From af491ecd10f96da4bd1f06b8a7a01a0aa9d0f516 Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Thu, 29 Nov 2012 01:40:07 +0000 Subject: [PATCH] in progress --- .../org/forester/archaeopteryx/Configuration.java | 6 +- .../org/forester/archaeopteryx/ControlPanel.java | 14 + .../src/org/forester/archaeopteryx/TreePanel.java | 4729 ++++++++++---------- 3 files changed, 2391 insertions(+), 2358 deletions(-) diff --git a/forester/java/src/org/forester/archaeopteryx/Configuration.java b/forester/java/src/org/forester/archaeopteryx/Configuration.java index d232fdd..ad38502 100644 --- a/forester/java/src/org/forester/archaeopteryx/Configuration.java +++ b/forester/java/src/org/forester/archaeopteryx/Configuration.java @@ -150,6 +150,7 @@ public final class Configuration { final static int edit_node_data = 14; final static int sort_descendents = 15; final static int get_ext_desc_data = 16; + final static int select_nodes = 17; // --------------------------- // Display options for trees // --------------------------- @@ -178,7 +179,7 @@ public final class Configuration { { "Open Sequence Web", "display" }, { "Open Taxonomy Web", "display" }, { "Blast", "display" }, { "Cut Subtree", "display" }, { "Copy Subtree", "display" }, { "Paste Subtree", "display" }, { "Delete Subtree/Node", "display" }, { "Add New Node", "display" }, { "Edit Node Data", "display" }, - { "Sort Descendants", "display" }, { "Return", "display" } }; + { "Sort Descendants", "display" }, { "Return", "display" }, { "Select Node(s)", "display" } }; // This option is selected in the dropdown int default_clickto = Configuration.display_node_data; // -------------- @@ -415,6 +416,9 @@ public final class Configuration { else if ( name.equals( "edit_node_data" ) ) { index = Configuration.edit_node_data; } + else if ( name.equals( "select_nodes" ) ) { + index = Configuration.select_nodes; + } else if ( name.equals( "display_node_popup" ) ) { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "configuration key [display_node_popup] is deprecated" ); diff --git a/forester/java/src/org/forester/archaeopteryx/ControlPanel.java b/forester/java/src/org/forester/archaeopteryx/ControlPanel.java index d7df705..1dee33f 100644 --- a/forester/java/src/org/forester/archaeopteryx/ControlPanel.java +++ b/forester/java/src/org/forester/archaeopteryx/ControlPanel.java @@ -134,6 +134,7 @@ final class ControlPanel extends JPanel implements ActionListener { private int _paste_subtree_item; private int _add_new_node_item; private int _edit_node_data_item; + private int _select_nodes_item; private int _get_ext_desc_data; private int _blast_item; // zooming and quick tree manipulation buttons: @@ -1195,6 +1196,9 @@ final class ControlPanel extends JPanel implements ActionListener { else if ( action == _edit_node_data_item ) { setActionWhenNodeClicked( NodeClickAction.EDIT_NODE_DATA ); } + else if ( action == _select_nodes_item ) { + setActionWhenNodeClicked( NodeClickAction.SELECT_NODES ); + } else if ( action == _get_ext_desc_data ) { setActionWhenNodeClicked( NodeClickAction.GET_EXT_DESC_DATA ); } @@ -1483,6 +1487,15 @@ final class ControlPanel extends JPanel implements ActionListener { } cb_index++; } + if ( _configuration.doDisplayClickToOption( Configuration.select_nodes ) ) { + _select_nodes_item = cb_index; + addClickToOption( Configuration.select_nodes, + _configuration.getClickToTitle( Configuration.select_nodes ) ); + if ( default_option == Configuration.select_nodes ) { + selected_index = cb_index; + } + cb_index++; + } } // Set default selection and its action _click_to_combobox.setSelectedIndex( selected_index ); @@ -2010,6 +2023,7 @@ final class ControlPanel extends JPanel implements ActionListener { PASTE_SUBTREE, ADD_NEW_NODE, EDIT_NODE_DATA, + SELECT_NODES, SORT_DESCENDENTS, GET_EXT_DESC_DATA, BLAST; diff --git a/forester/java/src/org/forester/archaeopteryx/TreePanel.java b/forester/java/src/org/forester/archaeopteryx/TreePanel.java index 924eae9..fb1316b 100644 --- a/forester/java/src/org/forester/archaeopteryx/TreePanel.java +++ b/forester/java/src/org/forester/archaeopteryx/TreePanel.java @@ -288,6 +288,26 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee .getNumberOfDigitsAfterCommaForBranchLengthValues() ); } + @Override + final public void actionPerformed( final ActionEvent e ) { + boolean done = false; + final JMenuItem node_popup_menu_item = ( JMenuItem ) e.getSource(); + 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 ] ) { + // Set this as the new default click-to action + _main_panel.getControlPanel().setClickToAction( index ); + final PhylogenyNode node = ( PhylogenyNode ) _node_popup_menu + .getClientProperty( NODE_POPMENU_NODE_CLIENT_PROPERTY ); + handleClickToAction( _control_panel.getActionWhenNodeClicked(), node ); + done = true; + } + } + repaint(); + requestFocusInWindow(); + } + public void checkForVectorProperties( final Phylogeny phy ) { final DescriptiveStatistics stats = new BasicDescriptiveStatistics(); for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) { @@ -347,220 +367,238 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } } - @Override - final public void actionPerformed( final ActionEvent e ) { - boolean done = false; - final JMenuItem node_popup_menu_item = ( JMenuItem ) e.getSource(); - 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 ] ) { - // Set this as the new default click-to action - _main_panel.getControlPanel().setClickToAction( index ); - final PhylogenyNode node = ( PhylogenyNode ) _node_popup_menu - .getClientProperty( NODE_POPMENU_NODE_CLIENT_PROPERTY ); - handleClickToAction( _control_panel.getActionWhenNodeClicked(), node ); - done = true; - } - } - repaint(); - requestFocusInWindow(); + public synchronized Hashtable getImageMap() { + return getMainPanel().getImageMap(); } - 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 public MainPanel getMainPanel() { + return _main_panel; } - 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() ); - } + /** + * Get a pointer to the phylogeny + * + * @return a pointer to the phylogeny + */ + public final Phylogeny getPhylogeny() { + return _phylogeny; } - final Color getGraphicsForNodeBoxWithColorForParentBranch( final PhylogenyNode node ) { - if ( getControlPanel().isColorBranches() && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) { - return ( PhylogenyMethods.getBranchColorValue( node ) ); + @Override + final public void mouseWheelMoved( final MouseWheelEvent e ) { + final int notches = e.getWheelRotation(); + if ( inOvVirtualRectangle( e ) ) { + if ( !isInOvRect() ) { + setInOvRect( true ); + repaint(); + } } else { - return ( getTreeColorSet().getBranchColor() ); + if ( isInOvRect() ) { + setInOvRect( false ); + repaint(); + } } - } - - final private void blast( final PhylogenyNode node ) { - if ( !isCanBlast( node ) ) { - JOptionPane.showMessageDialog( this, - "Insufficient information present", - "Cannot Blast", - JOptionPane.INFORMATION_MESSAGE ); - return; + if ( e.isControlDown() ) { + if ( notches < 0 ) { + getTreeFontSet().increaseFontSize(); + getControlPanel().displayedPhylogenyMightHaveChanged( true ); + } + else { + getTreeFontSet().decreaseFontSize(); + getControlPanel().displayedPhylogenyMightHaveChanged( true ); + } } - 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 ( 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 ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) { - if ( ForesterUtil.seqIsLikelyToBeAa( node.getNodeData().getSequence().getMolecularSequence() ) ) { - type = 'p'; - } - else { - type = 'n'; + } + 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 ); } } - if ( type == '?' ) { - if ( SequenceIdParser.isProtein( query ) ) { - type = 'p'; - } - else { - type = 'n'; + } + else { + if ( notches < 0 ) { + for( int i = 0; i < ( -notches ); ++i ) { + getControlPanel().zoomInY( Constants.WHEEL_ZOOM_IN_FACTOR ); + getControlPanel().displayedPhylogenyMightHaveChanged( false ); } } - 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(); + else { + for( int i = 0; i < notches; ++i ) { + getControlPanel().zoomOutY( Constants.WHEEL_ZOOM_OUT_FACTOR ); + getControlPanel().displayedPhylogenyMightHaveChanged( false ); } } } } - } - - final void calcMaxDepth() { - if ( _phylogeny != null ) { - _circ_max_depth = PhylogenyMethods.calculateMaxDepth( _phylogeny ); + 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 { + 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 ); + } + } } + requestFocus(); + requestFocusInWindow(); + requestFocus(); } - /** - * Calculate the length of the distance between the given node and its - * parent. + @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 setArrowCursor() { + setCursor( ARROW_CURSOR ); + repaint(); + } + + public final void setEdited( final boolean edited ) { + _edited = edited; + } + + public synchronized void setImageMap( final Hashtable image_map ) { + getMainPanel().setImageMap( image_map ); + } + + /** + * Set parameters for printing the displayed tree * - * @param node - * @param ext_node_x - * @factor - * @return the distance value + * @param x + * @param y */ - final private float calculateBranchLengthToParent( final PhylogenyNode node, final float factor ) { - if ( getControlPanel().isDrawPhylogram() ) { - if ( node.getDistanceToParent() < 0.0 ) { - return 0.0f; + public 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(); } - return ( float ) ( getXcorrectionFactor() * node.getDistanceToParent() ); - } - else { - if ( ( factor == 0 ) || isNonLinedUpCladogram() ) { - return getXdistance(); + 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; + } } - return getXdistance() * factor; + 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 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(); - } + /** + * 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 ); } - return c; } final void calculateLongestExtNodeInfo() { @@ -644,21 +682,6 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } } - 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; @@ -711,13 +734,6 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee 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 ); - } - /** * Collapse the tree from the given node * @@ -765,60 +781,6 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee 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 ); - 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 ) ); - } - 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 ); - } - else { - intitial_color = getTreeColorSet().getBranchColor(); - } - _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() { - if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) { - return; - } - setWaitCursor(); - AptxUtil.removeBranchColors( _phylogeny ); - AptxUtil.colorPhylogenyAccordingToConfidenceValues( _phylogeny, this ); - _control_panel.setColorBranches( true ); - if ( _control_panel.getColorBranchesCb() != null ) { - _control_panel.getColorBranchesCb().setSelected( true ); - } - setArrowCursor(); - repaint(); - } - final void colorRank( final String rank ) { if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) { return; @@ -864,228 +826,25 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } } - final private void copySubtree( final PhylogenyNode node ) { - if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) { - errorMessageNoCutCopyPasteInUnrootedDisplay(); + final void confColor() { + if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) { 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() ); + setWaitCursor(); + AptxUtil.removeBranchColors( _phylogeny ); + AptxUtil.colorPhylogenyAccordingToConfidenceValues( _phylogeny, this ); + _control_panel.setColorBranches( true ); + if ( _control_panel.getColorBranchesCb() != null ) { + _control_panel.getColorBranchesCb().setSelected( true ); } - node_ids.add( node.getId() ); - setCopiedAndPastedNodes( node_ids ); + setArrowCursor(); repaint(); } - final private void cutSubtree( final PhylogenyNode node ) { - if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) { - errorMessageNoCutCopyPasteInUnrootedDisplay(); - return; + final void decreaseDomainStructureEvalueThreshold() { + if ( _domain_structure_e_value_thr_exp > -20 ) { + _domain_structure_e_value_thr_exp -= 1; } - 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 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 = 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 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 ); - } - } - - 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 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 ); } /** @@ -1113,24 +872,6 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee return null; } - 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 Configuration getConfiguration() { return _configuration; } @@ -1139,14 +880,6 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee return _control_panel; } - final private Set getCopiedAndPastedNodes() { - return getMainPanel().getCopiedAndPastedNodes(); - } - - final private Phylogeny getCutOrCopiedTree() { - return getMainPanel().getCutOrCopiedTree(); - } - final int getDomainStructureEvalueThreshold() { return _domain_structure_e_value_thr_exp; } @@ -1155,38 +888,17 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee 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() { @@ -1196,14 +908,6 @@ 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; } @@ -1212,55 +916,18 @@ 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 private float getOvYDistance() { - return _ov_y_distance; - } - - final private int getOvYPosition() { - return _ov_y_position; - } - - final private int getOvYStart() { - return _ov_y_start; - } - - /** - * Get a pointer to the phylogeny - * - * @return a pointer to the phylogeny - */ - public 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; } + DescriptiveStatistics getStatisticsForExpressionValues() { + return _statistics_for_vector_data; + } + /** * Find a color for this species name. * @@ -1286,18 +953,6 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee 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; } @@ -1310,197 +965,12 @@ 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; - case SORT_DESCENDENTS: - sortDescendants( node ); - break; - case GET_EXT_DESC_DATA: - showExtDescNodeData( node ); - break; - default: - throw new IllegalArgumentException( "unknown action: " + action ); - } - } - - 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_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_CODE: - if ( n.getNodeData().isHasTaxonomy() - && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) { - data.add( n.getNodeData().getTaxonomy().getTaxonomyCode() ); - } - break; - case UNKNOWN: - AptxUtil.showExtDescNodeDataUserSelectedHelper( getControlPanel(), n, data ); - break; - default: - throw new IllegalArgumentException( "unknown data element: " - + getOptions().getExtDescNodeDataToReturn() ); - } - } // for loop - if ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.CONSOLE ) { - for( final String d : data ) { - if ( !ForesterUtil.isEmpty( d ) ) { - System.out.println( d ); - } - } - } - else if ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.WINODW ) { - final StringBuilder sb = new StringBuilder(); - for( final String d : data ) { - if ( !ForesterUtil.isEmpty( d ) ) { - sb.append( d ); - sb.append( "\n" ); - } - } - if ( sb.length() < 1 ) { - AptxUtil.showInformationMessage( this, - "No Appropriate Data (" + obtainTitleForExtDescNodeData() + ")", - "Descendants of selected node do not contain selected data" ); - } - else { - final String title = "External Descendants " - + ( getOptions().getExtDescNodeDataToReturn() == NODE_DATA.UNKNOWN ? "Data" - : obtainTitleForExtDescNodeData() ) + " (" + data.size() + "/" - + node.getNumberOfExternalNodes() + ") For Node " + node; - if ( getMainPanel().getMainFrame() == null ) { - // Must be "E" applet version. - final ArchaeopteryxE ae = ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet(); - final String s = sb.toString().trim(); - ae.showTextFrame( s, title ); - ae.setCurrentExternalNodesDataBuffer( s ); - } - else { - getMainPanel().getMainFrame().showTextFrame( sb.toString(), title ); - } - } - } - } - - 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_ACC: - return "Sequence Accessors"; - case TAXONOMY_SCIENTIFIC_NAME: - return "Scientific Names"; - case TAXONOMY_CODE: - return "Taxonomy Codes"; - case UNKNOWN: - return "User Selected Data"; - default: - throw new IllegalArgumentException( "unknown data element: " - + getOptions().getExtDescNodeDataToReturn() ); - } - } - 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; @@ -1511,25 +981,6 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee 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; @@ -1583,28 +1034,10 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee + 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() ) ); - } - final boolean isApplet() { return getMainPanel() instanceof MainPanelApplets; } - final private boolean isCanBlast( final PhylogenyNode node ) { - if ( !node.getNodeData().isHasSequence() && ForesterUtil.isEmpty( node.getName() ) ) { - return false; - } - return Blast.isContainsQueryForBlast( node ); - } - final boolean isCanCollapse() { return ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.UNROOTED ); } @@ -1626,37 +1059,6 @@ 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() ); @@ -1671,43 +1073,18 @@ 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; } @@ -1716,331 +1093,87 @@ 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(); + 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; } + getMainPanel().getCurrentScrollPane().getViewport() + .setViewPosition( new Point( ForesterUtil.roundToInt( x ), ForesterUtil.roundToInt( y ) ) ); + setInOvRect( true ); + repaint(); } 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 ); + final PhylogenyNode node = findNode( e.getX(), e.getY() ); + if ( node != null ) { + if ( !node.isRoot() && node.getParent().isCollapse() ) { + return; + } + _highlight_node = node; + // Check if shift key is down + if ( ( e.getModifiers() & InputEvent.SHIFT_MASK ) != 0 ) { + // Yes, so add to _found_nodes + if ( getFoundNodes() == null ) { + setFoundNodes( new HashSet() ); } + getFoundNodes().add( node.getId() ); + // Check if control key is down + } + else if ( ( e.getModifiers() & InputEvent.CTRL_MASK ) != 0 ) { + // Yes, so pop-up menu + displayNodePopupMenu( node, e.getX(), e.getY() ); + // Handle unadorned click } 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; + // Check for right mouse button + if ( e.getModifiers() == 4 ) { + displayNodePopupMenu( node, e.getX(), e.getY() ); } else { - final int max_y = getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getMaximum() - - getMainPanel().getCurrentScrollPane().getVerticalScrollBar().getVisibleAmount(); - if ( scroll_position.y >= max_y ) { - scroll_position.y = max_y; - } + // if not in _found_nodes, clear _found_nodes + handleClickToAction( _control_panel.getActionWhenNodeClicked(), node ); } - repaint(); - getMainPanel().getCurrentScrollPane().getViewport().setViewPosition( scroll_position ); } } - else if ( ( e.getKeyCode() == KeyEvent.VK_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 ] ) ) { - _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() && !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 ] ); - } - } - - 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(); - 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(); - } - else { - final PhylogenyNode node = findNode( e.getX(), e.getY() ); - if ( node != null ) { - if ( !node.isRoot() && node.getParent().isCollapse() ) { - return; - } - _highlight_node = node; - // Check if shift key is down - if ( ( e.getModifiers() & InputEvent.SHIFT_MASK ) != 0 ) { - // Yes, so add to _found_nodes - if ( getFoundNodes() == null ) { - setFoundNodes( new HashSet() ); - } - getFoundNodes().add( node.getId() ); - // Check if control key is down - } - else if ( ( e.getModifiers() & InputEvent.CTRL_MASK ) != 0 ) { - // Yes, so pop-up menu - displayNodePopupMenu( node, e.getX(), e.getY() ); - // Handle unadorned click - } - else { - // Check for right mouse button - if ( e.getModifiers() == 4 ) { - displayNodePopupMenu( node, e.getX(), e.getY() ); - } - else { - // if not in _found_nodes, clear _found_nodes - handleClickToAction( _control_panel.getActionWhenNodeClicked(), node ); - } - } - } - else { - // no node was clicked - _highlight_node = null; + else { + // no node was clicked + _highlight_node = null; } } repaint(); @@ -2147,122 +1280,1848 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee if ( isInOv() ) { setInOv( false ); } - 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 ) - || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.COPY_SUBTREE ) - || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.PASTE_SUBTREE ) - || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.DELETE_NODE_OR_SUBTREE ) - || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.REROOT ) - || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.ADD_NEW_NODE ) ) { - setCursor( CUT_CURSOR ); + 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 ) + || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.COPY_SUBTREE ) + || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.PASTE_SUBTREE ) + || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.DELETE_NODE_OR_SUBTREE ) + || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.REROOT ) + || ( getControlPanel().getActionWhenNodeClicked() == NodeClickAction.ADD_NEW_NODE ) ) { + setCursor( CUT_CURSOR ); + } + else { + setCursor( HAND_CURSOR ); + if ( getControlPanel().isNodeDescPopup() ) { + showNodeDataPopup( e, node ); + } + } + } + else { + setCursor( ARROW_CURSOR ); + } + } + } + + final void mouseReleasedInBrowserPanel( final MouseEvent e ) { + setCursor( ARROW_CURSOR ); + } + + final void multiplyUrtFactor( final float f ) { + _urt_factor *= f; + } + + final JApplet obtainApplet() { + return ( ( MainPanelApplets ) getMainPanel() ).getApplet(); + } + + final void paintBranchCircular( final PhylogenyNode p, + final PhylogenyNode c, + final Graphics2D g, + final boolean radial_labels, + final boolean to_pdf, + final boolean to_graphics_file ) { + final double angle = _urt_nodeid_angle_map.get( c.getId() ); + final double root_x = _root.getXcoord(); + final double root_y = _root.getYcoord(); + final double dx = root_x - p.getXcoord(); + final double dy = root_y - p.getYcoord(); + final double parent_radius = Math.sqrt( ( dx * dx ) + ( dy * dy ) ); + final double arc = ( _urt_nodeid_angle_map.get( p.getId() ) ) - angle; + assignGraphicsForBranchWithColorForParentBranch( c, false, g, to_pdf, to_graphics_file ); + if ( ( c.isFirstChildNode() || c.isLastChildNode() ) + && ( ( Math.abs( parent_radius * arc ) > 1.5 ) || to_pdf || to_graphics_file ) ) { + final double r2 = 2.0 * parent_radius; + drawArc( root_x - parent_radius, root_y - parent_radius, r2, r2, ( -angle - arc ), arc, g ); + } + drawLine( c.getXcoord(), + c.getYcoord(), + root_x + ( Math.cos( angle ) * parent_radius ), + root_y + ( Math.sin( angle ) * parent_radius ), + g ); + paintNodeBox( c.getXcoord(), c.getYcoord(), c, g, to_pdf, to_graphics_file, 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 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 ); + } + } + 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 ); + } + } + 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(); + 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() ); + } + else { + if ( getFoundNodes() == null ) { + setFoundNodes( new HashSet() ); + } + getFoundNodes().add( node.getId() ); + } + } + + final void setControlPanel( final ControlPanel atv_control ) { + _control_panel = atv_control; + } + + 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() ) { + if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) + && !getMainPanel().getOptions().isShowDefaultNodeShapes() + && ( ( getControlPanel() != null ) && !getControlPanel().isShowDomainArchitectures() ) ) { + _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(); + } + + 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 = 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(); + AptxUtil.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 ); + } + } + + 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 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(); + } + } + } + } + } + + /** + * 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 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; + } + + 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 ) { + 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; + } + _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 ) ); + } + 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 ); + } + else { + intitial_color = getTreeColorSet().getBranchColor(); + } + _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 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() ) { + 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 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 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 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 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 ); + } + } + if ( e.getModifiersEx() == InputEvent.CTRL_DOWN_MASK ) { + if ( ( e.getKeyCode() == KeyEvent.VK_DELETE ) || ( e.getKeyCode() == KeyEvent.VK_HOME ) + || ( e.getKeyCode() == KeyEvent.VK_F ) ) { + getMainPanel().getTreeFontSet().mediumFonts(); + getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true ); + } + else if ( ( e.getKeyCode() == KeyEvent.VK_SUBTRACT ) || ( e.getKeyCode() == KeyEvent.VK_MINUS ) ) { + getMainPanel().getTreeFontSet().decreaseFontSize(); + getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true ); + } + else if ( plusPressed( e.getKeyCode() ) ) { + getMainPanel().getTreeFontSet().increaseFontSize(); + getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( true ); + } + } + else { + if ( ( e.getKeyCode() == KeyEvent.VK_DELETE ) || ( e.getKeyCode() == KeyEvent.VK_HOME ) + || ( e.getKeyCode() == KeyEvent.VK_F ) ) { + getControlPanel().showWhole(); + } + else if ( ( e.getKeyCode() == KeyEvent.VK_UP ) || ( e.getKeyCode() == KeyEvent.VK_DOWN ) + || ( e.getKeyCode() == KeyEvent.VK_LEFT ) || ( e.getKeyCode() == KeyEvent.VK_RIGHT ) ) { + if ( e.getModifiersEx() == InputEvent.SHIFT_DOWN_MASK ) { + if ( e.getKeyCode() == KeyEvent.VK_UP ) { + getMainPanel().getControlPanel().zoomInY( Constants.WHEEL_ZOOM_IN_FACTOR ); + getMainPanel().getControlPanel().displayedPhylogenyMightHaveChanged( false ); + } + 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 { - setCursor( HAND_CURSOR ); - if ( getControlPanel().isNodeDescPopup() ) { - showNodeDataPopup( e, node ); + 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 { - setCursor( ARROW_CURSOR ); + else if ( e.getKeyCode() == KeyEvent.VK_X ) { + switchDisplaygetPhylogenyGraphicsType(); + repaint(); } - } - } - - final void mouseReleasedInBrowserPanel( final MouseEvent e ) { - setCursor( ARROW_CURSOR ); - } - - @Override - final public void mouseWheelMoved( final MouseWheelEvent e ) { - final int notches = e.getWheelRotation(); - if ( inOvVirtualRectangle( e ) ) { - if ( !isInOvRect() ) { - setInOvRect( true ); + else if ( e.getKeyCode() == KeyEvent.VK_C ) { + cycleColors(); repaint(); } - } - else { - if ( isInOvRect() ) { - setInOvRect( false ); + else if ( getOptions().isShowOverview() && isOvOn() && ( e.getKeyCode() == KeyEvent.VK_O ) ) { + MainFrame.cycleOverview( getOptions(), this ); repaint(); } - } - if ( e.isControlDown() ) { - if ( notches < 0 ) { - getTreeFontSet().increaseFontSize(); - getControlPanel().displayedPhylogenyMightHaveChanged( true ); + else if ( getOptions().isShowOverview() && isOvOn() && ( e.getKeyCode() == KeyEvent.VK_I ) ) { + increaseOvSize(); } - else { - getTreeFontSet().decreaseFontSize(); - getControlPanel().displayedPhylogenyMightHaveChanged( true ); + else if ( getOptions().isShowOverview() && isOvOn() && ( e.getKeyCode() == KeyEvent.VK_U ) ) { + decreaseOvSize(); } + e.consume(); } - 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 ); - } + } + + 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 ] ) ) { + _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; } - 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 ); - } + _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 ( notches < 0 ) { - for( int i = 0; i < ( -notches ); ++i ) { - getControlPanel().zoomInY( Constants.WHEEL_ZOOM_IN_FACTOR ); - getControlPanel().displayedPhylogenyMightHaveChanged( false ); - } + else if ( title.equals( Configuration.clickto_options[ Configuration.copy_subtree ][ 0 ] ) ) { + if ( !getOptions().isEditable() ) { + continue; } - else { - for( int i = 0; i < notches; ++i ) { - getControlPanel().zoomOutY( Constants.WHEEL_ZOOM_OUT_FACTOR ); - getControlPanel().displayedPhylogenyMightHaveChanged( false ); - } + _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 ( 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_ACC: + return "Sequence Accessors"; + case TAXONOMY_SCIENTIFIC_NAME: + return "Scientific Names"; + case TAXONOMY_CODE: + return "Taxonomy Codes"; + case UNKNOWN: + return "User Selected Data"; + default: + throw new IllegalArgumentException( "unknown data element: " + + getOptions().getExtDescNodeDataToReturn() ); + } } final private void openSeqWeb( final PhylogenyNode node ) { @@ -2372,82 +3231,23 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } if ( !ForesterUtil.isEmpty( uri_str ) ) { try { - JApplet applet = null; - if ( isApplet() ) { - applet = obtainApplet(); - } - AptxUtil.launchWebBrowser( new URI( uri_str ), isApplet(), applet, "_aptx_tax" ); - } - catch ( final IOException e ) { - AptxUtil.showErrorMessage( this, e.toString() ); - e.printStackTrace(); - } - catch ( final URISyntaxException e ) { - AptxUtil.showErrorMessage( this, e.toString() ); - e.printStackTrace(); - } - } - else { - cannotOpenBrowserWarningMessage( "taxonomic" ); - } - } - - final void 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; + JApplet applet = null; + if ( isApplet() ) { + applet = obtainApplet(); + } + AptxUtil.launchWebBrowser( new URI( uri_str ), isApplet(), applet, "_aptx_tax" ); + } + catch ( final IOException e ) { + AptxUtil.showErrorMessage( this, e.toString() ); + e.printStackTrace(); + } + catch ( final URISyntaxException e ) { + AptxUtil.showErrorMessage( this, e.toString() ); + e.printStackTrace(); } - 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 ); + else { + cannotOpenBrowserWarningMessage( "taxonomic" ); } } @@ -2644,80 +3444,6 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } } - 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 ) ); - } - - 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 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 private double paintCirculars( final PhylogenyNode n, final Phylogeny phy, final float center_x, @@ -2849,29 +3575,6 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee 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 private void paintConfidenceValues( final Graphics2D g, final PhylogenyNode node, final boolean to_pdf, @@ -3273,131 +3976,52 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee x += getTreeFontSet()._fm_large.stringWidth( _sb.toString() ) + 5; } final Annotation ann = node.getNodeData().getSequence().getAnnotation( 0 ); - if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) { - g.setColor( Color.BLACK ); - } - else { - g.setColor( calculateColorForAnnotation( ann ) ); - } - final String ann_str = ann.asSimpleText().toString(); - 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 ); - } - if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) - || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) - || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) { - if ( ( getControlPanel().isShowBinaryCharacters() || getControlPanel().isShowBinaryCharacterCounts() ) - && node.getNodeData().isHasBinaryCharacters() ) { - if ( _sb.length() > 0 ) { - x += getTreeFontSet()._fm_large.stringWidth( _sb.toString() ) + 5; - } - if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) { - g.setColor( Color.BLACK ); - } - else { - g.setColor( getTreeColorSet().getBinaryDomainCombinationsColor() ); - } - if ( getControlPanel().isShowBinaryCharacters() ) { - TreePanel.drawString( node.getNodeData().getBinaryCharacters().getPresentCharactersAsStringBuffer() - .toString(), node.getXcoord() + x + 1 + half_box_size, node.getYcoord() - + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g ); - paintGainedAndLostCharacters( g, node, node.getNodeData().getBinaryCharacters() - .getGainedCharactersAsStringBuffer().toString(), node.getNodeData().getBinaryCharacters() - .getLostCharactersAsStringBuffer().toString() ); - } - else { - TreePanel.drawString( " " + node.getNodeData().getBinaryCharacters().getPresentCount(), - node.getXcoord() + x + 4 + half_box_size, - node.getYcoord() - + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), - g ); - paintGainedAndLostCharacters( g, node, "+" - + node.getNodeData().getBinaryCharacters().getGainedCount(), "-" - + node.getNodeData().getBinaryCharacters().getLostCount() ); - } - } - } - } - - private 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( getPartAfterColon( p.getRef() ) ); - sb.append( "=" ); - sb.append( p.getValue() ); - if ( !ForesterUtil.isEmpty( p.getUnit() ) ) { - sb.append( getPartAfterColon( p.getUnit() ) ); - } - } - return sb; - } - - final private static String getPartAfterColon( final String s ) { - final int i = s.indexOf( ':' ); - if ( ( i < 1 ) || ( i == ( s.length() - 1 ) ) ) { - return s; - } - return s.substring( i + 1, s.length() ); - } - - private double drawTaxonomyImage( final double x, final double y, final PhylogenyNode node, final Graphics2D g ) { - final List us = new ArrayList(); - for( final Taxonomy t : node.getNodeData().getTaxonomies() ) { - for( final Uri uri : t.getUris() ) { - us.add( uri ); - } - } - 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; - } + if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) { + g.setColor( Color.BLACK ); + } + else { + g.setColor( calculateColorForAnnotation( ann ) ); + } + final String ann_str = ann.asSimpleText().toString(); + 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 ); + } + if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) + || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) + || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) { + if ( ( getControlPanel().isShowBinaryCharacters() || getControlPanel().isShowBinaryCharacterCounts() ) + && node.getNodeData().isHasBinaryCharacters() ) { + if ( _sb.length() > 0 ) { + x += getTreeFontSet()._fm_large.stringWidth( _sb.toString() ) + 5; + } + if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) { + g.setColor( Color.BLACK ); + } + else { + g.setColor( getTreeColorSet().getBinaryDomainCombinationsColor() ); + } + if ( getControlPanel().isShowBinaryCharacters() ) { + TreePanel.drawString( node.getNodeData().getBinaryCharacters().getPresentCharactersAsStringBuffer() + .toString(), node.getXcoord() + x + 1 + half_box_size, node.getYcoord() + + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g ); + paintGainedAndLostCharacters( g, node, node.getNodeData().getBinaryCharacters() + .getGainedCharactersAsStringBuffer().toString(), node.getNodeData().getBinaryCharacters() + .getLostCharactersAsStringBuffer().toString() ); + } + else { + TreePanel.drawString( " " + node.getNodeData().getBinaryCharacters().getPresentCount(), + node.getXcoord() + x + 4 + half_box_size, + node.getYcoord() + + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), + g ); + paintGainedAndLostCharacters( g, node, "+" + + node.getNodeData().getBinaryCharacters().getGainedCount(), "-" + + node.getNodeData().getBinaryCharacters().getLostCount() ); } } } - return offset; } final private void paintNodeDataUnrootedCirc( final Graphics2D g, @@ -3747,264 +4371,62 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee 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() ); - if ( rv != null ) { - 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 ) { - 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 ); - } - } - 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 ); - } - } - 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 ); + ////////////// + 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 ); + 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 ); } } @@ -4186,18 +4608,6 @@ 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, @@ -4396,166 +4806,38 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee repaint(); } - @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 ); - } - } - - 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(); - 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 ) ); + 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 { - x = TreePanel.MOVE - + getLongestExtNodeInfo() - + ForesterUtil.roundToInt( getXdistance() - * ( PhylogenyMethods.calculateMaxDepth( getPhylogeny() ) + 1 ) ); + sb.append( " " ); } - } - setPreferredSize( new Dimension( x, y ) ); - } - - public final void setArrowCursor() { - setCursor( ARROW_CURSOR ); - repaint(); - } - - final void setControlPanel( final ControlPanel atv_control ) { - _control_panel = atv_control; - } - - final private void setCopiedAndPastedNodes( final Set nodeIds ) { - getMainPanel().setCopiedAndPastedNodes( nodeIds ); - } - - final private void setCutOrCopiedTree( final Phylogeny cut_or_copied_tree ) { - getMainPanel().setCutOrCopiedTree( cut_or_copied_tree ); - } - - public 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 Property p = properties.getProperty( ref ); + sb.append( getPartAfterColon( p.getRef() ) ); + sb.append( "=" ); + sb.append( p.getValue() ); + if ( !ForesterUtil.isEmpty( p.getUnit() ) ) { + sb.append( getPartAfterColon( p.getUnit() ) ); + } + } + return sb; } - final void setLastMouseDragPointY( final float y ) { - _last_drag_point_y = y; + final private void setCopiedAndPastedNodes( final Set nodeIds ) { + getMainPanel().setCopiedAndPastedNodes( nodeIds ); } - final void setLongestExtNodeInfo( final int i ) { - _longest_ext_node_info = i; + final private void setCutOrCopiedTree( final Phylogeny cut_or_copied_tree ) { + getMainPanel().setCutOrCopiedTree( cut_or_copied_tree ); } - final void setMediumFonts() { - getTreeFontSet().mediumFonts(); + final private void setInOv( final boolean in_ov ) { + _in_ov = in_ov; } final private void setOvMaxHeight( final float ov_max_height ) { @@ -4566,10 +4848,6 @@ 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; } @@ -4594,72 +4872,6 @@ 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 - */ - public 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; } @@ -4668,73 +4880,6 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee _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 ) - && !getMainPanel().getOptions().isShowDefaultNodeShapes() - && ( ( getControlPanel() != null ) && !getControlPanel().isShowDomainArchitectures() ) ) { - _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 - */ - public final void setTree( final Phylogeny t ) { - setNodeInPreorderToNull(); - _phylogeny = t; - } - - final void setNodeInPreorderToNull() { - _nodes_in_preorder = null; - } - - final void setTreeFile( final File treefile ) { - _treefile = treefile; - } - final private void setUpUrtFactor() { final int d = getVisibleRect().width < getVisibleRect().height ? getVisibleRect().width : getVisibleRect().height; @@ -4761,21 +4906,96 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee _urt_factor_ov = urt_factor_ov; } - public 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; - } - - final void setYdistance( final float y ) { - _y_distance = y; + 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_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_CODE: + if ( n.getNodeData().isHasTaxonomy() + && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) { + data.add( n.getNodeData().getTaxonomy().getTaxonomyCode() ); + } + break; + case UNKNOWN: + AptxUtil.showExtDescNodeDataUserSelectedHelper( getControlPanel(), n, data ); + break; + default: + throw new IllegalArgumentException( "unknown data element: " + + getOptions().getExtDescNodeDataToReturn() ); + } + } // for loop + if ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.CONSOLE ) { + for( final String d : data ) { + if ( !ForesterUtil.isEmpty( d ) ) { + System.out.println( d ); + } + } + } + else if ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.WINODW ) { + final StringBuilder sb = new StringBuilder(); + for( final String d : data ) { + if ( !ForesterUtil.isEmpty( d ) ) { + sb.append( d ); + sb.append( "\n" ); + } + } + if ( sb.length() < 1 ) { + AptxUtil.showInformationMessage( this, + "No Appropriate Data (" + obtainTitleForExtDescNodeData() + ")", + "Descendants of selected node do not contain selected data" ); + } + else { + final String title = "External Descendants " + + ( getOptions().getExtDescNodeDataToReturn() == NODE_DATA.UNKNOWN ? "Data" + : obtainTitleForExtDescNodeData() ) + " (" + data.size() + "/" + + node.getNumberOfExternalNodes() + ") For Node " + node; + if ( getMainPanel().getMainFrame() == null ) { + // Must be "E" applet version. + final ArchaeopteryxE ae = ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet(); + final String s = sb.toString().trim(); + ae.showTextFrame( s, title ); + ae.setCurrentExternalNodesDataBuffer( s ); + } + else { + getMainPanel().getMainFrame().showTextFrame( sb.toString(), title ); + } + } + } } final private void showNodeDataPopup( final MouseEvent e, final PhylogenyNode node ) { @@ -5015,123 +5235,6 @@ 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; - } - 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 = 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() { - 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 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 private void switchDisplaygetPhylogenyGraphicsType() { switch ( getPhylogenyGraphicsType() ) { case RECTANGULAR: @@ -5193,103 +5296,6 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } } - final void taxColor() { - if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) { - return; - } - setWaitCursor(); - AptxUtil.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 ) ); } @@ -5298,6 +5304,14 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee g.drawString( str, ( int ) ( x + 0.5 ), ( int ) ( y + 0.5 ) ); } + final private static String getPartAfterColon( final String s ) { + final int i = s.indexOf( ':' ); + if ( ( i < 1 ) || ( i == ( s.length() - 1 ) ) ) { + return s; + } + return s.substring( i + 1, s.length() ); + } + final private static boolean isSequenceEmpty( final Sequence seq ) { return ( seq.getAccession() == null ) && ForesterUtil.isEmpty( seq.getName() ) && ForesterUtil.isEmpty( seq.getSymbol() ); @@ -5314,12 +5328,21 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee || ( 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 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 private class SubtreeColorizationActionListener implements ActionListener { @@ -5340,12 +5363,4 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } } } - - public synchronized void setImageMap( final Hashtable image_map ) { - getMainPanel().setImageMap( image_map ); - } - - public synchronized Hashtable getImageMap() { - return getMainPanel().getImageMap(); - } } -- 1.7.10.2