFrame( s, title ); - } + else if ( getControlPanel().isShowSeqNames() || getControlPanel().isShowSeqSymbols() + || getControlPanel().isShowGeneNames() ) { + pri = DESCENDANT_SORT_PRIORITY.SEQUENCE; } + PhylogenyMethods.sortNodeDescendents( node, pri ); + setNodeInPreorderToNull(); + _phylogeny.externalNodesHaveChanged(); + _phylogeny.clearHashIdToNodeMap(); + _phylogeny.recalculateNumberOfExternalDescendants( true ); + resetNodeIdToDistToLeafMap(); + setEdited( true ); } + repaint(); } - final private void showNodeDataPopup( final MouseEvent e, final PhylogenyNode node ) { - try { - if ( ( node.getName().length() > 0 ) - || ( node.getNodeData().isHasTaxonomy() && !TreePanelUtil.isTaxonomyEmpty( node.getNodeData() - .getTaxonomy() ) ) - || ( node.getNodeData().isHasSequence() && !TreePanelUtil.isSequenceEmpty( node.getNodeData() - .getSequence() ) ) || ( node.getNodeData().isHasDate() ) - || ( node.getNodeData().isHasDistribution() ) || node.getBranchData().isHasConfidences() ) { - _popup_buffer.setLength( 0 ); - short lines = 0; - if ( node.getName().length() > 0 ) { - lines++; - _popup_buffer.append( node.getName() ); - } - if ( node.getNodeData().isHasTaxonomy() - && !TreePanelUtil.isTaxonomyEmpty( node.getNodeData().getTaxonomy() ) ) { - lines++; - boolean enc_data = false; - final Taxonomy tax = node.getNodeData().getTaxonomy(); - if ( _popup_buffer.length() > 0 ) { - _popup_buffer.append( "\n" ); - } - if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) { - _popup_buffer.append( "[" ); - _popup_buffer.append( tax.getTaxonomyCode() ); - _popup_buffer.append( "]" ); - enc_data = true; - } - if ( !ForesterUtil.isEmpty( tax.getScientificName() ) ) { - if ( enc_data ) { - _popup_buffer.append( " " ); - } - _popup_buffer.append( tax.getScientificName() ); - enc_data = true; - } - if ( !ForesterUtil.isEmpty( tax.getCommonName() ) ) { - if ( enc_data ) { - _popup_buffer.append( " (" ); - } - else { - _popup_buffer.append( "(" ); - } - _popup_buffer.append( tax.getCommonName() ); - _popup_buffer.append( ")" ); - enc_data = true; - } - if ( !ForesterUtil.isEmpty( tax.getAuthority() ) ) { - if ( enc_data ) { - _popup_buffer.append( " (" ); - } - else { - _popup_buffer.append( "(" ); - } - _popup_buffer.append( tax.getAuthority() ); - _popup_buffer.append( ")" ); - enc_data = true; - } - if ( !ForesterUtil.isEmpty( tax.getRank() ) ) { - if ( enc_data ) { - _popup_buffer.append( " [" ); - } - else { - _popup_buffer.append( "[" ); - } - _popup_buffer.append( tax.getRank() ); - _popup_buffer.append( "]" ); - enc_data = true; - } - if ( tax.getSynonyms().size() > 0 ) { - if ( enc_data ) { - _popup_buffer.append( " " ); - } - _popup_buffer.append( "[" ); - int counter = 1; - for( final String syn : tax.getSynonyms() ) { - if ( !ForesterUtil.isEmpty( syn ) ) { - enc_data = true; - _popup_buffer.append( syn ); - if ( counter < tax.getSynonyms().size() ) { - _popup_buffer.append( ", " ); - } - } - counter++; - } - _popup_buffer.append( "]" ); - } - if ( !enc_data ) { - if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getValue() ) ) { - if ( !ForesterUtil.isEmpty( tax.getIdentifier().getProvider() ) ) { - _popup_buffer.append( "[" ); - _popup_buffer.append( tax.getIdentifier().getProvider() ); - _popup_buffer.append( "] " ); - } - _popup_buffer.append( tax.getIdentifier().getValue() ); - } - } - } - if ( node.getNodeData().isHasSequence() - && !TreePanelUtil.isSequenceEmpty( node.getNodeData().getSequence() ) ) { - lines++; - boolean enc_data = false; - if ( _popup_buffer.length() > 0 ) { - _popup_buffer.append( "\n" ); - } - final Sequence seq = node.getNodeData().getSequence(); - if ( seq.getAccession() != null ) { - _popup_buffer.append( "[" ); - if ( !ForesterUtil.isEmpty( seq.getAccession().getSource() ) ) { - _popup_buffer.append( seq.getAccession().getSource() ); - _popup_buffer.append( ":" ); - } - _popup_buffer.append( seq.getAccession().getValue() ); - _popup_buffer.append( "]" ); - enc_data = true; - } - if ( !ForesterUtil.isEmpty( seq.getSymbol() ) ) { - if ( enc_data ) { - _popup_buffer.append( " [" ); - } - else { - _popup_buffer.append( "[" ); - } - _popup_buffer.append( seq.getSymbol() ); - _popup_buffer.append( "]" ); - enc_data = true; - } - if ( !ForesterUtil.isEmpty( seq.getGeneName() ) ) { - if ( enc_data ) { - _popup_buffer.append( " [" ); - } - else { - _popup_buffer.append( "[" ); - } - _popup_buffer.append( seq.getGeneName() ); - _popup_buffer.append( "]" ); - enc_data = true; - } - if ( !ForesterUtil.isEmpty( seq.getName() ) ) { - if ( enc_data ) { - _popup_buffer.append( " " ); - } - _popup_buffer.append( seq.getName() ); - } - } - if ( node.getNodeData().isHasDate() ) { - lines++; - if ( _popup_buffer.length() > 0 ) { - _popup_buffer.append( "\n" ); - } - _popup_buffer.append( node.getNodeData().getDate().asSimpleText() ); - } - if ( node.getNodeData().isHasDistribution() ) { - lines++; - if ( _popup_buffer.length() > 0 ) { - _popup_buffer.append( "\n" ); - } - _popup_buffer.append( node.getNodeData().getDistribution().asSimpleText() ); - } - if ( node.getBranchData().isHasConfidences() ) { - final List confs = node.getBranchData().getConfidences(); - for( final Confidence confidence : confs ) { - lines++; - if ( _popup_buffer.length() > 0 ) { - _popup_buffer.append( "\n" ); - } - if ( !ForesterUtil.isEmpty( confidence.getType() ) ) { - _popup_buffer.append( "[" ); - _popup_buffer.append( confidence.getType() ); - _popup_buffer.append( "] " ); - } - _popup_buffer - .append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence.getValue(), - getOptions() - .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) ); - if ( confidence.getStandardDeviation() != Confidence.CONFIDENCE_DEFAULT_VALUE ) { - _popup_buffer.append( " (sd=" ); - _popup_buffer.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence - .getStandardDeviation(), getOptions() - .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) ); - _popup_buffer.append( ")" ); - } - } - } - if ( node.getNodeData().isHasProperties() ) { - final PropertiesMap properties = node.getNodeData().getProperties(); - for( final String ref : properties.getPropertyRefs() ) { - _popup_buffer.append( "\n" ); - final Property p = properties.getProperty( ref ); - _popup_buffer.append( TreePanelUtil.getPartAfterColon( p.getRef() ) ); - _popup_buffer.append( "=" ); - _popup_buffer.append( p.getValue() ); - if ( !ForesterUtil.isEmpty( p.getUnit() ) ) { - _popup_buffer.append( TreePanelUtil.getPartAfterColon( p.getUnit() ) ); - } - } - } - if ( _popup_buffer.length() > 0 ) { - if ( !getConfiguration().isUseNativeUI() ) { - _rollover_popup - .setBorder( BorderFactory.createLineBorder( getTreeColorSet().getBranchColor() ) ); - _rollover_popup.setBackground( getTreeColorSet().getBackgroundColor() ); - 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 { - _rollover_popup.setForeground( getTreeColorSet().getSequenceColor() ); - } - } - else { - _rollover_popup.setBorder( BorderFactory.createLineBorder( Color.BLACK ) ); - } - _rollover_popup.setText( _popup_buffer.toString() ); - _node_desc_popup = PopupFactory.getSharedInstance().getPopup( null, - _rollover_popup, - e.getLocationOnScreen().x + 10, - e.getLocationOnScreen().y - - ( lines * 20 ) ); - _node_desc_popup.show(); - } + final void subTree( final PhylogenyNode node ) { + if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) { + JOptionPane.showMessageDialog( this, + "Cannot get a sub/super tree in unrooted display", + "Attempt to get sub/super tree in unrooted display", + JOptionPane.WARNING_MESSAGE ); + return; + } + if ( node.isExternal() ) { + JOptionPane.showMessageDialog( this, + "Cannot get a subtree of a external node", + "Attempt to get subtree of external node", + JOptionPane.WARNING_MESSAGE ); + return; + } + if ( node.isRoot() && !isCurrentTreeIsSubtree() ) { + JOptionPane.showMessageDialog( this, + "Cannot get a subtree of the root node", + "Attempt to get subtree of root node", + JOptionPane.WARNING_MESSAGE ); + return; + } + setNodeInPreorderToNull(); + if ( !node.isExternal() && !node.isRoot() && ( _subtree_index <= ( TreePanel.MAX_SUBTREES - 1 ) ) ) { + _sub_phylogenies[ _subtree_index ] = _phylogeny; + _sub_phylogenies_temp_roots[ _subtree_index ] = node; + ++_subtree_index; + _phylogeny = TreePanelUtil.subTree( node, _phylogeny ); + if ( _phylogeny.getRoot().isCollapse() ) { + _phylogeny.getRoot().setCollapse( false ); } + _phylogeny.externalNodesHaveChanged(); + _phylogeny.clearHashIdToNodeMap(); + _phylogeny.recalculateNumberOfExternalDescendants( true ); + updateSubSuperTreeButton(); + getMainPanel().getControlPanel().search0(); + getMainPanel().getControlPanel().search1(); + resetRankCollapseRankValue(); + resetDepthCollapseDepthValue(); + getMainPanel().getControlPanel().updateDomainStructureEvaluethresholdDisplay(); + getMainPanel().getControlPanel().updateDepthCollapseDepthDisplay(); + getMainPanel().getControlPanel().updateRankCollapseRankDisplay(); } - catch ( final Exception ex ) { - // Do nothing. + else if ( node.isRoot() && isCurrentTreeIsSubtree() ) { + superTree(); + } + _main_panel.getControlPanel().showWhole(); + repaint(); + } + + final void superTree() { + setNodeInPreorderToNull(); + final PhylogenyNode temp_root = _sub_phylogenies_temp_roots[ _subtree_index - 1 ]; + for( final PhylogenyNode n : temp_root.getDescendants() ) { + n.setParent( temp_root ); + } + _sub_phylogenies[ _subtree_index ] = null; + _sub_phylogenies_temp_roots[ _subtree_index ] = null; + _phylogeny = _sub_phylogenies[ --_subtree_index ]; + _phylogeny.externalNodesHaveChanged(); + _phylogeny.clearHashIdToNodeMap(); + _phylogeny.recalculateNumberOfExternalDescendants( true ); + getMainPanel().getControlPanel().search0(); + getMainPanel().getControlPanel().search1(); + resetRankCollapseRankValue(); + resetDepthCollapseDepthValue(); + getMainPanel().getControlPanel().updateDomainStructureEvaluethresholdDisplay(); + getMainPanel().getControlPanel().updateDepthCollapseDepthDisplay(); + getMainPanel().getControlPanel().updateRankCollapseRankDisplay(); + updateSubSuperTreeButton(); + } + + final void orderSubtree( final PhylogenyNode node ) { + if ( node.isExternal() ) { + return; + } + DESCENDANT_SORT_PRIORITY pri = DESCENDANT_SORT_PRIORITY.NODE_NAME; + if ( getControlPanel().isShowTaxonomyScientificNames() || getControlPanel().isShowTaxonomyCode() ) { + pri = DESCENDANT_SORT_PRIORITY.TAXONOMY; } + else if ( getControlPanel().isShowSeqNames() || getControlPanel().isShowSeqSymbols() + || getControlPanel().isShowGeneNames() ) { + pri = DESCENDANT_SORT_PRIORITY.SEQUENCE; + } + PhylogenyMethods.orderAppearanceX( node, true, pri ); + setNodeInPreorderToNull(); + getPhylogeny().externalNodesHaveChanged(); + getPhylogeny().clearHashIdToNodeMap(); + getPhylogeny().recalculateNumberOfExternalDescendants( true ); + resetNodeIdToDistToLeafMap(); + setEdited( true ); + getControlPanel().displayedPhylogenyMightHaveChanged( true ); + repaint(); } - final private void showNodeEditFrame( final PhylogenyNode n ) { - if ( _node_frame_index < TreePanel.MAX_NODE_FRAMES ) { - // pop up edit box for single node - _node_frames[ _node_frame_index ] = new NodeFrame( n, _phylogeny, this, _node_frame_index, "" ); - _node_frame_index++; + final void swap( final PhylogenyNode node ) { + if ( node.isExternal() || ( node.getNumberOfDescendants() < 2 ) ) { + return; } - else { - JOptionPane.showMessageDialog( this, "too many node windows are open" ); + if ( node.getNumberOfDescendants() > 2 ) { + JOptionPane.showMessageDialog( this, + "Cannot swap descendants of nodes with more than 2 descendants", + "Cannot swap descendants", + JOptionPane.ERROR_MESSAGE ); + return; + } + if ( !node.isExternal() ) { + node.swapChildren(); + setNodeInPreorderToNull(); + _phylogeny.externalNodesHaveChanged(); + _phylogeny.clearHashIdToNodeMap(); + _phylogeny.recalculateNumberOfExternalDescendants( true ); + resetNodeIdToDistToLeafMap(); + setEdited( true ); } + repaint(); } - final private void showNodeFrame( final PhylogenyNode n ) { - if ( _node_frame_index < TreePanel.MAX_NODE_FRAMES ) { - // pop up edit box for single node - _node_frames[ _node_frame_index ] = new NodeFrame( n, _phylogeny, this, _node_frame_index ); - _node_frame_index++; + final void taxColor() { + if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) { + return; } - else { - JOptionPane.showMessageDialog( this, "too many node windows are open" ); + setWaitCursor(); + TreePanelUtil.colorPhylogenyAccordingToExternalTaxonomy( _phylogeny, this ); + _control_panel.setColorBranches( true ); + if ( _control_panel.getUseVisualStylesCb() != null ) { + _control_panel.getUseVisualStylesCb().setSelected( true ); } + setEdited( true ); + setArrowCursor(); + repaint(); } - final private void switchDisplaygetPhylogenyGraphicsType() { - switch ( getPhylogenyGraphicsType() ) { - case RECTANGULAR: - setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ); - getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ); - break; - case EURO_STYLE: - setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED ); - getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.ROUNDED ); - break; - case ROUNDED: - setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED ); - getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CURVED ); - break; - case CURVED: - setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR ); - getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.TRIANGULAR ); - break; - case TRIANGULAR: - setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX ); - getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CONVEX ); - break; - case CONVEX: - setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED ); - getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.UNROOTED ); + final void updateOvSettings() { + switch ( getOptions().getOvPlacement() ) { + case LOWER_LEFT: + setOvXPosition( OV_BORDER ); + setOvYPosition( ForesterUtil.roundToInt( getVisibleRect().height - OV_BORDER - getOvMaxHeight() ) ); + setOvYStart( ForesterUtil.roundToInt( getOvYPosition() + ( getOvMaxHeight() / 2 ) ) ); break; - case UNROOTED: - setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ); - getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ); + case LOWER_RIGHT: + setOvXPosition( ForesterUtil.roundToInt( getVisibleRect().width - OV_BORDER - getOvMaxWidth() ) ); + setOvYPosition( ForesterUtil.roundToInt( getVisibleRect().height - OV_BORDER - getOvMaxHeight() ) ); + setOvYStart( ForesterUtil.roundToInt( getOvYPosition() + ( getOvMaxHeight() / 2 ) ) ); break; - case CIRCULAR: - setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ); - getOptions().setPhylogenyGraphicsType( PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ); + case UPPER_RIGHT: + setOvXPosition( ForesterUtil.roundToInt( getVisibleRect().width - OV_BORDER - getOvMaxWidth() ) ); + setOvYPosition( OV_BORDER ); + setOvYStart( ForesterUtil.roundToInt( OV_BORDER + ( getOvMaxHeight() / 2 ) ) ); break; default: - throw new RuntimeException( "unkwnown display type: " + getPhylogenyGraphicsType() ); + setOvXPosition( OV_BORDER ); + setOvYPosition( OV_BORDER ); + setOvYStart( ForesterUtil.roundToInt( OV_BORDER + ( getOvMaxHeight() / 2 ) ) ); + break; } - if ( getControlPanel().getDynamicallyHideData() != null ) { - if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) { - getControlPanel().getDynamicallyHideData().setEnabled( false ); + } + + final void updateOvSizes() { + if ( ( getWidth() > ( 1.05 * getVisibleRect().width ) ) + || ( getHeight() > ( 1.05 * getVisibleRect().height ) ) ) { + setOvOn( true ); + float l = getLongestExtNodeInfo(); + final float w_ratio = getOvMaxWidth() / getWidth(); + l *= w_ratio; + final int ext_nodes = _phylogeny.getRoot().getNumberOfExternalNodes(); + setOvYDistance( getOvMaxHeight() / ( 2 * ext_nodes ) ); + float ov_xdist = 0; + if ( !isNonLinedUpCladogram() ) { + ov_xdist = ( ( getOvMaxWidth() - l ) / ( ext_nodes ) ); } else { - getControlPanel().getDynamicallyHideData().setEnabled( true ); + ov_xdist = ( ( getOvMaxWidth() - l ) / ( PhylogenyMethods.calculateMaxDepth( _phylogeny ) ) ); + } + float ydist = ( float ) ( ( getOvMaxWidth() / ( ext_nodes * 2.0 ) ) ); + if ( ov_xdist < 0.0 ) { + ov_xdist = 0.0f; + } + if ( ydist < 0.0 ) { + ydist = 0.0f; + } + setOvXDistance( ov_xdist ); + final double height = _phylogeny.calculateHeight( !_options.isCollapsedWithAverageHeigh() ); + if ( height > 0 ) { + final float ov_corr = ( float ) ( ( ( getOvMaxWidth() - l ) - getOvXDistance() ) / height ); + setOvXcorrectionFactor( ov_corr > 0 ? ov_corr : 0 ); + } + else { + setOvXcorrectionFactor( 0 ); } } - if ( isPhyHasBranchLengths() && ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) { - getControlPanel().setDrawPhylogramEnabled( true ); + else { + setOvOn( false ); + } + } + + void updateSetOfCollapsedExternalNodes() { + final Phylogeny phy = getPhylogeny(); + _collapsed_external_nodeid_set.clear(); + if ( phy != null ) { + 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() ); + ext_node.setCollapse( true ); + continue E; + } + n = n.getParent(); + } + } + } + } + + final void updateSubSuperTreeButton() { + if ( _subtree_index < 1 ) { + getControlPanel().deactivateButtonToReturnToSuperTree(); } else { - getControlPanel().setDrawPhylogramEnabled( false ); + getControlPanel().activateButtonToReturnToSuperTree( _subtree_index ); } - if ( getMainPanel().getMainFrame() == null ) { - // Must be "E" applet version. - ( ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet() ) - .setSelectedTypeInTypeMenu( getPhylogenyGraphicsType() ); + } + + final void updateButtonToUncollapseAll() { + if ( PhylogenyMethods.isHasCollapsedNodes( _phylogeny ) ) { + getControlPanel().activateButtonToUncollapseAll(); } else { - getMainPanel().getMainFrame().setSelectedTypeInTypeMenu( getPhylogenyGraphicsType() ); + getControlPanel().deactivateButtonToUncollapseAll(); + } + } + + final void zoomInDomainStructure() { + if ( _domain_structure_width < 2000 ) { + _domain_structure_width *= 1.2; + } + } + + final void zoomOutDomainStructure() { + if ( _domain_structure_width > 20 ) { + _domain_structure_width *= 0.8; } } @@ -6003,64 +6399,141 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee g.drawString( str, x, y ); } - final private static boolean plusPressed( final int key_code ) { - return ( ( key_code == KeyEvent.VK_ADD ) || ( key_code == KeyEvent.VK_PLUS ) - || ( key_code == KeyEvent.VK_EQUALS ) || ( key_code == KeyEvent.VK_SEMICOLON ) || ( key_code == KeyEvent.VK_1 ) ); + final private void drawStringX( final String str, final float x, final float y, final Graphics2D g ) { + //TODO + //FIXME + if ( getAttributedStringMap() == null /*&& getAttributedStringMap().containsKey(str) */ ) { + final AttributedString as = new AttributedString( str ); + //Font plainFont = new Font("Times New Roman", Font.PLAIN, 24); + as.addAttribute( TextAttribute.FONT, g.getFont() ); + as.addAttribute( TextAttribute.UNDERLINE, TextAttribute.UNDERLINE_ON, 1, 3 ); + as.addAttribute( TextAttribute.SUPERSCRIPT, TextAttribute.SUPERSCRIPT_SUPER, 3, 4 ); + as.addAttribute( TextAttribute.FOREGROUND, Color.BLUE, 1, 2 ); + as.addAttribute( TextAttribute.FOREGROUND, Color.PINK, 3, 5 ); + as.addAttribute( TextAttribute.STRIKETHROUGH, TextAttribute.STRIKETHROUGH_ON, 2, 4 ); + g.drawString( as.getIterator(), x, y ); + } + else { + g.drawString( str, x, y ); + } } - final private class NodeColorizationActionListener implements ActionListener { + private final Map getAttributedStringMap() { + return _attributed_string_map; + } - List _additional_nodes = null; - JColorChooser _chooser = null; - PhylogenyNode _node = null; + private final void setAttributedStringMap( final Map attributed_string_map ) { + _attributed_string_map = attributed_string_map; + } - NodeColorizationActionListener( final JColorChooser chooser, final PhylogenyNode node ) { - _chooser = chooser; - _node = node; - } + final private static boolean plusPressed( final int key_code ) { + return ( ( key_code == KeyEvent.VK_ADD ) || ( key_code == KeyEvent.VK_PLUS ) + || ( key_code == KeyEvent.VK_EQUALS ) || ( key_code == KeyEvent.VK_SEMICOLON ) + || ( key_code == KeyEvent.VK_1 ) ); + } - NodeColorizationActionListener( final JColorChooser chooser, - final PhylogenyNode node, - final List additional_nodes ) { - _chooser = chooser; - _node = node; - _additional_nodes = additional_nodes; + public void decreaseDepthCollapseLevel() { + if ( ( _phylogeny != null ) && ( _phylogeny.getNumberOfExternalNodes() > 2 ) ) { + if ( _depth_collapse_level <= 1 ) { + _depth_collapse_level = PhylogenyMethods.calculateMaxDepth( _phylogeny ); + uncollapseAll(); + } + else { + --_depth_collapse_level; + PhylogenyMethods.collapseToDepth( _phylogeny, _depth_collapse_level ); + } } + } - @Override - public void actionPerformed( final ActionEvent e ) { - final Color c = _chooser.getColor(); - if ( c != null ) { - colorizeNodes( c, _node, _additional_nodes ); + public void increaseDepthCollapseLevel() { + if ( ( _phylogeny != null ) && ( _phylogeny.getNumberOfExternalNodes() > 2 ) ) { + final int max = PhylogenyMethods.calculateMaxDepth( _phylogeny ); + if ( _depth_collapse_level >= max ) { + _depth_collapse_level = 1; + } + else { + ++_depth_collapse_level; } + PhylogenyMethods.collapseToDepth( _phylogeny, _depth_collapse_level ); } } - final private class SubtreeColorizationActionListener implements ActionListener { - - List _additional_nodes = null; - JColorChooser _chooser = null; - PhylogenyNode _node = null; + public void decreaseRankCollapseLevel() { + if ( ( _phylogeny != null ) && ( _phylogeny.getNumberOfExternalNodes() > 2 ) ) { + final String ranks[] = PhylogenyMethods.obtainPresentRanksSorted( _phylogeny ); + if ( ranks.length > 1 ) { + if ( _rank_collapse_level <= 0 ) { + _rank_collapse_level = ranks.length - 1; + uncollapseAll(); + } + else { + --_rank_collapse_level; + PhylogenyMethods.collapseToRank( _phylogeny, + mapToAbsoluteRankLevel( ranks, _rank_collapse_level ) ); + } + } + } + } - SubtreeColorizationActionListener( final JColorChooser chooser, final PhylogenyNode node ) { - _chooser = chooser; - _node = node; + public void increaseRankCollapseLevel() { + if ( ( _phylogeny != null ) && ( _phylogeny.getNumberOfExternalNodes() > 2 ) ) { + final String ranks[] = PhylogenyMethods.obtainPresentRanksSorted( _phylogeny ); + if ( ranks.length > 1 ) { + if ( _rank_collapse_level >= ( ranks.length - 1 ) ) { + _rank_collapse_level = 0; + PhylogenyMethods.collapseToRank( _phylogeny, + mapToAbsoluteRankLevel( ranks, _rank_collapse_level ) ); + } + else if ( _rank_collapse_level == ( ranks.length - 2 ) ) { + ++_rank_collapse_level; + uncollapseAll(); + } + else { + ++_rank_collapse_level; + PhylogenyMethods.collapseToRank( _phylogeny, + mapToAbsoluteRankLevel( ranks, _rank_collapse_level ) ); + } + } } + } - SubtreeColorizationActionListener( final JColorChooser chooser, - final PhylogenyNode node, - final List additional_nodes ) { - _chooser = chooser; - _node = node; - _additional_nodes = additional_nodes; + private final static int mapToAbsoluteRankLevel( final String present_ranks_sorted[], + final int rank_collapse_level ) { + final String rank_str = present_ranks_sorted[ rank_collapse_level ]; + if ( !TaxonomyUtil.RANK_TO_INT.containsKey( rank_str ) ) { + throw new IllegalStateException( "unexpected exception: cannot find rank " + rank_str ); } + return TaxonomyUtil.RANK_TO_INT.get( rank_str ); + } - @Override - public void actionPerformed( final ActionEvent e ) { - final Color c = _chooser.getColor(); - if ( c != null ) { - colorizeSubtree( c, _node, _additional_nodes ); - } + private final void uncollapseAll() { + final PhylogenyNodeIterator it = new PreorderTreeIterator( _phylogeny ); + while ( it.hasNext() ) { + it.next().setCollapse( false ); } } + + final int resetDepthCollapseDepthValue() { + return _depth_collapse_level = -1; + } + + final int getDepthCollapseDepthValue() { + return _depth_collapse_level; + } + + final void setDepthCollapseDepthValue( final int depth_collapse_level ) { + _depth_collapse_level = depth_collapse_level; + } + + final int resetRankCollapseRankValue() { + return _rank_collapse_level = -1; + } + + final int getRankCollapseRankValue() { + return _rank_collapse_level; + } + + final void setRankCollapseRankValue( final int rank_collapse_level ) { + _rank_collapse_level = rank_collapse_level; + } }