X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FTreePanel.java;h=3ad39351f9b3cc2b4e81eb2fe38aeaee38c3c1a9;hb=7bbb45295594e9574ee64a32fac17a93b5aa6ade;hp=c020b28de7b0b599f4c5fdfad2b4f2e25fd6c541;hpb=eee996a6476a1e3d84c07f8f690dcde3ff4b2ef5;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/TreePanel.java b/forester/java/src/org/forester/archaeopteryx/TreePanel.java index c020b28..3ad3935 100644 --- a/forester/java/src/org/forester/archaeopteryx/TreePanel.java +++ b/forester/java/src/org/forester/archaeopteryx/TreePanel.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.archaeopteryx; @@ -34,9 +34,9 @@ import java.awt.GradientPaint; import java.awt.Graphics; import java.awt.Graphics2D; import java.awt.Point; -import java.awt.Polygon; import java.awt.Rectangle; import java.awt.RenderingHints; +import java.awt.Stroke; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.awt.event.FocusAdapter; @@ -54,6 +54,7 @@ import java.awt.geom.Arc2D; import java.awt.geom.CubicCurve2D; import java.awt.geom.Ellipse2D; import java.awt.geom.Line2D; +import java.awt.geom.Path2D; import java.awt.geom.QuadCurve2D; import java.awt.geom.Rectangle2D; import java.awt.image.BufferedImage; @@ -75,7 +76,11 @@ import java.util.HashMap; import java.util.HashSet; import java.util.Hashtable; import java.util.List; +import java.util.Map.Entry; import java.util.Set; +import java.util.SortedMap; +import java.util.SortedSet; +import java.util.TreeMap; import javax.swing.BorderFactory; import javax.swing.JApplet; @@ -89,21 +94,30 @@ import javax.swing.JTextArea; import javax.swing.Popup; import javax.swing.PopupFactory; +import org.forester.archaeopteryx.Configuration.EXT_NODE_DATA_RETURN_ON; import org.forester.archaeopteryx.ControlPanel.NodeClickAction; import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE; import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION; import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE; import org.forester.archaeopteryx.phylogeny.data.RenderableDomainArchitecture; import org.forester.archaeopteryx.phylogeny.data.RenderableVector; +import org.forester.archaeopteryx.tools.Blast; +import org.forester.archaeopteryx.tools.ImageLoader; import org.forester.io.parsers.phyloxml.PhyloXmlUtil; +import org.forester.io.writers.SequenceWriter; import org.forester.phylogeny.Phylogeny; import org.forester.phylogeny.PhylogenyMethods; +import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY; import org.forester.phylogeny.PhylogenyNode; import org.forester.phylogeny.data.Annotation; import org.forester.phylogeny.data.BranchColor; import org.forester.phylogeny.data.Confidence; import org.forester.phylogeny.data.Event; -import org.forester.phylogeny.data.PhylogenyData; +import org.forester.phylogeny.data.NodeData.NODE_DATA; +import org.forester.phylogeny.data.NodeVisualization; +import org.forester.phylogeny.data.NodeVisualization.NodeFill; +import org.forester.phylogeny.data.NodeVisualization.NodeShape; +import org.forester.phylogeny.data.PhylogenyDataUtil; import org.forester.phylogeny.data.PropertiesMap; import org.forester.phylogeny.data.Property; import org.forester.phylogeny.data.Sequence; @@ -116,117 +130,123 @@ import org.forester.util.BasicDescriptiveStatistics; import org.forester.util.DescriptiveStatistics; import org.forester.util.ForesterConstants; import org.forester.util.ForesterUtil; +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 BOX_SIZE = 4; - private final static int HALF_BOX_SIZE = TreePanel.BOX_SIZE / 2; - 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 HALF_BOX_SIZE_PLUS_WIGGLE = HALF_BOX_SIZE + WIGGLE; - private final static int LIMIT_FOR_HQ_RENDERING = 1000; - // 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 boolean _phy_has_branch_lengths; - private final Rectangle2D _ov_rectangle = new Rectangle2D.Float(); - private boolean _in_ov_rect = false; - private boolean _in_ov = false; - private final Rectangle _ov_virtual_rectangle = new Rectangle(); - final private static double _180_OVER_PI = 180.0 / Math.PI; - private static final float ROUNDED_D = 8; - private int _circ_max_depth; - private int _circ_num_ext_nodes; - 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(); - 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 Popup _node_desc_popup; - private JTextArea _rollover_popup; - //private final short _skip_counter = 0; - private final StringBuffer _popup_buffer = new StringBuffer(); - final private static Font POPUP_FONT = new Font( Configuration.getDefaultFontFamilyName(), - Font.PLAIN, - 12 ); - private static final boolean DRAW_MEAN_COUNTS = true; //TODO remove me later - private Sequence _query_sequence = null; - private final FontRenderContext _frc = new FontRenderContext( null, - false, - false ); + private static final BasicStroke STROKE_2 = new BasicStroke( 2f ); + private static final BasicStroke STROKE_1 = new BasicStroke( 1f ); + private static final BasicStroke STROKE_075 = new BasicStroke( 0.75f ); + private static final BasicStroke STROKE_05 = new BasicStroke( 0.5f ); + private static final BasicStroke STROKE_025 = new BasicStroke( 0.25f ); + private static final BasicStroke STROKE_01 = new BasicStroke( 0.1f ); + private static final BasicStroke STROKE_005 = new BasicStroke( 0.05f ); + private static final float PI = ( float ) ( Math.PI ); + private static final double TWO_PI = 2 * Math.PI; + private static final float ONEHALF_PI = ( float ) ( 1.5 * Math.PI ); + private static final float HALF_PI = ( float ) ( Math.PI / 2.0 ); + private static final float ANGLE_ROTATION_UNIT = ( float ) ( Math.PI / 32 ); + private static final short OV_BORDER = 10; + final static Cursor CUT_CURSOR = Cursor.getPredefinedCursor( Cursor.CROSSHAIR_CURSOR ); + final static Cursor MOVE_CURSOR = Cursor.getPredefinedCursor( Cursor.MOVE_CURSOR ); + final static Cursor ARROW_CURSOR = Cursor.getPredefinedCursor( Cursor.DEFAULT_CURSOR ); + final static Cursor 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 = 2000; + private final static int CONFIDENCE_LEFT_MARGIN = 4; + private final RenderingHints _rendering_hints = new RenderingHints( RenderingHints.KEY_RENDERING, + RenderingHints.VALUE_RENDER_DEFAULT ); + private File _treefile = null; + private 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 Path2D.Float _polygon = new Path2D.Float(); + private final StringBuilder _sb = new StringBuilder(); + private JColorChooser _color_chooser = null; + private double _scale_distance = 0.0; + private String _scale_label = null; + private final CubicCurve2D _cubic_curve = new CubicCurve2D.Float(); + private final QuadCurve2D _quad_curve = new QuadCurve2D.Float(); + private final Line2D _line = new Line2D.Float(); + private final Ellipse2D _ellipse = new Ellipse2D.Float(); + private final Rectangle2D _rectangle = new Rectangle2D.Float(); + private 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 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(); + private AffineTransform _at; + private double _max_distance_to_root = -1; + private int _dynamic_hiding_factor = 0; + private boolean _edited = false; + private Popup _node_desc_popup; + private JTextArea _rollover_popup; + private 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 DescriptiveStatistics _statistics_for_vector_data; + private PhylogenyNode[] _nodes_in_preorder = null; + private StringBuilder _current_external_nodes_data_buffer = new StringBuilder(); + private int _current_external_nodes_data_buffer_change_counter = 0; + private Set _current_external_nodes = null; // private Image offscreenImage; // private Graphics offscreenGraphics; // private Dimension offscreenDimension; @@ -261,7 +281,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee _main_panel = tjp; _configuration = configuration; _phylogeny = t; - _phy_has_branch_lengths = ForesterUtil.isHasAtLeastOneBranchLengthLargerThanZero( _phylogeny ); + _phy_has_branch_lengths = AptxUtil.isHasAtLeastOneBranchLengthLargerThanZero( _phylogeny ); init(); // if ( !_phylogeny.isEmpty() ) { _phylogeny.recalculateNumberOfExternalDescendants( true ); @@ -278,70 +298,11 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee .getNumberOfDigitsAfterCommaForBranchLengthValues() ); } - public 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; - } - int i = -1; - try { - i = Integer.parseInt( index_str ); - } - 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; - } - if ( i < 0 ) { - JOptionPane.showMessageDialog( this, - "Attempt to use negative index for vector data", - "Problem with Vector Data", - JOptionPane.ERROR_MESSAGE ); - return; - } - 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 ] ); - } - node.getNodeData().setVector( vector_l ); - } - } - if ( stats.getN() > 0 ) { - _statistics_for_vector_data = stats; - } - } - + @Override final public void actionPerformed( final ActionEvent e ) { - int index; boolean done = false; final JMenuItem node_popup_menu_item = ( JMenuItem ) e.getSource(); - for( index = 0; ( index < _node_popup_menu_items.length ) && !done; index++ ) { + for( int index = 0; ( index < _node_popup_menu_items.length ) && !done; index++ ) { // NOTE: index corresponds to the indices of click-to options // in the control panel. if ( node_popup_menu_item == _node_popup_menu_items[ index ] ) { @@ -357,174 +318,283 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee requestFocusInWindow(); } - final private void addEmptyNode( final PhylogenyNode node ) { - if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) { - errorMessageNoCutCopyPasteInUnrootedDisplay(); - return; - } - final String label = getASimpleTextRepresentationOfANode( 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 + "?"; - } - 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; - } - phy.addAsSibling( node ); - } - else { - phy.addAsChild( node ); - } - _phylogeny.externalNodesHaveChanged(); - _phylogeny.hashIDs(); - _phylogeny.recalculateNumberOfExternalDescendants( true ); - resetNodeIdToDistToLeafMap(); - setEdited( true ); - repaint(); + public synchronized Hashtable getImageMap() { + return getMainPanel().getImageMap(); } - 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().getFoundColor() ); - } - else if ( getControlPanel().isColorBranches() && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) { - g.setColor( PhylogenyMethods.getBranchColorValue( node ) ); - } - else if ( to_pdf ) { - g.setColor( getTreeColorSet().getBranchColorForPdf() ); - } - else { - g.setColor( getTreeColorSet().getBranchColor() ); - } + final public MainPanel getMainPanel() { + return _main_panel; } - final void assignGraphicsForNodeBoxWithColorForParentBranch( final PhylogenyNode node, final Graphics g ) { - if ( getControlPanel().isColorBranches() && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) { - g.setColor( PhylogenyMethods.getBranchColorValue( node ) ); - } - else { - g.setColor( getTreeColorSet().getBranchColor() ); - } + /** + * Get a pointer to the phylogeny + * + * @return a pointer to the phylogeny + */ + public final Phylogeny getPhylogeny() { + return _phylogeny; } - final private void blast( final PhylogenyNode node ) { - if ( !isCanBlast( node ) ) { - JOptionPane.showMessageDialog( this, - "No sequence information present", - "Cannot Blast", - JOptionPane.WARNING_MESSAGE ); - return; + @Override + final public void mouseWheelMoved( final MouseWheelEvent e ) { + final int notches = e.getWheelRotation(); + if ( inOvVirtualRectangle( e ) ) { + if ( !isInOvRect() ) { + setInOvRect( true ); + repaint(); + } } - if ( node.getNodeData().isHasSequence() ) { - String name = ""; - if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getName() ) ) { - name = node.getNodeData().getSequence().getName(); + else { + if ( isInOvRect() ) { + setInOvRect( false ); + repaint(); } - else if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getSymbol() ) ) { - name = node.getNodeData().getSequence().getSymbol(); + } + if ( e.isControlDown() ) { + if ( notches < 0 ) { + getTreeFontSet().increaseFontSize(); + getControlPanel().displayedPhylogenyMightHaveChanged( true ); } - else if ( node.getNodeData().getSequence().getAccession() != null ) { - name = node.getNodeData().getSequence().getAccession().getValue(); + else { + getTreeFontSet().decreaseFontSize( 1, false ); + getControlPanel().displayedPhylogenyMightHaveChanged( true ); } - if ( !ForesterUtil.isEmpty( name ) ) { - try { - System.out.println( "trying: " + name ); - final Blast s = new Blast(); - s.go( name ); + } + else if ( e.isShiftDown() ) { + if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) + || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) { + if ( notches < 0 ) { + for( int i = 0; i < ( -notches ); ++i ) { + setStartingAngle( ( getStartingAngle() % TWO_PI ) + ANGLE_ROTATION_UNIT ); + getControlPanel().displayedPhylogenyMightHaveChanged( false ); + } } - catch ( final Exception e ) { - e.printStackTrace(); + else { + for( int i = 0; i < notches; ++i ) { + setStartingAngle( ( getStartingAngle() % TWO_PI ) - ANGLE_ROTATION_UNIT ); + if ( getStartingAngle() < 0 ) { + setStartingAngle( TWO_PI + getStartingAngle() ); + } + getControlPanel().displayedPhylogenyMightHaveChanged( false ); + } } } - } - } - - final void calcMaxDepth() { - if ( _phylogeny != null ) { - _circ_max_depth = PhylogenyMethods.calculateMaxDepth( _phylogeny ); - } - } - - /** - * 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; + else { + if ( notches < 0 ) { + for( int i = 0; i < ( -notches ); ++i ) { + getControlPanel().zoomInY( Constants.WHEEL_ZOOM_IN_FACTOR ); + getControlPanel().displayedPhylogenyMightHaveChanged( false ); + } + } + else { + for( int i = 0; i < notches; ++i ) { + getControlPanel().zoomOutY( Constants.WHEEL_ZOOM_OUT_FACTOR ); + getControlPanel().displayedPhylogenyMightHaveChanged( false ); + } + } } - return ( float ) ( getXcorrectionFactor() * node.getDistanceToParent() ); } else { - if ( ( factor == 0 ) || isNonLinedUpCladogram() ) { - return getXdistance(); + 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().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().displayedPhylogenyMightHaveChanged( false ); + } } - return getXdistance() * factor; } + requestFocus(); + requestFocusInWindow(); + requestFocus(); } - final private Color calculateColorForAnnotation( final PhylogenyData ann ) { - Color c = getTreeColorSet().getAnnotationColor(); - if ( getControlPanel().isColorAccordingToAnnotation() && ( getControlPanel().getAnnotationColors() != null ) ) { - c = getControlPanel().getAnnotationColors().get( ann.asSimpleText().toString() ); - if ( c == null ) { - c = getTreeColorSet().getAnnotationColor(); - } - } - return c; + @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 + final public int print( final Graphics g, final PageFormat page_format, final int page_index ) + throws PrinterException { + if ( page_index > 0 ) { + return ( NO_SUCH_PAGE ); + } + else { + final Graphics2D g2d = ( Graphics2D ) g; + g2d.translate( page_format.getImageableX(), page_format.getImageableY() ); + // Turn off double buffering !? + paintPhylogeny( g2d, true, false, 0, 0, 0, 0 ); + // Turn double buffering back on !? + return ( PAGE_EXISTS ); + } + } + + public final void setEdited( final boolean edited ) { + _edited = edited; + } + + public synchronized void setImageMap( final Hashtable image_map ) { + getMainPanel().setImageMap( image_map ); + } + + /** + * Set a phylogeny tree. + * + * @param t + * an instance of a Phylogeny + */ + public final void setTree( final Phylogeny t ) { + setNodeInPreorderToNull(); + _phylogeny = t; + } + + public final void setWaitCursor() { + setCursor( WAIT_CURSOR ); + repaint(); + } + + @Override + public void update( final Graphics g ) { + 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(); + } + } + } + } + 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(); + // } + // } + } + } + // + } } final void calculateLongestExtNodeInfo() { if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) { return; } - int longest = 20; + int max_length = ForesterUtil.roundToInt( ( getSize().getWidth() - MOVE ) + * Constants.EXT_NODE_INFO_LENGTH_MAX_RATIO ); + if ( max_length < 40 ) { + max_length = 40; + } + int longest = 30; for( final PhylogenyNode node : _phylogeny.getExternalNodes() ) { int sum = 0; if ( node.isCollapse() ) { @@ -550,10 +620,15 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee if ( getControlPanel().isShowAnnotation() && ( node.getNodeData().getSequence().getAnnotations() != null ) && !node.getNodeData().getSequence().getAnnotations().isEmpty() ) { - sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getAnnotation( 0 ) - .asSimpleText() + sum += getTreeFontSet()._fm_large.stringWidth( TreePanelUtil.createAnnotationString( node + .getNodeData().getSequence().getAnnotations(), getOptions().isShowAnnotationRefSource() ) + " " ); } + if ( getControlPanel().isShowDomainArchitectures() + && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) { + sum += ( ( RenderableDomainArchitecture ) node.getNodeData().getSequence().getDomainArchitecture() ) + .getRenderingSize().getWidth(); + } } if ( node.getNodeData().isHasTaxonomy() ) { final Taxonomy tax = node.getNodeData().getTaxonomy(); @@ -568,46 +643,29 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee sum += getTreeFontSet()._fm_large_italic.stringWidth( tax.getCommonName() + " ()" ); } } + if ( getControlPanel().isShowProperties() && node.getNodeData().isHasProperties() ) { + sum += getTreeFontSet()._fm_large.stringWidth( propertiesToString( node ).toString() ); + } if ( getControlPanel().isShowBinaryCharacters() && node.getNodeData().isHasBinaryCharacters() ) { sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getBinaryCharacters() .getGainedCharactersAsStringBuffer().toString() ); } - if ( getControlPanel().isShowDomainArchitectures() && node.getNodeData().isHasSequence() - && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) { - sum += ( ( RenderableDomainArchitecture ) node.getNodeData().getSequence().getDomainArchitecture() ) - .getRenderingSize().getWidth(); - } - if ( sum >= Constants.EXT_NODE_INFO_LENGTH_MAX ) { - setLongestExtNodeInfo( Constants.EXT_NODE_INFO_LENGTH_MAX ); + if ( sum >= max_length ) { + setLongestExtNodeInfo( max_length ); return; } if ( sum > longest ) { longest = sum; } } - if ( longest >= Constants.EXT_NODE_INFO_LENGTH_MAX ) { - setLongestExtNodeInfo( Constants.EXT_NODE_INFO_LENGTH_MAX ); + if ( longest >= max_length ) { + setLongestExtNodeInfo( max_length ); } else { setLongestExtNodeInfo( longest ); } } - final private float calculateOvBranchLengthToParent( final PhylogenyNode node, final int factor ) { - if ( getControlPanel().isDrawPhylogram() ) { - if ( node.getDistanceToParent() < 0.0 ) { - return 0.0f; - } - return ( float ) ( getOvXcorrectionFactor() * node.getDistanceToParent() ); - } - else { - if ( ( factor == 0 ) || isNonLinedUpCladogram() ) { - return getOvXDistance(); - } - return getOvXDistance() * factor; - } - } - final void calculateScaleDistance() { if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) { return; @@ -641,30 +699,90 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } final Color calculateTaxonomyBasedColor( final Taxonomy tax ) { - String species = tax.getTaxonomyCode(); - if ( ForesterUtil.isEmpty( species ) ) { - species = tax.getScientificName(); - if ( ForesterUtil.isEmpty( species ) ) { - species = tax.getCommonName(); - } - } - if ( ForesterUtil.isEmpty( species ) ) { + if ( ForesterUtil.isEmpty( tax.getTaxonomyCode() ) && ForesterUtil.isEmpty( tax.getScientificName() ) ) { return getTreeColorSet().getTaxonomyColor(); } - // Look in species hash - Color c = getControlPanel().getSpeciesColors().get( species ); + 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 ) { - c = Util.calculateColorFromString( species ); - getControlPanel().getSpeciesColors().put( species, c ); + if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) { + c = TreePanelUtil.calculateColorFromString( tax.getTaxonomyCode(), true ); + getControlPanel().getSpeciesColors().put( tax.getTaxonomyCode(), c ); + } + else { + c = TreePanelUtil.calculateColorFromString( tax.getScientificName(), true ); + getControlPanel().getSpeciesColors().put( tax.getScientificName(), c ); + } } return c; } - 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 ); + 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; + } + int i = -1; + try { + i = Integer.parseInt( index_str ); + } + 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; + } + if ( i < 0 ) { + JOptionPane.showMessageDialog( this, + "Attempt to use negative index for vector data", + "Problem with Vector Data", + JOptionPane.ERROR_MESSAGE ); + return; + } + 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 ] ); + } + node.getNodeData().setVector( vector_l ); + } + } + if ( stats.getN() > 0 ) { + _statistics_for_vector_data = stats; + } + } + + void clearCurrentExternalNodesDataBuffer() { + setCurrentExternalNodesDataBuffer( new StringBuilder() ); } /** @@ -683,10 +801,13 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } if ( !node.isExternal() && !node.isRoot() ) { final boolean collapse = !node.isCollapse(); - Util.collapseSubtree( node, collapse ); + TreePanelUtil.collapseSubtree( node, collapse ); + updateSetOfCollapsedExternalNodes(); _phylogeny.recalculateNumberOfExternalDescendants( true ); resetNodeIdToDistToLeafMap(); calculateLongestExtNodeInfo(); + setNodeInPreorderToNull(); + _control_panel.displayedPhylogenyMightHaveChanged( true ); resetPreferredSize(); updateOvSizes(); _main_panel.adjustJScrollPane(); @@ -699,53 +820,62 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee return; } setWaitCursor(); - Util.collapseSpeciesSpecificSubtrees( _phylogeny ); + TreePanelUtil.collapseSpeciesSpecificSubtrees( _phylogeny ); + updateSetOfCollapsedExternalNodes(); _phylogeny.recalculateNumberOfExternalDescendants( true ); resetNodeIdToDistToLeafMap(); calculateLongestExtNodeInfo(); + setNodeInPreorderToNull(); resetPreferredSize(); _main_panel.adjustJScrollPane(); setArrowCursor(); repaint(); } - final private void colorizeSubtree( final Color c, 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 ); + final void colorRank( final String rank ) { + if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) { return; } - _control_panel.setColorBranches( true ); - if ( _control_panel.getColorBranchesCb() != null ) { - _control_panel.getColorBranchesCb().setSelected( true ); - } - for( final PreorderTreeIterator it = new PreorderTreeIterator( node ); it.hasNext(); ) { - it.next().getBranchData().setBranchColor( new BranchColor( c ) ); + setWaitCursor(); + AptxUtil.removeBranchColors( _phylogeny ); + final int colorizations = TreePanelUtil.colorPhylogenyAccordingToRanks( _phylogeny, rank, this ); + if ( colorizations > 0 ) { + _control_panel.setColorBranches( true ); + if ( _control_panel.getColorBranchesCb() != null ) { + _control_panel.getColorBranchesCb().setSelected( true ); + } + if ( _control_panel.getColorAccSpeciesCb() != null ) { + _control_panel.getColorAccSpeciesCb().setSelected( false ); + } + _options.setColorLabelsSameAsParentBranch( true ); + _control_panel.repaint(); } + setArrowCursor(); repaint(); - } - - final private void colorSubtree( final PhylogenyNode node ) { - Color intitial_color = null; - if ( getControlPanel().isColorBranches() && ( PhylogenyMethods.getBranchColorValue( node ) != null ) - && ( ( ( !node.isRoot() && ( node.getParent().getNumberOfDescendants() < 3 ) ) ) || ( node.isRoot() ) ) ) { - intitial_color = PhylogenyMethods.getBranchColorValue( node ); + 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 ); } else { - intitial_color = getTreeColorSet().getBranchColor(); + 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 ); } - _color_chooser.setColor( intitial_color ); - _color_chooser.setPreviewPanel( new JPanel() ); - final JDialog dialog = JColorChooser - .createDialog( this, - "Subtree colorization", - true, - _color_chooser, - new SubtreeColorizationActionListener( _color_chooser, node ), - null ); - dialog.setVisible( true ); } final void confColor() { @@ -753,7 +883,8 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee return; } setWaitCursor(); - Util.colorPhylogenyAccordingToConfidenceValues( _phylogeny, this ); + AptxUtil.removeBranchColors( _phylogeny ); + TreePanelUtil.colorPhylogenyAccordingToConfidenceValues( _phylogeny, this ); _control_panel.setColorBranches( true ); if ( _control_panel.getColorBranchesCb() != null ) { _control_panel.getColorBranchesCb().setSelected( true ); @@ -762,179 +893,10 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee repaint(); } - final private void copySubtree( final PhylogenyNode node ) { - if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) { - errorMessageNoCutCopyPasteInUnrootedDisplay(); - return; - } - 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() ); + final void decreaseDomainStructureEvalueThreshold() { + if ( _domain_structure_e_value_thr_exp > -20 ) { + _domain_structure_e_value_thr_exp -= 1; } - node_ids.add( node.getId() ); - setCopiedAndPastedNodes( node_ids ); - repaint(); - } - - 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 = getASimpleTextRepresentationOfANode( node ); - final int r = JOptionPane.showConfirmDialog( null, - "Cut subtree" + label + "?", - "Confirm Cutting of Subtree", - JOptionPane.YES_NO_OPTION ); - if ( r != JOptionPane.OK_OPTION ) { - return; - } - setCopiedAndPastedNodes( null ); - setCutOrCopiedTree( _phylogeny.copy( node ) ); - _phylogeny.deleteSubtree( node, true ); - _phylogeny.hashIDs(); - _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() ); - } - } - - final void decreaseDomainStructureEvalueThreshold() { - if ( _domain_structure_e_value_thr_exp > -20 ) { - _domain_structure_e_value_thr_exp -= 1; - } - } - - final private void decreaseOvSize() { - if ( ( getOvMaxWidth() > 20 ) && ( getOvMaxHeight() > 20 ) ) { - setOvMaxWidth( getOvMaxWidth() - 5 ); - setOvMaxHeight( getOvMaxHeight() - 5 ); - updateOvSettings(); - getControlPanel().displayedPhylogenyMightHaveChanged( false ); - } - } - - final private void deleteNodeOrSubtree( final PhylogenyNode node ) { - if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) { - errorMessageNoCutCopyPasteInUnrootedDisplay(); - return; - } - if ( node.isRoot() ) { - JOptionPane.showMessageDialog( this, - "Cannot delete entire tree", - "Attempt to delete entire tree", - JOptionPane.ERROR_MESSAGE ); - return; - } - final String label = getASimpleTextRepresentationOfANode( 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 ] ); - boolean node_only = true; - if ( r == 1 ) { - node_only = false; - } - else if ( r != 0 ) { - return; - } - if ( node_only ) { - PhylogenyMethods.removeNode( node, _phylogeny ); - } - else { - _phylogeny.deleteSubtree( node, true ); - } - _phylogeny.externalNodesHaveChanged(); - _phylogeny.hashIDs(); - _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 ); - } - - 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; - } - _line.setLine( x1, y1, x2, y2 ); - g.draw( _line ); - } - - 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 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 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 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 ); } /** @@ -948,37 +910,20 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) { return null; } + final int half_box_size_plus_wiggle = ( getOptions().getDefaultNodeShapeSize() / 2 ) + WIGGLE; for( final PhylogenyNodeIterator iter = _phylogeny.iteratorPostorder(); iter.hasNext(); ) { final PhylogenyNode node = iter.next(); if ( ( _phylogeny.isRooted() || !node.isRoot() || ( node.getNumberOfDescendants() > 2 ) ) - && ( ( node.getXcoord() - HALF_BOX_SIZE_PLUS_WIGGLE ) <= x ) - && ( ( node.getXcoord() + HALF_BOX_SIZE_PLUS_WIGGLE ) >= x ) - && ( ( node.getYcoord() - HALF_BOX_SIZE_PLUS_WIGGLE ) <= y ) - && ( ( node.getYcoord() + HALF_BOX_SIZE_PLUS_WIGGLE ) >= y ) ) { + && ( ( node.getXcoord() - half_box_size_plus_wiggle ) <= x ) + && ( ( node.getXcoord() + half_box_size_plus_wiggle ) >= x ) + && ( ( node.getYcoord() - half_box_size_plus_wiggle ) <= y ) + && ( ( node.getYcoord() + half_box_size_plus_wiggle ) >= y ) ) { return node; } } return null; } - final private String getASimpleTextRepresentationOfANode( 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 Configuration getConfiguration() { return _configuration; } @@ -987,54 +932,33 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee return _control_panel; } - final private Set getCopiedAndPastedNodes() { - return getMainPanel().getCopiedAndPastedNodes(); + String getCurrentExternalNodesDataBufferAsString() { + return _current_external_nodes_data_buffer.toString(); } - final private Phylogeny getCutOrCopiedTree() { - return getMainPanel().getCutOrCopiedTree(); + int getCurrentExternalNodesDataBufferChangeCounter() { + return _current_external_nodes_data_buffer_change_counter; } final int getDomainStructureEvalueThreshold() { return _domain_structure_e_value_thr_exp; } - final Set getFoundNodes() { + final Set getFoundNodes() { return _found_nodes; } - final private float getLastDragPointX() { - return _last_drag_point_x; - } - - final private float getLastDragPointY() { - return _last_drag_point_y; - } - - final int getLongestExtNodeInfo() { - return _longest_ext_node_info; - } - - final public MainPanel getMainPanel() { - return _main_panel; - } - - 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 Color getGraphicsForNodeBoxWithColorForParentBranch( final PhylogenyNode node ) { + if ( getControlPanel().isColorBranches() && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) { + return ( PhylogenyMethods.getBranchColorValue( node ) ); } else { - return _nodeid_dist_to_leaf.get( node.getId() ); + return ( getTreeColorSet().getBranchColor() ); } } - final private double getMaxDistanceToRoot() { - if ( _max_distance_to_root < 0 ) { - recalculateMaxDistanceToRoot(); - } - return _max_distance_to_root; + final int getLongestExtNodeInfo() { + return _longest_ext_node_info; } final Options getOptions() { @@ -1044,14 +968,6 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee return _options; } - final private float getOvMaxHeight() { - return _ov_max_height; - } - - final private float getOvMaxWidth() { - return _ov_max_width; - } - final Rectangle2D getOvRectangle() { return _ov_rectangle; } @@ -1060,92 +976,43 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee return _ov_virtual_rectangle; } - 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 PHYLOGENY_GRAPHICS_TYPE getPhylogenyGraphicsType() { + return _graphics_type; } - final private float getOvYDistance() { - return _ov_y_distance; + final double getStartingAngle() { + return _urt_starting_angle; } - final private int getOvYPosition() { - return _ov_y_position; + DescriptiveStatistics getStatisticsForExpressionValues() { + return _statistics_for_vector_data; } - final private int getOvYStart() { - return _ov_y_start; + /** + * Find a color for this species name. + * + * @param species + * @return the species color + */ + final Color getTaxonomyBasedColor( final PhylogenyNode node ) { + if ( node.getNodeData().isHasTaxonomy() ) { + return calculateTaxonomyBasedColor( node.getNodeData().getTaxonomy() ); + } + // return non-colorized color + return getTreeColorSet().getTaxonomyColor(); } /** - * Get a pointer to the phylogeny - * - * @return a pointer to the phylogeny + * @return pointer to colorset for tree drawing */ - final Phylogeny getPhylogeny() { - return _phylogeny; - } - - final PHYLOGENY_GRAPHICS_TYPE getPhylogenyGraphicsType() { - return _graphics_type; - } - - final private double getScaleDistance() { - return _scale_distance; - } - - final private String getScaleLabel() { - return _scale_label; - } - - final double getStartingAngle() { - return _urt_starting_angle; - } - - /** - * Find a color for this species name. - * - * @param species - * @return the species color - */ - final Color getTaxonomyBasedColor( final PhylogenyNode node ) { - if ( node.getNodeData().isHasTaxonomy() ) { - return calculateTaxonomyBasedColor( node.getNodeData().getTaxonomy() ); - } - // return non-colorized color - return getTreeColorSet().getTaxonomyColor(); - } - - /** - * @return pointer to colorset for tree drawing - */ - final TreeColorSet getTreeColorSet() { - return getMainPanel().getTreeColorSet(); + final TreeColorSet getTreeColorSet() { + return getMainPanel().getTreeColorSet(); } final File getTreeFile() { return _treefile; } - final private TreeFontSet getTreeFontSet() { - return getMainPanel().getTreeFontSet(); - } - - final private float getUrtFactor() { - return _urt_factor; - } - - final private float getUrtFactorOv() { - return _urt_factor_ov; - } - final float getXcorrectionFactor() { return _x_correction_factor; } @@ -1158,104 +1025,12 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee return _y_distance; } - 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 OPEN_SEQ_WEB: - openSeqWeb( node ); - break; - case BLAST: - blast( node ); - break; - case OPEN_TAX_WEB: - openTaxWeb( 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; - default: - throw new IllegalArgumentException( "unknown action: " + action ); - } - } - final void increaseDomainStructureEvalueThreshold() { if ( _domain_structure_e_value_thr_exp < 3 ) { _domain_structure_e_value_thr_exp += 1; } } - 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 void inferCommonPartOfScientificNames() { - if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) { - return; - } - setWaitCursor(); - Util.inferCommonPartOfScientificNames( _phylogeny ); - setArrowCursor(); - repaint(); - } - - 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 initializeOvSettings() { - setOvMaxHeight( getConfiguration().getOvMaxHeight() ); - setOvMaxWidth( getConfiguration().getOvMaxWidth() ); - } - final void initNodeData() { if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) { return; @@ -1296,41 +1071,23 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } 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 ) ); + 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 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 boolean inOvVirtualRectangle( final MouseEvent e ) { - return ( inOvVirtualRectangle( e.getX(), e.getY() ) ); + 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 isApplet() { return getMainPanel() instanceof MainPanelApplets; } - final private boolean isCanBlast( final PhylogenyNode node ) { - return ( node.getNodeData().isHasSequence() && ( ( ( node.getNodeData().getSequence().getAccession() != null ) && !ForesterUtil - .isEmpty( node.getNodeData().getSequence().getAccession().getValue() ) ) - || !ForesterUtil.isEmpty( node.getNodeData().getSequence().getName() ) || !ForesterUtil.isEmpty( node - .getNodeData().getSequence().getSymbol() ) ) ); - } - final boolean isCanCollapse() { return ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ); } @@ -1352,37 +1109,6 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable() ); } - final private boolean isCanOpenSeqWeb( final PhylogenyNode node ) { - if ( node.getNodeData().isHasSequence() - && ( node.getNodeData().getSequence().getAccession() != null ) - && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() ) - && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getValue() ) - && getConfiguration().isHasWebLink( node.getNodeData().getSequence().getAccession().getSource() - .toLowerCase() ) ) { - return true; - } - return false; - } - - final private boolean isCanOpenTaxWeb( final PhylogenyNode node ) { - if ( node.getNodeData().isHasTaxonomy() - && ( ( ( node.getNodeData().getTaxonomy().getIdentifier() != null ) - && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getIdentifier().getProvider() ) - && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getIdentifier().getValue() ) && getConfiguration() - .isHasWebLink( node.getNodeData().getTaxonomy().getIdentifier().getProvider().toLowerCase() ) ) - || ( !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() ) && node - .getNodeData().getTaxonomy().getIdentifier().getValue().startsWith( "http://" ) ) ) ) { - return true; - } - else { - return false; - } - } - final boolean isCanPaste() { return ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) && getOptions().isEditable() && ( getCutOrCopiedTree() != null ) && !getCutOrCopiedTree().isEmpty() ); @@ -1397,43 +1123,18 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee .isRoot() || ( _subtree_index > 0 ) ) ); } - final boolean isEdited() { - return _edited; - } - - final private boolean isInFoundNodes( final PhylogenyNode node ) { - return ( ( getFoundNodes() != null ) && getFoundNodes().contains( node.getId() ) ); + final boolean isCurrentTreeIsSubtree() { + return ( _subtree_index > 0 ); } - final private boolean isInOv() { - return _in_ov; + final boolean isEdited() { + return _edited; } final boolean isInOvRect() { return _in_ov_rect; } - 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 boolean isOvOn() { return _ov_on; } @@ -1442,291 +1143,52 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee return _phy_has_branch_lengths; } - final private boolean isUniformBranchLengthsForCladogram() { - return getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP; + 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 private void keyPressedCalls( final KeyEvent e ) { - if ( isOvOn() && ( getMousePosition() != null ) && ( getMousePosition().getLocation() != null ) ) { - if ( inOvVirtualRectangle( getMousePosition().x, getMousePosition().y ) ) { - if ( !isInOvRect() ) { - setInOvRect( true ); - } - } - else if ( isInOvRect() ) { - setInOvRect( false ); + 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 ( 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 ); + if ( y < 0 ) { + y = 0; } - else if ( ( e.getKeyCode() == KeyEvent.VK_SUBTRACT ) || ( e.getKeyCode() == KeyEvent.VK_MINUS ) ) { - getMainPanel().getTreeFontSet().decreaseFontSize(); - getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true ); + final double max_x = getWidth() - getVisibleRect().width; + final double max_y = getHeight() - getVisibleRect().height; + if ( x > max_x ) { + x = max_x; } - else if ( plusPressed( e.getKeyCode() ) ) { - getMainPanel().getTreeFontSet().increaseFontSize(); - getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true ); + if ( y > max_y ) { + y = max_y; } - } - 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 ); - } - else if ( e.getKeyCode() == KeyEvent.VK_DOWN ) { - getMainPanel().getControlPanel().zoomOutY( Constants.WHEEL_ZOOM_OUT_FACTOR ); - getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false ); - } - 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 ); - } - else if ( e.getKeyCode() == KeyEvent.VK_RIGHT ) { - getMainPanel().getControlPanel().zoomInX( Constants.WHEEL_ZOOM_IN_FACTOR, - Constants.WHEEL_ZOOM_IN_FACTOR ); - getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false ); - } - } - else { - 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; - } - else { - final int max_x = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getMaximum() - - getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getVisibleAmount(); - if ( scroll_position.x >= max_x ) { - scroll_position.x = max_x; - } - } - 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; - } - } - repaint(); - getMainPanel().getCurrentScrollPane().getViewport().setViewPosition( scroll_position ); - } - } - 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 ); - } - 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 ); - } - 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 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 { - getMainPanel().getMainFrame().getlabelDirectionCbmi().setSelected( selected ); - } - 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(); - } - 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 ] ) ) { - _node_popup_menu_items[ i ].setEnabled( isCanOpenSeqWeb( node ) ); - } - 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 ] ) ) { - if ( Constants.__RELEASE || Constants.__SNAPSHOT_RELEASE ) { - continue; - } - _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; - } - } - 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() ); - } - 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 ) ); - } - _node_popup_menu_items[ i ].addActionListener( this ); - _node_popup_menu.add( _node_popup_menu_items[ i ] ); - } - } - - 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; - } - setWaitCursor(); - PhylogenyMethods.midpointRoot( _phylogeny ); - resetNodeIdToDistToLeafMap(); - setArrowCursor(); - 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; - } - 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; - } - if ( y > max_y ) { - y = max_y; - } - getMainPanel().getCurrentScrollPane().getViewport() - .setViewPosition( new Point( ForesterUtil.roundToInt( x ), ForesterUtil.roundToInt( y ) ) ); - setInOvRect( true ); - repaint(); + getMainPanel().getCurrentScrollPane().getViewport() + .setViewPosition( new Point( ForesterUtil.roundToInt( x ), ForesterUtil.roundToInt( y ) ) ); + setInOvRect( true ); + repaint(); } else { final PhylogenyNode node = findNode( e.getX(), e.getY() ); @@ -1739,7 +1201,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee if ( ( e.getModifiers() & InputEvent.SHIFT_MASK ) != 0 ) { // Yes, so add to _found_nodes if ( getFoundNodes() == null ) { - setFoundNodes( new HashSet() ); + setFoundNodes( new HashSet() ); } getFoundNodes().add( node.getId() ); // Check if control key is down @@ -1804,8 +1266,8 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee 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() ); + 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 ) { @@ -1840,6 +1302,10 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee 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(); @@ -1871,8 +1337,14 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } final PhylogenyNode node = findNode( e.getX(), e.getY() ); if ( ( node != null ) && ( node.isRoot() || !node.getParent().isCollapse() ) ) { - // cursor is over a tree node - if ( ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.CUT_SUBTREE ) + if ( ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.GET_EXT_DESC_DATA ) ) { + for( final PhylogenyNode n : node.getAllExternalDescendants() ) { + addToCurrentExternalNodes( n.getId() ); + } + 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 ) @@ -1897,132 +1369,1902 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee setCursor( ARROW_CURSOR ); } - final public void mouseWheelMoved( final MouseWheelEvent e ) { - final int notches = e.getWheelRotation(); - if ( inOvVirtualRectangle( e ) ) { - if ( !isInOvRect() ) { - setInOvRect( true ); - repaint(); - } - } - else { - if ( isInOvRect() ) { + 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, isInFoundNodes( c ) + || isInCurrentExternalNodes( c ) ); + if ( c.isExternal() ) { + final boolean is_in_found_nodes = isInFoundNodes( 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 ); + } + } + + 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( getTreeColorSet().getFoundColor() ); + drawRectFilled( c.getXSecondary() - 1, c.getYSecondary() - 1, 3, 3, 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 { + //TODO remove me + System.out.println( "is collapse" + n.getName() ); + } + } + paintCirculars( phy.getRoot(), phy, center_x, center_y, radius, radial_labels, g, to_pdf, to_graphics_file ); + paintNodeBox( _root.getXcoord(), _root.getYcoord(), _root, g, to_pdf, to_graphics_file, isInFoundNodes( _root ) ); + } + + 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 ( getOptions().isPrintBlackAndWhite() ) { + g.setColor( Color.WHITE ); + } + g.fillRect( graphics_file_x, graphics_file_y, graphics_file_width, graphics_file_height ); + } + } + 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 { + 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 ); + } + 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 ( ( _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 PhylogenyNodeIterator it; + //for( it = _phylogeny.iteratorPreorder(); it.hasNext(); ) { + // paintNodeRectangular( g, it.next(), to_pdf, getControlPanel().isDynamicallyHideData() + // && ( dynamic_hiding_factor > 1 ), dynamic_hiding_factor, to_graphics_file ); + //} + for( final PhylogenyNode element : _nodes_in_preorder ) { + paintNodeRectangular( g, element, to_pdf, getControlPanel().isDynamicallyHideData() + && ( dynamic_hiding_factor > 1 ), dynamic_hiding_factor, to_graphics_file ); + } + 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 ); + } + } + 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 ) ( ( getTreeFontSet()._fm_large.getHeight() * 1.5 * getPhylogeny() + .getNumberOfExternalNodes() ) / ( TWO_PI * 10 ) ); + } + if ( getControlPanel().getDynamicallyHideData() != null ) { + if ( _dynamic_hiding_factor > 1 ) { + getControlPanel().setDynamicHidingIsOn( true ); + } + else { + getControlPanel().setDynamicHidingIsOn( false ); + } + } + 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 ); + } + } + 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 ) ( ( getTreeFontSet()._fm_large.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 ); + } + } + } + + final void recalculateMaxDistanceToRoot() { + _max_distance_to_root = PhylogenyMethods.calculateMaxDistanceToRoot( getPhylogeny() ); + } + + /** + * 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 ( 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; + } + getPhylogeny().reRoot( node ); + getPhylogeny().recalculateNumberOfExternalDescendants( true ); + resetNodeIdToDistToLeafMap(); + setNodeInPreorderToNull(); + resetPreferredSize(); + getMainPanel().adjustJScrollPane(); + setEdited( true ); + repaint(); + if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) { + getControlPanel().showWhole(); + } + } + + final void resetNodeIdToDistToLeafMap() { + _nodeid_dist_to_leaf = new HashMap(); + } + + final void resetPreferredSize() { + if ( ( getPhylogeny() == null ) || getPhylogeny().isEmpty() ) { + 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() ); + } + else { + if ( !isNonLinedUpCladogram() && !isUniformBranchLengthsForCladogram() ) { + x = TreePanel.MOVE + + getLongestExtNodeInfo() + + ForesterUtil.roundToInt( getXdistance() + * ( getPhylogeny().getRoot().getNumberOfExternalNodes() + 2 ) ); + } + else { + x = TreePanel.MOVE + + getLongestExtNodeInfo() + + ForesterUtil.roundToInt( getXdistance() + * ( PhylogenyMethods.calculateMaxDepth( getPhylogeny() ) + 1 ) ); + } + } + setPreferredSize( new Dimension( x, y ) ); + } + + final void selectNode( final PhylogenyNode node ) { + if ( ( getFoundNodes() != null ) && getFoundNodes().contains( node.getId() ) ) { + getFoundNodes().remove( node.getId() ); + getControlPanel().setSearchFoundCountsOnLabel( getFoundNodes().size() ); + if ( getFoundNodes().size() < 1 ) { + getControlPanel().searchReset(); + } + } + else { + getControlPanel().getSearchFoundCountsLabel().setVisible( true ); + getControlPanel().getSearchResetButton().setEnabled( true ); + getControlPanel().getSearchResetButton().setVisible( true ); + if ( getFoundNodes() == null ) { + setFoundNodes( new HashSet() ); + } + getFoundNodes().add( node.getId() ); + getControlPanel().setSearchFoundCountsOnLabel( getFoundNodes().size() ); + } + } + + 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 setFoundNodes( final Set found_nodes ) { + _found_nodes = 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 setLongestExtNodeInfo( final int i ) { + _longest_ext_node_info = i; + } + + 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 ); + } + else { + _rendering_hints.put( RenderingHints.KEY_RENDERING, RenderingHints.VALUE_RENDER_SPEED ); + } + } + 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 ); + } + } + + final void setTinyFonts() { + getTreeFontSet().tinyFonts(); + } + + 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.TAXONOMY; + if ( ( !getControlPanel().isShowTaxonomyScientificNames() && !getControlPanel().isShowTaxonomyCode() && !getControlPanel() + .isShowTaxonomyCommonNames() ) ) { + if ( ( getControlPanel().isShowSequenceAcc() || getControlPanel().isShowGeneNames() || getControlPanel() + .isShowGeneSymbols() ) ) { + pri = DESCENDANT_SORT_PRIORITY.SEQUENCE; + } + else if ( getControlPanel().isShowNodeNames() ) { + pri = DESCENDANT_SORT_PRIORITY.NODE_NAME; + } + } + 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; + } + 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 ); + updateSubSuperTreeButton(); + } + 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 ]; + 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; + } + if ( !node.isExternal() ) { + node.swapChildren(); + setNodeInPreorderToNull(); + _phylogeny.externalNodesHaveChanged(); + _phylogeny.clearHashIdToNodeMap(); + _phylogeny.recalculateNumberOfExternalDescendants( true ); + resetNodeIdToDistToLeafMap(); + setEdited( true ); + } + repaint(); + } + + final void taxColor() { + if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) { + return; + } + setWaitCursor(); + TreePanelUtil.colorPhylogenyAccordingToExternalTaxonomy( _phylogeny, this ); + _control_panel.setColorBranches( true ); + if ( _control_panel.getColorBranchesCb() != null ) { + _control_panel.getColorBranchesCb().setSelected( true ); + } + 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; + } + } + + 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 ) ) ); + } + 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.getHeight(); + if ( height > 0 ) { + final float ov_corr = ( float ) ( ( ( getOvMaxWidth() - l ) - getOvXDistance() ) / height ); + setOvXcorrectionFactor( ov_corr > 0 ? ov_corr : 0 ); + } + else { + setOvXcorrectionFactor( 0 ); + } + } + 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().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 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 private void addEmptyNode( final PhylogenyNode node ) { + if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) { + errorMessageNoCutCopyPasteInUnrootedDisplay(); + 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 + "?"; + } + 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; + } + 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().getFoundColor() ); + } + else if ( getControlPanel().isColorBranches() && ( 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'; + } + } + } + if ( type == '?' ) { + if ( SequenceIdParser.isProtein( query ) ) { + type = 'p'; + } + else { + type = 'n'; + } + } + JApplet applet = null; + if ( isApplet() ) { + applet = obtainApplet(); + } + try { + Blast.openNcbiBlastWeb( query, type == 'n', applet, this ); + } + catch ( final Exception e ) { + e.printStackTrace(); + } + if ( Constants.ALLOW_DDBJ_BLAST ) { + try { + System.out.println( "trying: " + query ); + final Blast s = new Blast(); + s.ddbjBlast( query ); + } + catch ( final Exception e ) { + e.printStackTrace(); + } + } + } + } + } + + private final int calcDynamicHidingFactor() { + return ( int ) ( 0.5 + ( getTreeFontSet()._fm_large.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() ); + } + else { + if ( ( factor == 0 ) || isNonLinedUpCladogram() ) { + return getXdistance(); + } + return getXdistance() * factor; + } + } + + 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 = TreePanelUtil.calculateColorFromString( ann_str, false ); + getControlPanel().getAnnotationColors().put( ann_str, c ); + } + if ( c == null ) { + c = getTreeColorSet().getAnnotationColor(); + } + } + } + return c; + } + + final private float calculateOvBranchLengthToParent( final PhylogenyNode node, final int factor ) { + if ( getControlPanel().isDrawPhylogram() ) { + if ( node.getDistanceToParent() < 0.0 ) { + return 0.0f; + } + return ( float ) ( getOvXcorrectionFactor() * node.getDistanceToParent() ); + } + else { + if ( ( factor == 0 ) || isNonLinedUpCladogram() ) { + return getOvXDistance(); + } + return getOvXDistance() * factor; + } + } + + 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 ); + } + + final private void colorizeSubtree( final Color c, + final PhylogenyNode node, + final List additional_nodes ) { + _control_panel.setColorBranches( true ); + if ( _control_panel.getColorBranchesCb() != null ) { + _control_panel.getColorBranchesCb().setSelected( true ); + } + if ( node != null ) { + for( final PreorderTreeIterator it = new PreorderTreeIterator( node ); it.hasNext(); ) { + it.next().getBranchData().setBranchColor( new BranchColor( c ) ); + } + } + if ( additional_nodes != null ) { + for( final PhylogenyNode n : additional_nodes ) { + n.getBranchData().setBranchColor( new BranchColor( c ) ); + } + } + 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 ( ( getFoundNodes() != null ) && !getFoundNodes().isEmpty() ) { + final List additional_nodes = new ArrayList(); + for( final Long id : getFoundNodes() ) { + additional_nodes.add( _phylogeny.getNode( id ) ); + } + 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 ); + dialog.setVisible( true ); + } + + 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(); + } + + 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 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 private void cycleColors() { + getMainPanel().getTreeColorSet().cycleColorScheme(); + for( final TreePanel tree_panel : getMainPanel().getTreePanels() ) { + tree_panel.setBackground( getMainPanel().getTreeColorSet().getBackgroundColor() ); + } + } + + final private void decreaseOvSize() { + if ( ( getOvMaxWidth() > 20 ) && ( getOvMaxHeight() > 20 ) ) { + setOvMaxWidth( getOvMaxWidth() - 5 ); + setOvMaxHeight( getOvMaxHeight() - 5 ); + updateOvSettings(); + getControlPanel().displayedPhylogenyMightHaveChanged( false ); + } + } + + 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 { + _phylogeny.deleteSubtree( node, true ); + } + _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 ); + } + + 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; + } + _line.setLine( x1, y1, x2, y2 ); + g.draw( _line ); + } + + 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 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 double x, + final double y, + final double width, + final double 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( ( float ) x, + ( float ) y, + color_1, + ( float ) ( x + width ), + ( float ) ( y + heigth ), + color_2, + false ) ); + g.fill( _ellipse ); + if ( color_border != null ) { + g.setPaint( color_border ); + g.draw( _ellipse ); + } + } + + 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 double x, + final double y, + final double width, + final double 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( ( float ) x, + ( float ) y, + color_1, + ( float ) ( x + width ), + ( float ) ( y + heigth ), + color_2, + false ) ); + g.fill( _rectangle ); + if ( color_border != null ) { + g.setPaint( color_border ); + g.draw( _rectangle ); + } + } + + 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 ); + } + } + 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; + } + + 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 private Set getCopiedAndPastedNodes() { + return getMainPanel().getCopiedAndPastedNodes(); + } + + final private Set getCurrentExternalNodes() { + return _current_external_nodes; + } + + final private Phylogeny getCutOrCopiedTree() { + return getMainPanel().getCutOrCopiedTree(); + } + + final private float getLastDragPointX() { + return _last_drag_point_x; + } + + final private float getLastDragPointY() { + return _last_drag_point_y; + } + + 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; + } + else { + return _nodeid_dist_to_leaf.get( node.getId() ); + } + } + + final private double getMaxDistanceToRoot() { + if ( _max_distance_to_root < 0 ) { + recalculateMaxDistanceToRoot(); + } + 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 double getScaleDistance() { + return _scale_distance; + } + + final private String getScaleLabel() { + return _scale_label; + } + + final private TreeFontSet getTreeFontSet() { + return getMainPanel().getTreeFontSet(); + } + + final private float getUrtFactor() { + return _urt_factor; + } + + final private float getUrtFactorOv() { + return _urt_factor_ov; + } + + 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 OPEN_SEQ_WEB: + openSeqWeb( node ); + break; + case BLAST: + blast( node ); + break; + case OPEN_TAX_WEB: + openTaxWeb( 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 increaseCurrentExternalNodesDataBufferChangeCounter() { + _current_external_nodes_data_buffer_change_counter++; + } + + 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 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 initializeOvSettings() { + setOvMaxHeight( getConfiguration().getOvMaxHeight() ); + setOvMaxWidth( getConfiguration().getOvMaxWidth() ); + } + + 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 boolean inOvVirtualRectangle( final MouseEvent e ) { + return ( inOvVirtualRectangle( e.getX(), e.getY() ) ); + } + + final private boolean isCanBlast( final PhylogenyNode node ) { + if ( !node.getNodeData().isHasSequence() && ForesterUtil.isEmpty( node.getName() ) ) { + return false; + } + return Blast.isContainsQueryForBlast( node ); + } + + final private String isCanOpenSeqWeb( final PhylogenyNode node ) { + String v = ForesterUtil.extractUniProtKbProteinSeqIdentifier( node ); + if ( ForesterUtil.isEmpty( v ) ) { + v = ForesterUtil.extractGenbankAccessor( node ); + } + if ( ForesterUtil.isEmpty( v ) ) { + v = ForesterUtil.extractRefSeqAccessorAccessor( node ); + } + if ( ForesterUtil.isEmpty( v ) ) { + v = ForesterUtil.extractGInumber( node ); + } + return v; + } + + 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 private boolean isInCurrentExternalNodes( final PhylogenyNode node ) { + return ( ( getCurrentExternalNodes() != null ) && getCurrentExternalNodes().contains( node.getId() ) ); + } + + final private boolean isInFoundNodes( final PhylogenyNode node ) { + return ( ( getFoundNodes() != null ) && getFoundNodes().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 boolean isUniformBranchLengthsForCladogram() { + return getOptions().getCladogramType() == CLADOGRAM_TYPE.TOTAL_NODE_SUM_DEP; + } + + final private void keyPressedCalls( final KeyEvent e ) { + if ( isOvOn() && ( getMousePosition() != null ) && ( getMousePosition().getLocation() != null ) ) { + if ( inOvVirtualRectangle( getMousePosition().x, getMousePosition().y ) ) { + if ( !isInOvRect() ) { + setInOvRect( true ); + } + } + else if ( isInOvRect() ) { setInOvRect( false ); - repaint(); } } - if ( e.isControlDown() ) { - if ( notches < 0 ) { - getTreeFontSet().increaseFontSize(); - getControlPanel().displayedPhylogenyMightHaveChanged( true ); + 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 { - getTreeFontSet().decreaseFontSize(); - 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.isShiftDown() ) { - if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) - || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) ) { - if ( notches < 0 ) { - for( int i = 0; i < ( -notches ); ++i ) { - setStartingAngle( ( getStartingAngle() % TWO_PI ) + ANGLE_ROTATION_UNIT ); - getControlPanel().displayedPhylogenyMightHaveChanged( false ); + 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 ); + } + else if ( e.getKeyCode() == KeyEvent.VK_DOWN ) { + getMainPanel().getControlPanel().zoomOutY( Constants.WHEEL_ZOOM_OUT_FACTOR ); + getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false ); + } + 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 ); + } + else if ( e.getKeyCode() == KeyEvent.VK_RIGHT ) { + getMainPanel().getControlPanel().zoomInX( Constants.WHEEL_ZOOM_IN_FACTOR, + Constants.WHEEL_ZOOM_IN_FACTOR ); + getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false ); } } else { - for( int i = 0; i < notches; ++i ) { - setStartingAngle( ( getStartingAngle() % TWO_PI ) - ANGLE_ROTATION_UNIT ); - if ( getStartingAngle() < 0 ) { - setStartingAngle( TWO_PI + getStartingAngle() ); + 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; + } + else { + final int max_x = getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getMaximum() + - getMainPanel().getCurrentScrollPane().getHorizontalScrollBar().getVisibleAmount(); + if ( scroll_position.x >= max_x ) { + scroll_position.x = max_x; } - getControlPanel().displayedPhylogenyMightHaveChanged( false ); } + 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; + } + } + repaint(); + getMainPanel().getCurrentScrollPane().getViewport().setViewPosition( scroll_position ); + } + } + 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 ); + } + 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 ); + } + 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 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 { + getMainPanel().getMainFrame().getlabelDirectionCbmi().setSelected( selected ); + } + 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(); + } + 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 ); + } + } + 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 ( notches < 0 ) { - for( int i = 0; i < ( -notches ); ++i ) { - getControlPanel().zoomInY( Constants.WHEEL_ZOOM_IN_FACTOR ); - getControlPanel().displayedPhylogenyMightHaveChanged( false ); - } - } - else { - for( int i = 0; i < notches; ++i ) { - getControlPanel().zoomOutY( Constants.WHEEL_ZOOM_OUT_FACTOR ); - getControlPanel().displayedPhylogenyMightHaveChanged( false ); - } + else if ( title.equals( Configuration.clickto_options[ Configuration.paste_subtree ][ 0 ] ) ) { + if ( !getOptions().isEditable() ) { + continue; } + _node_popup_menu_items[ i ].setEnabled( isCanPaste() ); } - } - 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().displayedPhylogenyMightHaveChanged( false ); + else if ( title.equals( Configuration.clickto_options[ Configuration.edit_node_data ][ 0 ] ) ) { + if ( !getOptions().isEditable() ) { + continue; } } - 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().displayedPhylogenyMightHaveChanged( false ); + else if ( title.equals( Configuration.clickto_options[ Configuration.add_new_node ][ 0 ] ) ) { + if ( !getOptions().isEditable() ) { + continue; } } + 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 ] ); } - requestFocus(); - requestFocusInWindow(); - requestFocus(); - } - - final void multiplyUrtFactor( final float f ) { - _urt_factor *= f; } - final JApplet obtainApplet() { - return ( ( MainPanelApplets ) getMainPanel() ).getApplet(); + private final String obtainTitleForExtDescNodeData() { + switch ( getOptions().getExtDescNodeDataToReturn() ) { + case NODE_NAME: + return "Node 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() ); + } } final private void openSeqWeb( final PhylogenyNode node ) { - if ( !isCanOpenSeqWeb( node ) ) { + if ( ForesterUtil.isEmpty( isCanOpenSeqWeb( node ) ) ) { cannotOpenBrowserWarningMessage( "sequence" ); return; } - String uri_str = null; - final Sequence seq = node.getNodeData().getSequence(); - final String source = seq.getAccession().getSource().toLowerCase(); - String url; - if ( source.toLowerCase().equals( "ncbi" ) ) { - url = Constants.NCBI_ALL_DATABASE_SEARCH; - } - else { - final WebLink weblink = getConfiguration().getWebLink( source ); - url = weblink.getUrl().toString(); - } - try { - uri_str = url + URLEncoder.encode( seq.getAccession().getValue(), ForesterConstants.UTF8 ); - } - catch ( final UnsupportedEncodingException e ) { - Util.showErrorMessage( this, e.toString() ); - e.printStackTrace(); - } + final String uri_str = TreePanelUtil.createUriForSeqWeb( node, getConfiguration(), this ); if ( !ForesterUtil.isEmpty( uri_str ) ) { try { - JApplet applet = null; - if ( isApplet() ) { - applet = obtainApplet(); - } - Util.launchWebBrowser( new URI( uri_str ), isApplet(), applet, "_aptx_seq" ); + AptxUtil.launchWebBrowser( new URI( uri_str ), + isApplet(), + isApplet() ? obtainApplet() : null, + "_aptx_seq" ); } catch ( final IOException e ) { - Util.showErrorMessage( this, e.toString() ); + AptxUtil.showErrorMessage( this, e.toString() ); e.printStackTrace(); } catch ( final URISyntaxException e ) { - Util.showErrorMessage( this, e.toString() ); + AptxUtil.showErrorMessage( this, e.toString() ); e.printStackTrace(); } } @@ -2038,36 +3280,38 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } String uri_str = null; final Taxonomy tax = node.getNodeData().getTaxonomy(); - if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getProvider() ) - && getConfiguration().isHasWebLink( tax.getIdentifier().getProvider().toLowerCase() ) ) { - final String type = tax.getIdentifier().getProvider().toLowerCase(); - final WebLink weblink = getConfiguration().getWebLink( type ); + if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getValue() ) + && tax.getIdentifier().getValue().startsWith( "http://" ) ) { try { - uri_str = weblink.getUrl() + URLEncoder.encode( tax.getIdentifier().getValue(), ForesterConstants.UTF8 ); + uri_str = new URI( tax.getIdentifier().getValue() ).toString(); } - catch ( final UnsupportedEncodingException e ) { - Util.showErrorMessage( this, e.toString() ); + catch ( final URISyntaxException e ) { + AptxUtil.showErrorMessage( this, e.toString() ); + uri_str = null; e.printStackTrace(); } } - else if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getValue() ) - && tax.getIdentifier().getValue().startsWith( "http://" ) ) { + 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 = new URI( tax.getIdentifier().getValue() ).toString(); + uri_str = "http://www.uniprot.org/taxonomy/" + + URLEncoder.encode( tax.getIdentifier().getValue(), ForesterConstants.UTF8 ); } - catch ( final URISyntaxException e ) { - Util.showErrorMessage( this, e.toString() ); - uri_str = null; + catch ( final UnsupportedEncodingException e ) { + AptxUtil.showErrorMessage( this, e.toString() ); e.printStackTrace(); } } else if ( !ForesterUtil.isEmpty( tax.getScientificName() ) ) { try { - uri_str = "http://www.eol.org/search?q=" + uri_str = "http://www.uniprot.org/taxonomy/?query=" + URLEncoder.encode( tax.getScientificName(), ForesterConstants.UTF8 ); } catch ( final UnsupportedEncodingException e ) { - Util.showErrorMessage( this, e.toString() ); + AptxUtil.showErrorMessage( this, e.toString() ); e.printStackTrace(); } } @@ -2077,34 +3321,33 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee + URLEncoder.encode( tax.getTaxonomyCode(), ForesterConstants.UTF8 ); } catch ( final UnsupportedEncodingException e ) { - Util.showErrorMessage( this, e.toString() ); + AptxUtil.showErrorMessage( this, e.toString() ); e.printStackTrace(); } } else if ( !ForesterUtil.isEmpty( tax.getCommonName() ) ) { try { - uri_str = "http://www.eol.org/search?q=" + uri_str = "http://www.uniprot.org/taxonomy/?query=" + URLEncoder.encode( tax.getCommonName(), ForesterConstants.UTF8 ); } catch ( final UnsupportedEncodingException e ) { - Util.showErrorMessage( this, e.toString() ); + AptxUtil.showErrorMessage( this, e.toString() ); e.printStackTrace(); } } if ( !ForesterUtil.isEmpty( uri_str ) ) { try { - JApplet applet = null; - if ( isApplet() ) { - applet = obtainApplet(); - } - Util.launchWebBrowser( new URI( uri_str ), isApplet(), applet, "_aptx_tax" ); + AptxUtil.launchWebBrowser( new URI( uri_str ), + isApplet(), + isApplet() ? obtainApplet() : null, + "_aptx_tax" ); } catch ( final IOException e ) { - Util.showErrorMessage( this, e.toString() ); + AptxUtil.showErrorMessage( this, e.toString() ); e.printStackTrace(); } catch ( final URISyntaxException e ) { - Util.showErrorMessage( this, e.toString() ); + AptxUtil.showErrorMessage( this, e.toString() ); e.printStackTrace(); } } @@ -2113,65 +3356,6 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } } - 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, isInFoundNodes( c ) ); - if ( c.isExternal() ) { - final boolean is_in_found_nodes = isInFoundNodes( 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 ); - } - } - - 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 ) ) { - g.setColor( getTreeColorSet().getFoundColor() ); - drawRectFilled( c.getXSecondary() - 1, c.getYSecondary() - 1, 3, 3, g ); - } - } - final private void paintBranchLength( final Graphics2D g, final PhylogenyNode node, final boolean to_pdf, @@ -2243,7 +3427,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee final private void paintBranchRectangular( final Graphics2D g, final float x1, final float x2, - float y1, + final float y1, final float y2, final PhylogenyNode node, final boolean to_pdf, @@ -2264,131 +3448,87 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee g.draw( _cubic_curve ); } else { - float x2a = x2; - float x1a = x1; - // draw the vertical line - boolean draw_horizontal = true; + final float x2a = x2; + final float x1a = x1; float y2_r = 0; if ( node.isFirstChildNode() || node.isLastChildNode() || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) { - boolean draw_vertical = true; - final PhylogenyNode parent = node.getParent(); - if ( ( ( getOptions().isShowNodeBoxes() && !to_pdf && !to_graphics_file ) || ( ( getControlPanel() - .isEvents() ) && ( parent != null ) && parent.isHasAssignedEvent() ) ) - && ( _phylogeny.isRooted() || !( ( parent != null ) && parent.isRoot() ) ) - && !( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() && !parent - .isDuplication() ) ) { - if ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) - && ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) { - if ( Math.abs( y2 - y1 ) <= TreePanel.HALF_BOX_SIZE ) { - draw_vertical = false; - } - else { - if ( y1 < y2 ) { - y1 += TreePanel.HALF_BOX_SIZE; - } - else { - if ( !to_pdf ) { - y1 -= TreePanel.HALF_BOX_SIZE + 1; - } - else { - y1 -= TreePanel.HALF_BOX_SIZE; - } - } - } - } - if ( ( x2 - x1 ) <= TreePanel.HALF_BOX_SIZE ) { - draw_horizontal = false; - } - else if ( !draw_vertical ) { - x1a += TreePanel.HALF_BOX_SIZE; - } - if ( ( ( x2 - x1a ) > TreePanel.HALF_BOX_SIZE ) - && !( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() && !node - .isDuplication() ) ) { - x2a -= TreePanel.HALF_BOX_SIZE; - } + if ( !to_graphics_file + && !to_pdf + && ( ( ( y2 < ( getVisibleRect().getMinY() - 20 ) ) && ( y1 < ( getVisibleRect().getMinY() - 20 ) ) ) || ( ( y2 > ( getVisibleRect() + .getMaxY() + 20 ) ) && ( y1 > ( getVisibleRect().getMaxY() + 20 ) ) ) ) ) { + // Do nothing. } - if ( draw_vertical ) { - if ( !to_graphics_file - && !to_pdf - && ( ( ( y2 < getVisibleRect().getMinY() - 20 ) && ( y1 < getVisibleRect().getMinY() - 20 ) ) || ( ( y2 > getVisibleRect() - .getMaxY() + 20 ) && ( y1 > getVisibleRect().getMaxY() + 20 ) ) ) ) { - // Do nothing. - } - else { - if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) { - float x2c = x1 + EURO_D; - if ( x2c > x2a ) { - x2c = x2a; - } - drawLine( x1, y1, x2c, y2, g ); + else { + if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) { + float x2c = x1 + EURO_D; + if ( x2c > x2a ) { + x2c = x2a; } - else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) { - if ( y2 > y1 ) { - y2_r = y2 - ROUNDED_D; - if ( y2_r < y1 ) { - y2_r = y1; - } - drawLine( x1, y1, x1, y2_r, g ); - } - else { - y2_r = y2 + ROUNDED_D; - if ( y2_r > y1 ) { - y2_r = y1; - } - drawLine( x1, y1, x1, y2_r, g ); + drawLine( x1, y1, x2c, y2, g ); + } + else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) { + if ( y2 > y1 ) { + y2_r = y2 - ROUNDED_D; + if ( y2_r < y1 ) { + y2_r = y1; } + drawLine( x1, y1, x1, y2_r, g ); } else { - drawLine( x1, y1, x1, y2, g ); + y2_r = y2 + ROUNDED_D; + if ( y2_r > y1 ) { + y2_r = y1; + } + drawLine( x1, y1, x1, y2_r, g ); } } + else { + drawLine( x1, y1, x1, y2, g ); + } } } // draw the horizontal line if ( !to_graphics_file && !to_pdf - && ( ( y2 < getVisibleRect().getMinY() - 20 ) || ( y2 > getVisibleRect().getMaxY() + 20 ) ) ) { + && ( ( y2 < ( getVisibleRect().getMinY() - 20 ) ) || ( y2 > ( getVisibleRect().getMaxY() + 20 ) ) ) ) { return; } float x1_r = 0; - if ( draw_horizontal ) { - if ( !getControlPanel().isWidthBranches() || ( PhylogenyMethods.getBranchWidthValue( node ) == 1 ) ) { - if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) { - x1_r = x1a + ROUNDED_D; - if ( x1_r < x2a ) { - drawLine( x1_r, y2, x2a, y2, g ); - } - } - else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) { - final float x1c = x1a + EURO_D; - if ( x1c < x2a ) { - drawLine( x1c, y2, x2a, y2, g ); - } + if ( !getControlPanel().isWidthBranches() || ( PhylogenyMethods.getBranchWidthValue( node ) == 1 ) ) { + if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) { + x1_r = x1a + ROUNDED_D; + if ( x1_r < x2a ) { + drawLine( x1_r, y2, x2a, y2, g ); } - else { - drawLine( x1a, y2, x2a, y2, g ); + } + else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) { + final float x1c = x1a + EURO_D; + if ( x1c < x2a ) { + drawLine( x1c, y2, x2a, y2, g ); } } else { - final double w = PhylogenyMethods.getBranchWidthValue( node ); - if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) { - x1_r = x1a + ROUNDED_D; - if ( x1_r < x2a ) { - drawRectFilled( x1_r, y2 - ( w / 2 ), x2a - x1_r, w, g ); - } - } - else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) { - final float x1c = x1a + EURO_D; - if ( x1c < x2a ) { - drawRectFilled( x1c, y2 - ( w / 2 ), x2a - x1c, w, g ); - } + drawLine( x1a, y2, x2a, y2, g ); + } + } + else { + final double w = PhylogenyMethods.getBranchWidthValue( node ); + if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) { + x1_r = x1a + ROUNDED_D; + if ( x1_r < x2a ) { + drawRectFilled( x1_r, y2 - ( w / 2 ), x2a - x1_r, w, g ); } - else { - drawRectFilled( x1a, y2 - ( w / 2 ), x2a - x1a, w, g ); + } + else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) { + final float x1c = x1a + EURO_D; + if ( x1c < x2a ) { + drawRectFilled( x1c, y2 - ( w / 2 ), x2a - x1c, w, g ); } } + else { + drawRectFilled( x1a, y2 - ( w / 2 ), x2a - x1a, w, g ); + } } if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) { if ( x1_r > x2a ) { @@ -2404,55 +3544,10 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee g.draw( _arc ); } } - paintNodeBox( x2, y2, node, g, to_pdf, to_graphics_file, isInFoundNodes( node ) ); - } - - 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 ) { - _circ_num_ext_nodes = phy.getNumberOfExternalNodes(); - _root = phy.getRoot(); - _root.setXcoord( center_x ); - _root.setYcoord( center_y ); - paintNodeBox( _root.getXcoord(), _root.getYcoord(), _root, g, to_pdf, to_graphics_file, isInFoundNodes( _root ) ); - final boolean radial_labels = getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL; - double current_angle = starting_angle; - int i = 0; - for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) { - final PhylogenyNode n = it.next(); - n.setXcoord( ( float ) ( center_x + ( radius * Math.cos( current_angle ) ) ) ); - n.setYcoord( ( float ) ( center_y + ( radius * Math.sin( current_angle ) ) ) ); - _urt_nodeid_angle_map.put( n.getId(), current_angle ); - _urt_nodeid_index_map.put( n.getId(), i++ ); - current_angle += ( TWO_PI / _circ_num_ext_nodes ); - } - paintCirculars( phy.getRoot(), phy, center_x, center_y, radius, radial_labels, 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 ) { - _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 ); + if ( node.isExternal() ) { + paintNodeBox( x2, y2, node, g, to_pdf, to_graphics_file, isInFoundNodes( node ) + || isInCurrentExternalNodes( node ) ); } - paintCircularsLite( phy.getRoot(), phy, center_x, center_y, radius, g ); } final private double paintCirculars( final PhylogenyNode n, @@ -2464,9 +3559,9 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee final Graphics2D g, final boolean to_pdf, final boolean to_graphics_file ) { - if ( n.isExternal() ) { + if ( n.isExternal() || n.isCollapse() ) { //~~circ collapse if ( !_urt_nodeid_angle_map.containsKey( n.getId() ) ) { - System.out.println( "no " + n + ", fucker!" );//TODO + System.out.println( "no " + n + " =====>>>>>>> ERROR!" );//TODO } return _urt_nodeid_angle_map.get( n.getId() ); } @@ -2486,11 +3581,11 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } double r = 0; if ( !n.isRoot() ) { - r = 1 - ( ( ( double ) _circ_max_depth - PhylogenyMethods.calculateDepth( n ) ) / _circ_max_depth ); + 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 ) ) ); + 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 ); @@ -2515,11 +3610,11 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } float r = 0; if ( !n.isRoot() ) { - r = 1 - ( ( ( float ) _circ_max_depth - PhylogenyMethods.calculateDepth( n ) ) / _circ_max_depth ); + 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 ) ) ); + 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 ); } @@ -2531,21 +3626,22 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee final boolean to_graphics_file, final boolean to_pdf, final boolean is_in_found_nodes ) { + Color c = null; if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) { - g.setColor( Color.BLACK ); + c = Color.BLACK; } else if ( is_in_found_nodes ) { - g.setColor( getTreeColorSet().getFoundColor() ); + c = getTreeColorSet().getFoundColor(); } else if ( getControlPanel().isColorAccordingToTaxonomy() ) { - g.setColor( getTaxonomyBasedColor( node ) ); + c = getTaxonomyBasedColor( node ); } else if ( getOptions().isColorLabelsSameAsParentBranch() && getControlPanel().isColorBranches() && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) { - g.setColor( PhylogenyMethods.getBranchColorValue( node ) ); + c = PhylogenyMethods.getBranchColorValue( node ); } else { - g.setColor( getTreeColorSet().getCollapseFillColor() ); + c = getTreeColorSet().getCollapseFillColor(); } double d = node.getAllExternalDescendants().size(); if ( d > 1000 ) { @@ -2553,78 +3649,81 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } else { d = ( Math.log10( d ) * _y_distance ) / 2.5; - } - if ( d < BOX_SIZE ) { - d = BOX_SIZE; - } - _polygon.reset(); - _polygon.addPoint( ForesterUtil.roundToInt( node.getXcoord() - TreePanel.BOX_SIZE ), - ForesterUtil.roundToInt( node.getYcoord() ) ); - _polygon.addPoint( ForesterUtil.roundToInt( node.getXcoord() + TreePanel.BOX_SIZE ), - ForesterUtil.roundToInt( node.getYcoord() - d ) ); - _polygon.addPoint( ForesterUtil.roundToInt( node.getXcoord() + TreePanel.BOX_SIZE ), - ForesterUtil.roundToInt( node.getYcoord() + d ) ); - g.fillPolygon( _polygon ); - paintNodeData( g, node, to_graphics_file, to_pdf, is_in_found_nodes ); - } - - @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 - public void update( final Graphics g ) { - paint( g ); + } + 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() == NodeVisualization.NodeFill.SOLID ) { + g.setColor( c ); + g.fill( _polygon ); + } + else if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.NONE ) { + g.setColor( getBackground() ); + g.fill( _polygon ); + g.setColor( c ); + g.draw( _polygon ); + } + 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 ); } final private void paintConfidenceValues( final Graphics2D g, final PhylogenyNode node, final boolean to_pdf, final boolean to_graphics_file ) { - String conf_str = ""; final List confidences = node.getBranchData().getConfidences(); - if ( confidences.size() == 1 ) { - final double value = node.getBranchData().getConfidence( 0 ).getValue(); - if ( ( value == Confidence.CONFIDENCE_DEFAULT_VALUE ) || ( value < getOptions().getMinConfidenceValue() ) ) { - return; - } - conf_str = FORMATTER_CONFIDENCE.format( value ); - } - else if ( confidences.size() > 1 ) { - boolean one_ok = false; - boolean not_first = false; - Collections.sort( confidences ); - final StringBuilder sb = new StringBuilder(); - for( final Confidence confidence : confidences ) { - final double value = confidence.getValue(); - if ( value != Confidence.CONFIDENCE_DEFAULT_VALUE ) { - if ( value >= getOptions().getMinConfidenceValue() ) { - one_ok = true; - } - if ( not_first ) { - sb.append( "/" ); - } - else { - not_first = true; + // if ( confidences.size() == 1 ) { + // final double value = node.getBranchData().getConfidence( 0 ).getValue(); + // if ( ( value == Confidence.CONFIDENCE_DEFAULT_VALUE ) || ( value < getOptions().getMinConfidenceValue() ) ) { + // return; + // } + // conf_str = FORMATTER_CONFIDENCE.format( value ); + // } + // else if ( confidences.size() > 1 ) { + boolean one_ok = false; + boolean not_first = false; + Collections.sort( confidences ); + final StringBuilder sb = new StringBuilder(); + String conf_str = ""; + for( final Confidence confidence : confidences ) { + final double value = confidence.getValue(); + if ( value != Confidence.CONFIDENCE_DEFAULT_VALUE ) { + if ( value >= getOptions().getMinConfidenceValue() ) { + one_ok = true; + } + 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( ")" ); } - sb.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( value, getOptions() - .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) ); } } + //} if ( one_ok ) { conf_str = sb.toString(); } @@ -2655,8 +3754,10 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } final private void paintFoundNode( final int x, final int y, final Graphics2D g ) { + final int box_size = getOptions().getDefaultNodeShapeSize(); + final int half_box_size = getOptions().getDefaultNodeShapeSize() / 2; g.setColor( getTreeColorSet().getFoundColor() ); - g.fillRect( x - TreePanel.HALF_BOX_SIZE, y - TreePanel.HALF_BOX_SIZE, TreePanel.BOX_SIZE, TreePanel.BOX_SIZE ); + g.fillRect( x - half_box_size, y - half_box_size, box_size, box_size ); } final private void paintGainedAndLostCharacters( final Graphics2D g, @@ -2713,33 +3814,95 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee paintFoundNode( ForesterUtil.roundToInt( x ), ForesterUtil.roundToInt( y ), g ); } else { + Color outline_color = null; if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) { - g.setColor( Color.BLACK ); + outline_color = Color.BLACK; } - else if ( getControlPanel().isEvents() && Util.isHasAssignedEvent( node ) ) { + else if ( getControlPanel().isEvents() && TreePanelUtil.isHasAssignedEvent( node ) ) { final Event event = node.getNodeData().getEvent(); if ( event.isDuplication() ) { - g.setColor( getTreeColorSet().getDuplicationBoxColor() ); + outline_color = getTreeColorSet().getDuplicationBoxColor(); } else if ( event.isSpeciation() ) { - g.setColor( getTreeColorSet().getSpecBoxColor() ); + outline_color = getTreeColorSet().getSpecBoxColor(); } else if ( event.isSpeciationOrDuplication() ) { - g.setColor( getTreeColorSet().getDuplicationOrSpeciationColor() ); + outline_color = getTreeColorSet().getDuplicationOrSpeciationColor(); } } + else if ( getOptions().isTaxonomyColorizeNodeShapes() ) { + outline_color = getTaxonomyBasedColor( node ); + } else { - assignGraphicsForNodeBoxWithColorForParentBranch( node, g ); + outline_color = getGraphicsForNodeBoxWithColorForParentBranch( node ); + if ( to_pdf && ( outline_color == getTreeColorSet().getBranchColor() ) ) { + outline_color = getTreeColorSet().getBranchColorForPdf(); + } } - if ( ( getOptions().isShowNodeBoxes() && !to_pdf && !to_graphics_file ) + final int box_size = getOptions().getDefaultNodeShapeSize(); + final int half_box_size = box_size / 2; + if ( ( getOptions().isShowDefaultNodeShapesExternal() && node.isExternal() ) + || ( getOptions().isShowDefaultNodeShapesInternal() && node.isInternal() ) || ( getControlPanel().isEvents() && node.isHasAssignedEvent() ) ) { - if ( to_pdf || to_graphics_file ) { - if ( node.isDuplication() || !getOptions().isPrintBlackAndWhite() ) { - drawOvalFilled( x - HALF_BOX_SIZE, y - HALF_BOX_SIZE, BOX_SIZE, BOX_SIZE, g ); + if ( getOptions().getDefaultNodeShape() == NodeShape.CIRCLE ) { + if ( getOptions().getDefaultNodeFill() == NodeFill.GRADIENT ) { + drawOvalGradient( x - half_box_size, + y - half_box_size, + box_size, + box_size, + g, + to_pdf ? Color.WHITE : outline_color, + to_pdf ? outline_color : getBackground(), + outline_color ); + } + else if ( getOptions().getDefaultNodeFill() == NodeFill.NONE ) { + Color background = getBackground(); + if ( to_pdf ) { + background = Color.WHITE; + } + drawOvalGradient( x - half_box_size, + y - half_box_size, + box_size, + box_size, + g, + background, + background, + outline_color ); + } + else if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.SOLID ) { + g.setColor( outline_color ); + drawOvalFilled( x - half_box_size, y - half_box_size, box_size, box_size, g ); } } - else { - drawRectFilled( x - HALF_BOX_SIZE, y - HALF_BOX_SIZE, BOX_SIZE, BOX_SIZE, g ); + else if ( getOptions().getDefaultNodeShape() == NodeVisualization.NodeShape.RECTANGLE ) { + if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.GRADIENT ) { + drawRectGradient( x - half_box_size, + y - half_box_size, + box_size, + box_size, + g, + to_pdf ? Color.WHITE : outline_color, + to_pdf ? outline_color : getBackground(), + outline_color ); + } + else if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.NONE ) { + Color background = getBackground(); + if ( to_pdf ) { + background = Color.WHITE; + } + drawRectGradient( x - half_box_size, + y - half_box_size, + box_size, + box_size, + g, + background, + background, + outline_color ); + } + else if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.SOLID ) { + g.setColor( outline_color ); + drawRectFilled( x - half_box_size, y - half_box_size, box_size, box_size, g ); + } } } } @@ -2756,20 +3919,22 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee if ( getOptions().isShowBranchLengthValues() && ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) ) - && ( !node.isRoot() ) && ( node.getDistanceToParent() != PhylogenyNode.DISTANCE_DEFAULT ) ) { + && ( !node.isRoot() ) && ( node.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) ) { paintBranchLength( g, node, to_pdf, to_graphics_file ); } if ( !getControlPanel().isShowInternalData() && !node.isExternal() && !node.isCollapse() ) { return; } + _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 + TreePanel.HALF_BOX_SIZE, node.getYcoord(), node, g ); + x += drawTaxonomyImage( node.getXcoord() + 2 + half_box_size, node.getYcoord(), node, g ); } if ( ( getControlPanel().isShowTaxonomyCode() || getControlPanel().isShowTaxonomyScientificNames() || getControlPanel() .isShowTaxonomyCommonNames() ) && node.getNodeData().isHasTaxonomy() ) { @@ -2784,6 +3949,11 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee 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().isColorBranches() && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) { g.setColor( PhylogenyMethods.getBranchColorValue( node ) ); @@ -2794,11 +3964,16 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee else { g.setColor( getTreeColorSet().getSequenceColor() ); } - _sb.setLength( 0 ); if ( node.isCollapse() && ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) ) { - _sb.append( " [" ); - _sb.append( node.getAllExternalDescendants().size() ); - _sb.append( "]" ); + if ( _sb.length() > 0 ) { + _sb.setLength( 0 ); + _sb.append( "(" ); + _sb.append( node.getAllExternalDescendants().size() ); + _sb.append( ")" ); + } + } + else { + _sb.setLength( 0 ); } if ( getControlPanel().isShowNodeNames() && ( node.getName().length() > 0 ) ) { if ( _sb.length() > 0 ) { @@ -2830,6 +4005,12 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee _sb.append( node.getNodeData().getSequence().getAccession().getValue() ); } } + if ( getControlPanel().isShowProperties() && node.getNodeData().isHasProperties() ) { + if ( _sb.length() > 0 ) { + _sb.append( " " ); + } + _sb.append( propertiesToString( node ) ); + } g.setFont( getTreeFontSet().getLargeFont() ); if ( is_in_found_nodes ) { g.setFont( getTreeFontSet().getLargeFont().deriveFont( Font.BOLD ) ); @@ -2838,21 +4019,20 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee if ( !node.isExternal() && ( node.getNumberOfDescendants() == 1 ) ) { down_shift_factor = 1; } + final double pos_x = node.getXcoord() + x + 2 + half_box_size; + final double pos_y = ( node.getYcoord() + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ) ); + final String sb_str = _sb.toString(); // GUILHEM_BEG ______________ - final double posX = node.getXcoord() + x + 2 + TreePanel.HALF_BOX_SIZE; - final double posY = ( node.getYcoord() + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ) ); - final int CONFIDENCE_LEFT_MARGIN = 4; - final String sNodeText = _sb.toString(); if ( _control_panel.isShowSequenceRelations() && node.getNodeData().isHasSequence() && ( _query_sequence != null ) ) { int nodeTextBoundsWidth = 0; - if ( sNodeText.length() > 0 ) { - final Rectangle2D node_text_bounds = new TextLayout( sNodeText, g.getFont(), _frc ).getBounds(); //would like to remove this 'new', but how... + 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 ) posX - 1, ( int ) posY - 8, nodeTextBoundsWidth + 5, 11 ); + g.fillRect( ( int ) pos_x - 1, ( int ) pos_y - 8, nodeTextBoundsWidth + 5, 11 ); g.setColor( getTreeColorSet().getBackgroundColor() ); } } @@ -2864,24 +4044,24 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee && 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 + TreePanel.HALF_BOX_SIZE; + final double linePosX = node.getXcoord() + 2 + half_box_size; final String sConfidence = ( !getControlPanel().isShowSequenceRelationConfidence() || ( seqRelation .getConfidence() == null ) ) ? null : " (" + seqRelation.getConfidence().getValue() + ")"; if ( sConfidence != null ) { - double confidenceX = posX; - if ( sNodeText.length() > 0 ) { - confidenceX += new TextLayout( sNodeText, g.getFont(), _frc ).getBounds().getWidth() + double 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, posY, g ); + 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 ( ( 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 */ @@ -2889,16 +4069,16 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee else { nodeTextBoundsWidth += 2; } - g.drawLine( ( int ) linePosX + 1, 3 + ( int ) posY, ( int ) linePosX + x - + nodeTextBoundsWidth, 3 + ( int ) posY ); + g.drawLine( ( int ) linePosX + 1, 3 + ( int ) pos_y, ( int ) linePosX + x + + nodeTextBoundsWidth, 3 + ( int ) pos_y ); break; } } } } } - if ( sNodeText.length() > 0 ) { - TreePanel.drawString( sNodeText, posX, posY, g ); + if ( sb_str.length() > 0 ) { + TreePanel.drawString( sb_str, pos_x, pos_y, g ); } // GUILHEM_END _____________ // COMMENTED_OUT_BY_GUILHEM_BEG _______________ @@ -2914,15 +4094,15 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee if ( _sb.length() > 0 ) { x += getTreeFontSet()._fm_large.stringWidth( _sb.toString() ) + 5; } - final Annotation ann = node.getNodeData().getSequence().getAnnotation( 0 ); + final SortedSet ann = node.getNodeData().getSequence().getAnnotations(); if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) { g.setColor( Color.BLACK ); } - else { + else if ( getControlPanel().isColorAccordingToAnnotation() ) { g.setColor( calculateColorForAnnotation( ann ) ); } - final String ann_str = ann.asSimpleText().toString(); - TreePanel.drawString( ann_str, node.getXcoord() + x + 3 + TreePanel.HALF_BOX_SIZE, node.getYcoord() + final String ann_str = TreePanelUtil.createAnnotationString( ann, getOptions().isShowAnnotationRefSource() ); + TreePanel.drawString( ann_str, node.getXcoord() + x + 3 + half_box_size, node.getYcoord() + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g ); _sb.setLength( 0 ); _sb.append( ann_str ); @@ -2943,35 +4123,18 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } if ( getControlPanel().isShowBinaryCharacters() ) { TreePanel.drawString( node.getNodeData().getBinaryCharacters().getPresentCharactersAsStringBuffer() - .toString(), node.getXcoord() + x + 1 + TreePanel.HALF_BOX_SIZE, node.getYcoord() + .toString(), node.getXcoord() + x + 1 + half_box_size, node.getYcoord() + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g ); paintGainedAndLostCharacters( g, node, node.getNodeData().getBinaryCharacters() .getGainedCharactersAsStringBuffer().toString(), node.getNodeData().getBinaryCharacters() .getLostCharactersAsStringBuffer().toString() ); } else { - if ( DRAW_MEAN_COUNTS && node.isInternal() ) { - final List ec = node.getAllExternalDescendants(); - double sum = 0; - int count = 0; - for( final PhylogenyNode phylogenyNode : ec ) { - count++; - if ( phylogenyNode.getNodeData().getBinaryCharacters() != null ) { - sum += phylogenyNode.getNodeData().getBinaryCharacters().getPresentCount(); - } - } - final double mean = ForesterUtil.round( sum / count, 1 ); - TreePanel.drawString( " " + node.getNodeData().getBinaryCharacters().getPresentCount() + " [" - + mean + "]", node.getXcoord() + x + 4 + TreePanel.HALF_BOX_SIZE, node.getYcoord() - + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g ); - } - else { - TreePanel.drawString( " " + node.getNodeData().getBinaryCharacters().getPresentCount(), - node.getXcoord() + x + 4 + TreePanel.HALF_BOX_SIZE, - node.getYcoord() - + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), - g ); - } + TreePanel.drawString( " " + node.getNodeData().getBinaryCharacters().getPresentCount(), + node.getXcoord() + x + 4 + half_box_size, + node.getYcoord() + + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), + g ); paintGainedAndLostCharacters( g, node, "+" + node.getNodeData().getBinaryCharacters().getGainedCount(), "-" + node.getNodeData().getBinaryCharacters().getLostCount() ); @@ -2980,55 +4143,6 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } } - 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 ); - } - } - 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; - } - final private void paintNodeDataUnrootedCirc( final Graphics2D g, final PhylogenyNode node, final boolean to_pdf, @@ -3048,6 +4162,11 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee 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 { g.setColor( getTreeColorSet().getSequenceColor() ); } @@ -3164,12 +4283,12 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee final private void paintNodeLite( final Graphics2D g, final PhylogenyNode node ) { if ( node.isCollapse() ) { - if ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) { + if ( !node.isRoot() && !node.getParent().isCollapse() ) { paintCollapsedNode( g, node, false, false, false ); } return; } - if ( isInFoundNodes( node ) ) { + if ( isInFoundNodes( node ) || isInCurrentExternalNodes( node ) ) { g.setColor( getTreeColorSet().getFoundColor() ); drawRectFilled( node.getXSecondary() - 1, node.getYSecondary() - 1, 3, 3, g ); } @@ -3216,9 +4335,9 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee final boolean dynamically_hide, final int dynamic_hiding_factor, final boolean to_graphics_file ) { - final boolean is_in_found_nodes = isInFoundNodes( node ); + final boolean is_in_found_nodes = isInFoundNodes( node ) || isInCurrentExternalNodes( node ); if ( node.isCollapse() ) { - if ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) { + if ( ( !node.isRoot() && !node.getParent().isCollapse() ) ) { paintCollapsedNode( g, node, to_graphics_file, to_pdf, is_in_found_nodes ); } return; @@ -3227,7 +4346,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee ++_external_node_index; } // Confidence values - if ( getControlPanel().isShowBootstrapValues() + if ( getControlPanel().isShowConfidenceValues() && !node.isExternal() && !node.isRoot() && ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) @@ -3298,11 +4417,13 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee child_node.setYcoord( y2 ); y2 += _y_distance * child_node.getNumberOfExternalNodes(); } + paintNodeBox( node.getXcoord(), node.getYcoord(), node, g, to_pdf, to_graphics_file, isInFoundNodes( node ) + || isInCurrentExternalNodes( node ) ); } 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() < getTreeFontSet()._fm_large + && ( ( node.isExternal() && ( ( _external_node_index % dynamic_hiding_factor ) != 1 ) ) || ( !node + .isExternal() && ( ( new_x_min < 20 ) || ( ( _y_distance * node.getNumberOfExternalNodes() ) < getTreeFontSet()._fm_large .getHeight() ) ) ) ) ) { return; } @@ -3321,281 +4442,142 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee return; } if ( getControlPanel().isShowDomainArchitectures() && node.getNodeData().isHasSequence() - && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) { - RenderableDomainArchitecture rds = null; - if ( node.getNodeData().getSequence().getDomainArchitecture() instanceof RenderableDomainArchitecture ) { - try { - rds = ( RenderableDomainArchitecture ) node.getNodeData().getSequence().getDomainArchitecture(); - } - catch ( final ClassCastException cce ) { - cce.printStackTrace(); - return; - } - rds.setRenderingHeight( 6 ); - int x = 0; - if ( getControlPanel().isShowTaxonomyCode() && ( PhylogenyMethods.getSpecies( node ).length() > 0 ) ) { - x += getTreeFontSet()._fm_large_italic.stringWidth( PhylogenyMethods.getSpecies( node ) + " " ); - } - if ( getControlPanel().isShowNodeNames() && ( node.getName().length() > 0 ) ) { - x += getTreeFontSet()._fm_large.stringWidth( node.getName() + " " ); - } - rds.render( node.getXcoord() + x, node.getYcoord() - 3, g, this, to_pdf ); - } - } - ////////////// - if ( getControlPanel().isShowVectorData() && ( node.getNodeData().getVector() != null ) - && ( node.getNodeData().getVector().size() > 0 ) && ( getStatisticsForExpressionValues() != null ) ) { - final RenderableVector rv = RenderableVector.createInstance( node.getNodeData().getVector(), - getStatisticsForExpressionValues(), - getConfiguration() ); - int x = 0; - PhylogenyNode my_node = node; - if ( !getControlPanel().isDrawPhylogram() ) { - my_node = getPhylogeny().getFirstExternalNode(); - } - if ( getControlPanel().isShowTaxonomyCode() && ( PhylogenyMethods.getSpecies( my_node ).length() > 0 ) ) { - x += getTreeFontSet()._fm_large_italic.stringWidth( PhylogenyMethods.getSpecies( my_node ) + " " ); - } - if ( getControlPanel().isShowNodeNames() && ( my_node.getName().length() > 0 ) ) { - x += getTreeFontSet()._fm_large.stringWidth( my_node.getName() + " " ); - } - rv.render( my_node.getXcoord() + x, node.getYcoord() - 5, g, this, to_pdf ); - } - ////////////// - } - - 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().getFoundColor() ); - getOvRectangle().setRect( x, y, width, height ); - 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 ); - } - } - - 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 ) { - /* GUILHEM_BEG */ - // System.out.println( "p" + ( xxx++ ) ); - _query_sequence = _control_panel.getSelectedQuerySequence(); - /* GUILHEM_END */ - // 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 ( getOptions().isPrintBlackAndWhite() ) { - g.setColor( Color.WHITE ); - } - g.fillRect( graphics_file_x, graphics_file_y, graphics_file_width, graphics_file_height ); - } - } - 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 { - 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 ); - } - } - g.setStroke( new BasicStroke( 1 ) ); - } - 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 ( ( _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 = ( int ) ( getTreeFontSet()._fm_large.getHeight() / ( 1.5 * getYdistance() ) ); - if ( getControlPanel().isDynamicallyHideData() ) { - if ( dynamic_hiding_factor > 1 ) { - getControlPanel().setDynamicHidingIsOn( true ); - } - else { - getControlPanel().setDynamicHidingIsOn( false ); - } - } - final PhylogenyNodeIterator it; - for( it = _phylogeny.iteratorPreorder(); it.hasNext(); ) { - paintNodeRectangular( g, it.next(), to_pdf, getControlPanel().isDynamicallyHideData() - && ( dynamic_hiding_factor > 1 ), dynamic_hiding_factor, to_graphics_file ); - } - 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 ); - } - } - 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 ) ( ( getTreeFontSet()._fm_large.getHeight() * 1.5 * getPhylogeny() - .getNumberOfExternalNodes() ) / ( TWO_PI * 10 ) ); - } - if ( getControlPanel().getDynamicallyHideData() != null ) { - if ( _dynamic_hiding_factor > 1 ) { - getControlPanel().setDynamicHidingIsOn( true ); - } - else { - getControlPanel().setDynamicHidingIsOn( false ); + && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) { + RenderableDomainArchitecture rds = null; + if ( node.getNodeData().getSequence().getDomainArchitecture() instanceof RenderableDomainArchitecture ) { + try { + rds = ( RenderableDomainArchitecture ) node.getNodeData().getSequence().getDomainArchitecture(); } - } - 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 ); + catch ( final ClassCastException cce ) { + cce.printStackTrace(); } - else { - paintScale( g, graphics_file_x, graphics_file_y + graphics_file_height, to_pdf, to_graphics_file ); + if ( rds != null ) { + rds.setRenderingHeight( 6 ); + int x = 0; + if ( node.getNodeData().isHasTaxonomy() ) { + if ( getControlPanel().isShowTaxonomyCode() + && ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getTaxonomyCode() ) ) ) { + x += getTreeFontSet()._fm_large_italic.stringWidth( node.getNodeData().getTaxonomy() + .getTaxonomyCode() + + " " ); + } + if ( getControlPanel().isShowTaxonomyScientificNames() + && ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getScientificName() ) ) ) { + x += getTreeFontSet()._fm_large_italic.stringWidth( node.getNodeData().getTaxonomy() + .getScientificName() + + " " ); + } + if ( getControlPanel().isShowTaxonomyCommonNames() + && ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getCommonName() ) ) ) { + x += getTreeFontSet()._fm_large_italic.stringWidth( node.getNodeData().getTaxonomy() + .getCommonName() + + " " ); + } + } + if ( node.getNodeData().isHasSequence() ) { + if ( getControlPanel().isShowGeneNames() + && ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getName() ) ) ) { + x += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getName() + + " " ); + } + if ( getControlPanel().isShowGeneSymbols() + && ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getSymbol() ) ) ) { + x += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getSymbol() + + " " ); + } + if ( getControlPanel().isShowSequenceAcc() + && ( node.getNodeData().getSequence().getAccession() != null ) ) { + x += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence() + .getAccession().toString() + + " " ); + } + if ( getControlPanel().isShowAnnotation() + && ( node.getNodeData().getSequence().getAnnotations() != null ) + && ( !node.getNodeData().getSequence().getAnnotations().isEmpty() ) ) { + x += getTreeFontSet()._fm_large.stringWidth( TreePanelUtil.createAnnotationString( node + .getNodeData().getSequence().getAnnotations(), getOptions() + .isShowAnnotationRefSource() ) + + " " ); + } + } + if ( getControlPanel().isShowNodeNames() && !ForesterUtil.isEmpty( node.getName() ) ) { + x += getTreeFontSet()._fm_large.stringWidth( node.getName() + " " ); + } + rds.render( node.getXcoord() + x, node.getYcoord() - 3, g, this, to_pdf ); } } - 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 ) ( ( getTreeFontSet()._fm_large.getHeight() * 1.5 * getPhylogeny() - .getNumberOfExternalNodes() ) / ( TWO_PI * radius ) ); - } - if ( getControlPanel().getDynamicallyHideData() != null ) { - if ( _dynamic_hiding_factor > 1 ) { - getControlPanel().setDynamicHidingIsOn( true ); - } - else { - getControlPanel().setDynamicHidingIsOn( false ); + ////////////// + 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 ) { + int x = 0; + PhylogenyNode my_node = node; + if ( !getControlPanel().isDrawPhylogram() ) { + my_node = getPhylogeny().getFirstExternalNode(); } - } - 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 ); + if ( getControlPanel().isShowTaxonomyCode() && ( PhylogenyMethods.getSpecies( my_node ).length() > 0 ) ) { + x += getTreeFontSet()._fm_large_italic.stringWidth( PhylogenyMethods.getSpecies( my_node ) + " " ); } - else { - y_scale = ( double ) getWidth() / getHeight(); - y_pos = ForesterUtil.roundToInt( y_pos / y_scale ); + if ( getControlPanel().isShowNodeNames() && ( my_node.getName().length() > 0 ) ) { + x += getTreeFontSet()._fm_large.stringWidth( my_node.getName() + " " ); } - _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 ); + rv.render( my_node.getXcoord() + x, node.getYcoord() - 5, g, this, to_pdf ); + } + } + ////////////// + } + + 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().getFoundColor() ); + 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 private void paintPhylogenyLite( final Graphics2D g ) { - //System.out.println( getVisibleRect().x + " " + getVisibleRect().y ); _phylogeny .getRoot() .setXSecondary( ( float ) ( getVisibleRect().x + getOvXPosition() + ( MOVE / ( getVisibleRect().width / getOvRectangle() .getWidth() ) ) ) ); _phylogeny.getRoot().setYSecondary( ( getVisibleRect().y + getOvYStart() ) ); - final PhylogenyNodeIterator it; - for( it = _phylogeny.iteratorPreorder(); it.hasNext(); ) { - paintNodeLite( g, it.next() ); + final Stroke s = g.getStroke(); + g.setStroke( STROKE_05 ); + for( final PhylogenyNode element : _nodes_in_preorder ) { + paintNodeLite( g, element ); } + g.setStroke( s ); paintOvRectangle( g ); } @@ -3647,12 +4629,15 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee else { g.setColor( getTreeColorSet().getBranchLengthColor() ); } + 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 ); } + g.setStroke( s ); } final private int paintTaxonomy( final Graphics2D g, @@ -3683,7 +4668,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee else { g.setColor( getTreeColorSet().getTaxonomyColor() ); } - final double start_x = node.getXcoord() + 3 + TreePanel.HALF_BOX_SIZE + x_shift; + final double start_x = node.getXcoord() + 3 + ( getOptions().getDefaultNodeShapeSize() / 2 ) + x_shift; final double start_y = node.getYcoord() + ( getTreeFontSet()._fm_large.getAscent() / ( node.getNumberOfDescendants() == 1 ? 1 : 3.0 ) ); _sb.setLength( 0 ); @@ -3740,8 +4725,8 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } final String label = _sb.toString(); /* GUILHEM_BEG */ - if ( ( label.length() > 0 ) && ( node.getNodeData().isHasSequence() ) - && node.getNodeData().getSequence().equals( _query_sequence ) ) { + 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, @@ -3760,18 +4745,6 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } } - private void abbreviateScientificName( final String sn ) { - 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 private void paintUnrooted( final PhylogenyNode n, final double low_angle, final double high_angle, @@ -3782,7 +4755,6 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee if ( n.isRoot() ) { n.setXcoord( getWidth() / 2 ); n.setYcoord( getHeight() / 2 ); - paintNodeBox( n.getXcoord(), n.getYcoord(), n, g, to_pdf, to_graphics_file, isInFoundNodes( n ) ); } if ( n.isExternal() ) { paintNodeDataUnrootedCirc( g, @@ -3791,7 +4763,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee to_graphics_file, radial_labels, ( high_angle + low_angle ) / 2, - isInFoundNodes( n ) ); + isInFoundNodes( n ) || isInCurrentExternalNodes( n ) ); return; } final float num_enclosed = n.getNumberOfExternalNodes(); @@ -3830,16 +4802,20 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee 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 ); + 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 ); - paintNodeBox( new_x, new_y, desc, g, to_pdf, to_graphics_file, isInFoundNodes( desc ) ); paintUnrooted( desc, current_angle, current_angle + arc_size, radial_labels, g, to_pdf, to_graphics_file ); current_angle += arc_size; assignGraphicsForBranchWithColorForParentBranch( desc, false, g, to_pdf, to_graphics_file ); drawLine( x, y, new_x, new_y, g ); + paintNodeBox( new_x, new_y, desc, g, to_pdf, to_graphics_file, isInFoundNodes( desc ) + || isInCurrentExternalNodes( desc ) ); + } + if ( n.isRoot() ) { + paintNodeBox( n.getXcoord(), n.getYcoord(), n, g, to_pdf, to_graphics_file, isInFoundNodes( n ) ); } } @@ -3849,8 +4825,8 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee 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 ); + 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 ); } @@ -3877,213 +4853,120 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee 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 ); + 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 ) ) { + if ( isInFoundNodes( desc ) || isInCurrentExternalNodes( desc ) ) { g.setColor( getTreeColorSet().getFoundColor() ); drawRectFilled( desc.getXSecondary() - 1, desc.getYSecondary() - 1, 3, 3, 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 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 = getASimpleTextRepresentationOfANode( 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(); - buffer_phy.preOrderReId(); - 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 ); - _phylogeny.externalNodesHaveChanged(); - _phylogeny.hashIDs(); - _phylogeny.recalculateNumberOfExternalDescendants( true ); - resetNodeIdToDistToLeafMap(); - setEdited( true ); - if ( need_to_show_whole ) { - getControlPanel().showWhole(); - } - repaint(); - } - - final public int print( final Graphics g, final PageFormat page_format, final int page_index ) - throws PrinterException { - if ( page_index > 0 ) { - return ( NO_SUCH_PAGE ); - } - else { - final Graphics2D g2d = ( Graphics2D ) g; - g2d.translate( page_format.getImageableX(), page_format.getImageableY() ); - // Turn off double buffering !? - paintPhylogeny( g2d, true, false, 0, 0, 0, 0 ); - // Turn double buffering back on !? - return ( PAGE_EXISTS ); - } - } - - final void recalculateMaxDistanceToRoot() { - _max_distance_to_root = PhylogenyMethods.calculateMaxDistanceToRoot( getPhylogeny() ); - } - - /** - * 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; + drawLine( x, y, new_x, new_y, g ); } + } + + final private void pasteSubtree( final PhylogenyNode node ) { if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) { + errorMessageNoCutCopyPasteInUnrootedDisplay(); + return; + } + if ( ( getCutOrCopiedTree() == null ) || getCutOrCopiedTree().isEmpty() ) { JOptionPane.showMessageDialog( this, - "Cannot reroot in unrooted display type", - "Attempt to reroot tree in unrooted display", - JOptionPane.WARNING_MESSAGE ); + "No tree in buffer (need to copy or cut a subtree first)", + "Attempt to paste with empty buffer", + JOptionPane.ERROR_MESSAGE ); return; } - getPhylogeny().reRoot( node ); - getPhylogeny().recalculateNumberOfExternalDescendants( true ); - resetNodeIdToDistToLeafMap(); - resetPreferredSize(); - getMainPanel().adjustJScrollPane(); - repaint(); - if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.CIRCULAR ) { - getControlPanel().showWhole(); + 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; } - } - - final void resetNodeIdToDistToLeafMap() { - _nodeid_dist_to_leaf = new HashMap(); - } - - final void resetPreferredSize() { - if ( ( getPhylogeny() == null ) || getPhylogeny().isEmpty() ) { + else if ( r != 0 ) { 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() ); + 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 ( !isNonLinedUpCladogram() && !isUniformBranchLengthsForCladogram() ) { - x = TreePanel.MOVE - + getLongestExtNodeInfo() - + ForesterUtil.roundToInt( getXdistance() - * ( getPhylogeny().getRoot().getNumberOfExternalNodes() + 2 ) ); + if ( ( node.getNumberOfExternalNodes() == 1 ) && node.isRoot() ) { + need_to_show_whole = true; + _phylogeny = buffer_phy; } else { - x = TreePanel.MOVE - + getLongestExtNodeInfo() - + ForesterUtil.roundToInt( getXdistance() - * ( PhylogenyMethods.calculateMaxDepth( getPhylogeny() ) + 1 ) ); + buffer_phy.addAsChild( node ); } } - setPreferredSize( new Dimension( x, y ) ); - } - - final void setArrowCursor() { - setCursor( ARROW_CURSOR ); + 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 void setControlPanel( final ControlPanel atv_control ) { - _control_panel = atv_control; + 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 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() ) ); + } + } + return sb; } - final private void setCopiedAndPastedNodes( final Set nodeIds ) { + final private void setCopiedAndPastedNodes( final Set nodeIds ) { getMainPanel().setCopiedAndPastedNodes( nodeIds ); } @@ -4091,42 +4974,10 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee getMainPanel().setCutOrCopiedTree( cut_or_copied_tree ); } - final void setEdited( final boolean edited ) { - _edited = edited; - } - - final void setFoundNodes( final Set found_nodes ) { - _found_nodes = found_nodes; - } - final private void setInOv( final boolean in_ov ) { _in_ov = in_ov; } - 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 setLongestExtNodeInfo( final int i ) { - _longest_ext_node_info = i; - } - - final void setMediumFonts() { - getTreeFontSet().mediumFonts(); - } - final private void setOvMaxHeight( final float ov_max_height ) { _ov_max_height = ov_max_height; } @@ -4135,10 +4986,6 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee _ov_max_width = ov_max_width; } - final void setOvOn( final boolean ov_on ) { - _ov_on = ov_on; - } - final private void setOvXcorrectionFactor( final float f ) { _ov_x_correction_factor = f; } @@ -4163,138 +5010,36 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee _ov_y_start = ov_y_start; } - /** - * Set parameters for printing the displayed tree - * - * @param x - * @param y - */ - final void setParametersForPainting( 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(); - } - 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(); - } - } - - 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 private void setScaleLabel( final String scale_label ) { - _scale_label = scale_label; - } - - final void setSmallFonts() { - getTreeFontSet().smallFonts(); - } - - final void setStartingAngle( final double starting_angle ) { - _urt_starting_angle = starting_angle; - } - - 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 { - _rendering_hints.put( RenderingHints.KEY_RENDERING, RenderingHints.VALUE_RENDER_SPEED ); - } - } - if ( getMainPanel().getOptions().isAntialiasScreen() ) { - if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) { - _rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_OFF ); - } - else { - _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 ); - } - } - - final void setTinyFonts() { - getTreeFontSet().tinyFonts(); - } - - /** - * Set a phylogeny tree. - * - * @param t - * an instance of a Phylogeny - */ - final void setTree( final Phylogeny t ) { - _phylogeny = t; + _scale_distance = scale_distance; } - final void setTreeFile( final File treefile ) { - _treefile = treefile; + final private void setScaleLabel( final String scale_label ) { + _scale_label = scale_label; + } + + private final void setupStroke( final Graphics2D g ) { + 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 ) { + g.setStroke( STROKE_1 ); + } + else { + g.setStroke( STROKE_2 ); + } } final private void setUpUrtFactor() { @@ -4323,37 +5068,210 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee _urt_factor_ov = urt_factor_ov; } - final void setWaitCursor() { - setCursor( WAIT_CURSOR ); - repaint(); - } - - final void setXcorrectionFactor( final float f ) { - _x_correction_factor = f; - } - - final void setXdistance( final float x ) { - _x_distance = x; + private void showExtDescNodeData( final PhylogenyNode node ) { + final List data = new ArrayList(); + for( final PhylogenyNode n : node.getAllExternalDescendants() ) { + 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 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 ( 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 = ann.toString().trim(); + if ( ann_str.endsWith( "|" ) ) { + ann_str = ann_str.substring( 0, ann_str.length() - 1 ); + } + 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 = 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 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 { + setCurrentExternalNodesDataBuffer( sb ); + final String 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 ); + } + } + } } - final void setYdistance( final float y ) { - _y_distance = y; + private int makeSB( final List data, final Options optz, final StringBuilder sb ) { + final SortedMap map = new TreeMap(); + if ( ( optz.getExtDescNodeDataToReturn() != NODE_DATA.SEQUENCE_MOL_SEQ ) + && ( optz.getExtDescNodeDataToReturn() != NODE_DATA.SEQUENCE_MOL_SEQ_FASTA ) ) { + for( final String d : data ) { + if ( !ForesterUtil.isEmpty( d ) ) { + if ( map.containsKey( d ) ) { + map.put( d, map.get( d ) + 1 ); + } + else { + map.put( d, 1 ); + } + } + } + } + int size = 0; + if ( ( optz.getExtDescNodeDataToReturn() != NODE_DATA.SEQUENCE_MOL_SEQ ) + && ( optz.getExtDescNodeDataToReturn() != NODE_DATA.SEQUENCE_MOL_SEQ_FASTA ) ) { + for( final Entry e : map.entrySet() ) { + final String v = e.getKey(); + final Object c = e.getValue(); + sb.append( v ); + sb.append( "\t" ); + sb.append( c ); + sb.append( ForesterUtil.LINE_SEPARATOR ); + } + size = map.size(); + } + else { + for( final String d : data ) { + if ( !ForesterUtil.isEmpty( d ) ) { + sb.append( d ); + sb.append( ForesterUtil.LINE_SEPARATOR ); + } + } + size = data.size(); + } + return size; } final private void showNodeDataPopup( final MouseEvent e, final PhylogenyNode node ) { try { if ( ( node.getName().length() > 0 ) - || ( node.getNodeData().isHasTaxonomy() && !isTaxonomyEmpty( node.getNodeData().getTaxonomy() ) ) - || ( node.getNodeData().isHasSequence() && !isSequenceEmpty( node.getNodeData().getSequence() ) ) - || ( node.getNodeData().isHasDate() ) || ( node.getNodeData().isHasDistribution() ) - || node.getBranchData().isHasConfidences() ) { + || ( 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() && !isTaxonomyEmpty( node.getNodeData().getTaxonomy() ) ) { + if ( node.getNodeData().isHasTaxonomy() + && !TreePanelUtil.isTaxonomyEmpty( node.getNodeData().getTaxonomy() ) ) { lines++; boolean enc_data = false; final Taxonomy tax = node.getNodeData().getTaxonomy(); @@ -4435,7 +5353,8 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } } } - if ( node.getNodeData().isHasSequence() && !isSequenceEmpty( node.getNodeData().getSequence() ) ) { + if ( node.getNodeData().isHasSequence() + && !TreePanelUtil.isSequenceEmpty( node.getNodeData().getSequence() ) ) { lines++; boolean enc_data = false; if ( _popup_buffer.length() > 0 ) { @@ -4500,6 +5419,26 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee .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 ) { @@ -4557,81 +5496,6 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } } - 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; - } - 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 = subTree( node, _phylogeny ); - updateSubSuperTreeButton(); - } - else if ( node.isRoot() && isCurrentTreeIsSubtree() ) { - superTree(); - } - _main_panel.getControlPanel().showWhole(); - repaint(); - } - - final boolean isCurrentTreeIsSubtree() { - return ( _subtree_index > 0 ); - } - - final private static Phylogeny subTree( final PhylogenyNode new_root, final Phylogeny source_phy ) { - final Phylogeny new_phy = new Phylogeny(); - new_phy.setRooted( true ); - new_phy.setName( source_phy.getName() ); - new_phy.setDescription( source_phy.getDescription() ); - new_phy.setType( source_phy.getType() ); - new_phy.setDistanceUnit( source_phy.getDistanceUnit() ); - new_phy.setConfidence( source_phy.getConfidence() ); - new_phy.setIdentifier( source_phy.getIdentifier() ); - new_phy.setRoot( new_root.copyNodeDataShallow() ); - int i = 0; - for( final PhylogenyNode n : new_root.getDescendants() ) { - new_phy.getRoot().setChildNode( i++, n ); - } - return new_phy; - } - - final void superTree() { - 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() ) { - _phylogeny.swapChildren( node ); - } - repaint(); - } - final private void switchDisplaygetPhylogenyGraphicsType() { switch ( getPhylogenyGraphicsType() ) { case RECTANGULAR: @@ -4693,159 +5557,40 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } } - final void taxColor() { - if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) { - return; - } - setWaitCursor(); - Util.colorPhylogenyAccordingToExternalTaxonomy( _phylogeny, this ); - _control_panel.setColorBranches( true ); - if ( _control_panel.getColorBranchesCb() != null ) { - _control_panel.getColorBranchesCb().setSelected( 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; - } - } - - 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 ) ) ); - } - 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.getHeight(); - if ( height > 0 ) { - final float ov_corr = ( float ) ( ( ( getOvMaxWidth() - l ) - getOvXDistance() ) / height ); - setOvXcorrectionFactor( ov_corr > 0 ? ov_corr : 0 ); - } - else { - setOvXcorrectionFactor( 0 ); - } - } - else { - setOvOn( false ); - } - } - - 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; - } - } - - final private static void drawString( final int i, final double x, final double y, final Graphics2D g ) { - g.drawString( String.valueOf( i ), ( int ) ( x + 0.5 ), ( int ) ( y + 0.5 ) ); - } - final private static void drawString( final String str, final double x, final double y, final Graphics2D g ) { g.drawString( str, ( int ) ( x + 0.5 ), ( int ) ( y + 0.5 ) ); } - final private static boolean isSequenceEmpty( final Sequence seq ) { - return ( seq.getAccession() == null ) && ForesterUtil.isEmpty( seq.getName() ) - && ForesterUtil.isEmpty( seq.getSymbol() ); - } - - final private static boolean isTaxonomyEmpty( final Taxonomy tax ) { - return ( ( tax.getIdentifier() == null ) && ForesterUtil.isEmpty( tax.getTaxonomyCode() ) - && ForesterUtil.isEmpty( tax.getCommonName() ) && ForesterUtil.isEmpty( tax.getScientificName() ) && tax - .getSynonyms().isEmpty() ); - } - 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 ) ); } - void setStatisticsForExpressionValues( final DescriptiveStatistics statistics_for_expression_values ) { - _statistics_for_vector_data = statistics_for_expression_values; - } - - DescriptiveStatistics getStatisticsForExpressionValues() { - return _statistics_for_vector_data; - } - final private class SubtreeColorizationActionListener implements ActionListener { - JColorChooser _chooser; - PhylogenyNode _node; + JColorChooser _chooser = null; + PhylogenyNode _node = null; + List _additional_nodes = 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 ); + colorizeSubtree( c, _node, _additional_nodes ); } } } - - synchronized void setImageMap( final Hashtable image_map ) { - getMainPanel().setImageMap( image_map ); - } - - synchronized Hashtable getImageMap() { - return getMainPanel().getImageMap(); - } }