X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FTreePanel.java;h=bbf835790cb37bbd1699866fdc0d7669b1a1f378;hb=ceb6173a0256d06fffbe04756755bb18052622fc;hp=fcb1580967eb32747b9fe76c544c33d6181562c4;hpb=f2560d91ad4d0e4fb8b150f5ebeefb405d669bde;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/TreePanel.java b/forester/java/src/org/forester/archaeopteryx/TreePanel.java index fcb1580..bbf8357 100644 --- a/forester/java/src/org/forester/archaeopteryx/TreePanel.java +++ b/forester/java/src/org/forester/archaeopteryx/TreePanel.java @@ -129,111 +129,114 @@ import org.forester.util.SequenceIdParser; public final class TreePanel extends JPanel implements ActionListener, MouseWheelListener, Printable { - private static final float PI = ( float ) ( Math.PI ); - private static final double TWO_PI = 2 * Math.PI; - private static final float ONEHALF_PI = ( float ) ( 1.5 * Math.PI ); - private static final float HALF_PI = ( float ) ( Math.PI / 2.0 ); - private static final float ANGLE_ROTATION_UNIT = ( float ) ( Math.PI / 32 ); - private static final short OV_BORDER = 10; - final static Cursor CUT_CURSOR = Cursor.getPredefinedCursor( Cursor.CROSSHAIR_CURSOR ); - final static Cursor MOVE_CURSOR = Cursor.getPredefinedCursor( Cursor.MOVE_CURSOR ); - final static Cursor ARROW_CURSOR = Cursor.getPredefinedCursor( Cursor.DEFAULT_CURSOR ); - final static Cursor HAND_CURSOR = Cursor.getPredefinedCursor( Cursor.HAND_CURSOR ); - final static Cursor WAIT_CURSOR = Cursor.getPredefinedCursor( Cursor.WAIT_CURSOR ); - private final static long serialVersionUID = -978349745916505029L; - private final static int EURO_D = 10; - private final static String NODE_POPMENU_NODE_CLIENT_PROPERTY = "node"; - private final static int MIN_ROOT_LENGTH = 3; - private final static int MAX_SUBTREES = 100; - private final static int MAX_NODE_FRAMES = 10; - private final static int MOVE = 20; + private static final float PI = ( float ) ( Math.PI ); + private static final double TWO_PI = 2 * Math.PI; + private static final float ONEHALF_PI = ( float ) ( 1.5 * Math.PI ); + private static final float HALF_PI = ( float ) ( Math.PI / 2.0 ); + private static final float ANGLE_ROTATION_UNIT = ( float ) ( Math.PI / 32 ); + private static final short OV_BORDER = 10; + final static Cursor CUT_CURSOR = Cursor.getPredefinedCursor( Cursor.CROSSHAIR_CURSOR ); + final static Cursor MOVE_CURSOR = Cursor.getPredefinedCursor( Cursor.MOVE_CURSOR ); + final static Cursor ARROW_CURSOR = Cursor.getPredefinedCursor( Cursor.DEFAULT_CURSOR ); + final static Cursor HAND_CURSOR = Cursor.getPredefinedCursor( Cursor.HAND_CURSOR ); + final static Cursor WAIT_CURSOR = Cursor.getPredefinedCursor( Cursor.WAIT_CURSOR ); + private final static long serialVersionUID = -978349745916505029L; + private final static int EURO_D = 10; + private final static String NODE_POPMENU_NODE_CLIENT_PROPERTY = "node"; + private final static int MIN_ROOT_LENGTH = 3; + private final static int MAX_SUBTREES = 100; + private final static int MAX_NODE_FRAMES = 10; + private final static int MOVE = 20; private final static NumberFormat FORMATTER_CONFIDENCE; private final static NumberFormat FORMATTER_BRANCH_LENGTH; - private final static int WIGGLE = 2; - private final static int LIMIT_FOR_HQ_RENDERING = 1000; - private final static int CONFIDENCE_LEFT_MARGIN = 4; + private final static int WIGGLE = 2; + private final static int LIMIT_FOR_HQ_RENDERING = 1000; + private final static int CONFIDENCE_LEFT_MARGIN = 4; // TODO "rendering_hints" was static before. Need to make sure everything is OK with it not // being static anymore (02/20/2009). - private final RenderingHints _rendering_hints = new RenderingHints( RenderingHints.KEY_RENDERING, - RenderingHints.VALUE_RENDER_DEFAULT ); - private File _treefile = null; - private Configuration _configuration = null; - private final NodeFrame[] _node_frames = new NodeFrame[ TreePanel.MAX_NODE_FRAMES ]; - private int _node_frame_index = 0; - private Phylogeny _phylogeny = null; - private final Phylogeny[] _sub_phylogenies = new Phylogeny[ TreePanel.MAX_SUBTREES ]; - private final PhylogenyNode[] _sub_phylogenies_temp_roots = new PhylogenyNode[ TreePanel.MAX_SUBTREES ]; - private int _subtree_index = 0; - private MainPanel _main_panel = null; - private Set _found_nodes = null; - private PhylogenyNode _highlight_node = null; - private JPopupMenu _node_popup_menu = null; - private JMenuItem _node_popup_menu_items[] = null; - private int _longest_ext_node_info = 0; - private float _x_correction_factor = 0.0f; - private float _ov_x_correction_factor = 0.0f; - private float _x_distance = 0.0f; - private float _y_distance = 0.0f; - private PHYLOGENY_GRAPHICS_TYPE _graphics_type = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR; - private double _domain_structure_width = Constants.DOMAIN_STRUCTURE_DEFAULT_WIDTH; - private int _domain_structure_e_value_thr_exp = Constants.DOMAIN_STRUCTURE_E_VALUE_THR_DEFAULT_EXP; - private float _last_drag_point_x = 0; - private float _last_drag_point_y = 0; - private ControlPanel _control_panel = null; - private int _external_node_index = 0; - private final Polygon _polygon = new Polygon(); - private final StringBuilder _sb = new StringBuilder(); - private JColorChooser _color_chooser = null; - private double _scale_distance = 0.0; - private String _scale_label = null; - private final CubicCurve2D _cubic_curve = new CubicCurve2D.Float(); - private final QuadCurve2D _quad_curve = new QuadCurve2D.Float(); - private final Line2D _line = new Line2D.Float(); - private final Ellipse2D _ellipse = new Ellipse2D.Float(); - private final Rectangle2D _rectangle = new Rectangle2D.Float(); - private Options _options = null; - private float _ov_max_width = 0; - private float _ov_max_height = 0; - private int _ov_x_position = 0; - private int _ov_y_position = 0; - private int _ov_y_start = 0; - private float _ov_y_distance = 0; - private float _ov_x_distance = 0; - private boolean _ov_on = false; - private double _urt_starting_angle = ( float ) ( Math.PI / 2 ); - private float _urt_factor = 1; - private float _urt_factor_ov = 1; + private final RenderingHints _rendering_hints = new RenderingHints( RenderingHints.KEY_RENDERING, + RenderingHints.VALUE_RENDER_DEFAULT ); + private File _treefile = null; + private Configuration _configuration = null; + private final NodeFrame[] _node_frames = new NodeFrame[ TreePanel.MAX_NODE_FRAMES ]; + private int _node_frame_index = 0; + private Phylogeny _phylogeny = null; + private final Phylogeny[] _sub_phylogenies = new Phylogeny[ TreePanel.MAX_SUBTREES ]; + private final PhylogenyNode[] _sub_phylogenies_temp_roots = new PhylogenyNode[ TreePanel.MAX_SUBTREES ]; + private int _subtree_index = 0; + private MainPanel _main_panel = null; + private Set _found_nodes = null; + private PhylogenyNode _highlight_node = null; + private JPopupMenu _node_popup_menu = null; + private JMenuItem _node_popup_menu_items[] = null; + private int _longest_ext_node_info = 0; + private float _x_correction_factor = 0.0f; + private float _ov_x_correction_factor = 0.0f; + private float _x_distance = 0.0f; + private float _y_distance = 0.0f; + private PHYLOGENY_GRAPHICS_TYPE _graphics_type = PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR; + private double _domain_structure_width = Constants.DOMAIN_STRUCTURE_DEFAULT_WIDTH; + private int _domain_structure_e_value_thr_exp = Constants.DOMAIN_STRUCTURE_E_VALUE_THR_DEFAULT_EXP; + private float _last_drag_point_x = 0; + private float _last_drag_point_y = 0; + private ControlPanel _control_panel = null; + private int _external_node_index = 0; + private final Polygon _polygon = new Polygon(); + private final StringBuilder _sb = new StringBuilder(); + private JColorChooser _color_chooser = null; + private double _scale_distance = 0.0; + private String _scale_label = null; + private final CubicCurve2D _cubic_curve = new CubicCurve2D.Float(); + private final QuadCurve2D _quad_curve = new QuadCurve2D.Float(); + private final Line2D _line = new Line2D.Float(); + private final Ellipse2D _ellipse = new Ellipse2D.Float(); + private final Rectangle2D _rectangle = new Rectangle2D.Float(); + private Options _options = null; + private float _ov_max_width = 0; + private float _ov_max_height = 0; + private int _ov_x_position = 0; + private int _ov_y_position = 0; + private int _ov_y_start = 0; + private float _ov_y_distance = 0; + private float _ov_x_distance = 0; + private boolean _ov_on = false; + private double _urt_starting_angle = ( float ) ( Math.PI / 2 ); + private float _urt_factor = 1; + private float _urt_factor_ov = 1; private final boolean _phy_has_branch_lengths; - private final Rectangle2D _ov_rectangle = new Rectangle2D.Float(); - private boolean _in_ov_rect = false; - private boolean _in_ov = false; - private final Rectangle _ov_virtual_rectangle = new Rectangle(); - final private static double _180_OVER_PI = 180.0 / Math.PI; - private static final float ROUNDED_D = 8; + private final Rectangle2D _ov_rectangle = new Rectangle2D.Float(); + private boolean _in_ov_rect = false; + private boolean _in_ov = false; + private final Rectangle _ov_virtual_rectangle = new Rectangle(); + final private static double _180_OVER_PI = 180.0 / Math.PI; + private static final float ROUNDED_D = 8; private int _circ_max_depth; private PhylogenyNode _root; - final private Arc2D _arc = new Arc2D.Double(); - final private HashMap _urt_nodeid_angle_map = new HashMap(); - final private HashMap _urt_nodeid_index_map = new HashMap(); - final private Set _collapsed_external_nodeid_set = new HashSet(); - HashMap _nodeid_dist_to_leaf = new HashMap(); + final private Arc2D _arc = new Arc2D.Double(); + final private HashMap _urt_nodeid_angle_map = new HashMap(); + final private HashMap _urt_nodeid_index_map = new HashMap(); + final private Set _collapsed_external_nodeid_set = new HashSet(); + HashMap _nodeid_dist_to_leaf = new HashMap(); private AffineTransform _at; - private double _max_distance_to_root = -1; - private int _dynamic_hiding_factor = 0; - private boolean _edited = false; + private double _max_distance_to_root = -1; + private int _dynamic_hiding_factor = 0; + private boolean _edited = false; private Popup _node_desc_popup; private JTextArea _rollover_popup; - private final StringBuffer _popup_buffer = new StringBuffer(); - final private static Font POPUP_FONT = new Font( Configuration.getDefaultFontFamilyName(), - Font.PLAIN, - 12 ); - private Sequence _query_sequence = null; - private final FontRenderContext _frc = new FontRenderContext( null, - false, - false ); + private final StringBuffer _popup_buffer = new StringBuffer(); + final private static Font POPUP_FONT = new Font( Configuration + .getDefaultFontFamilyName(), + Font.PLAIN, + 12 ); + private Sequence _query_sequence = null; + private final FontRenderContext _frc = new FontRenderContext( null, + false, + false ); // expression values menu: private DescriptiveStatistics _statistics_for_vector_data; - private PhylogenyNode[] _nodes_in_preorder = null; + private PhylogenyNode[] _nodes_in_preorder = null; + private StringBuilder _current_external_nodes_data_buffer = new StringBuilder(); + private int _current_external_nodes_data_buffer_change_counter = 0; // private Image offscreenImage; // private Graphics offscreenGraphics; // private Dimension offscreenDimension; @@ -731,6 +734,10 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee return c; } + void clearCurrentExternalNodesDataBuffer() { + setCurrentExternalNodesDataBuffer( new StringBuilder() ); + } + /** * Collapse the tree from the given node * @@ -877,6 +884,14 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee return _control_panel; } + String getCurrentExternalNodesDataBufferAsString() { + return _current_external_nodes_data_buffer.toString(); + } + + int getCurrentExternalNodesDataBufferChangeCounter() { + return _current_external_nodes_data_buffer_change_counter; + } + final int getDomainStructureEvalueThreshold() { return _domain_structure_e_value_thr_exp; } @@ -1736,6 +1751,12 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee _control_panel = atv_control; } + void setCurrentExternalNodesDataBuffer( final StringBuilder sb ) { + increaseCurrentExternalNodesDataBufferChangeCounter(); + _current_external_nodes_data_buffer = sb; + System.out.println( sb.toString() ); //TODO ~~~~~~~~~~~~~~ REMOVEME + } + final void setFoundNodes( final Set found_nodes ) { _found_nodes = found_nodes; } @@ -2770,6 +2791,11 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } } + private void increaseCurrentExternalNodesDataBufferChangeCounter() { + _current_external_nodes_data_buffer_change_counter++; + System.out.println( _current_external_nodes_data_buffer_change_counter ); //TODO ~~~~~~~~~~~~~~ REMOVEME + } + final private void increaseOvSize() { if ( ( getOvMaxWidth() < ( getMainPanel().getCurrentScrollPane().getViewport().getVisibleRect().getWidth() / 2 ) ) && ( getOvMaxHeight() < ( getMainPanel().getCurrentScrollPane().getViewport().getVisibleRect() @@ -5004,25 +5030,10 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } } if ( sb.length() < 1 ) { - if ( getMainPanel().getMainFrame() == null ) { - // Must be "E" applet version. - ( ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet() ) - .setCurrentExternalNodesDataBuffer( "" ); - } - else { - getMainPanel().getMainFrame().setCurrentExternalNodesDataBuffer( "" ); - } + clearCurrentExternalNodesDataBuffer(); } else { - final String s = sb.toString().trim(); - if ( getMainPanel().getMainFrame() == null ) { - // Must be "E" applet version. - ( ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet() ) - .setCurrentExternalNodesDataBuffer( s ); - } - else { - getMainPanel().getMainFrame().setCurrentExternalNodesDataBuffer( s ); - } + setCurrentExternalNodesDataBuffer( sb ); } } else if ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.WINODW ) { @@ -5037,16 +5048,10 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee AptxUtil.showInformationMessage( this, "No Appropriate Data (" + obtainTitleForExtDescNodeData() + ")", "Descendants of selected node do not contain selected data" ); - if ( getMainPanel().getMainFrame() == null ) { - // Must be "E" applet version. - ( ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet() ) - .setCurrentExternalNodesDataBuffer( "" ); - } - else { - getMainPanel().getMainFrame().setCurrentExternalNodesDataBuffer( "" ); - } + clearCurrentExternalNodesDataBuffer(); } else { + setCurrentExternalNodesDataBuffer( sb ); final String title = "External Descendants " + ( getOptions().getExtDescNodeDataToReturn() == NODE_DATA.UNKNOWN ? "Data" : obtainTitleForExtDescNodeData() ) + " (" + data.size() + "/" @@ -5056,11 +5061,9 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee // Must be "E" applet version. final ArchaeopteryxE ae = ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet(); ae.showTextFrame( s, title ); - ae.setCurrentExternalNodesDataBuffer( s ); } else { getMainPanel().getMainFrame().showTextFrame( s, title ); - getMainPanel().getMainFrame().setCurrentExternalNodesDataBuffer( s ); } } }