.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(); ) {
}
}
- @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<String, BufferedImage> 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<String, BufferedImage> 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() {
}
}
- 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;
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
*
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;
}
}
- 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<PhylogenyNode> nodes = PhylogenyMethods.getAllDescendants( node );
- final Set<Integer> node_ids = new HashSet<Integer>( 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 );
}
/**
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;
}
return _control_panel;
}
- final private Set<Integer> getCopiedAndPastedNodes() {
- return getMainPanel().getCopiedAndPastedNodes();
- }
-
- final private Phylogeny getCutOrCopiedTree() {
- return getMainPanel().getCutOrCopiedTree();
- }
-
final int getDomainStructureEvalueThreshold() {
return _domain_structure_e_value_thr_exp;
}
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() {
return _options;
}
- final private float getOvMaxHeight() {
- return _ov_max_height;
- }
-
- final private float getOvMaxWidth() {
- return _ov_max_width;
- }
-
final Rectangle2D getOvRectangle() {
return _ov_rectangle;
}
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.
*
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;
}
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<String> data = new ArrayList<String>();
- 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;
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;
+ 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 );
}
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() );
.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;
}
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<Integer>() );
}
+ 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<String> 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<Integer>() );
- }
- 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();
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<Integer, Short>();
+ }
+
+ 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<Integer>() );
+ }
+ getFoundNodes().add( node.getId() );
+ }
+ }
+
+ final void setControlPanel( final ControlPanel atv_control ) {
+ _control_panel = atv_control;
+ }
+
+ final void setFoundNodes( final Set<Integer> 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<PhylogenyNode> nodes = PhylogenyMethods.getAllDescendants( node );
+ final Set<Integer> node_ids = new HashSet<Integer>( 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<Uri> us = new ArrayList<Uri>();
+ 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<Integer> 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<String> 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 ) {
}
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" );
}
}
}
}
- 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,
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,
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<Uri> us = new ArrayList<Uri>();
- 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,
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 );
}
}
}
}
- 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,
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<Integer, Short>();
- }
-
- 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<Integer> 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<Integer> 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<Integer> 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 ) {
_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;
}
_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;
}
_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;
_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<String> data = new ArrayList<String>();
+ 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 ) {
}
}
- 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:
}
}
- 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 ) );
}
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() );
|| ( 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 {
}
}
}
-
- public synchronized void setImageMap( final Hashtable<String, BufferedImage> image_map ) {
- getMainPanel().setImageMap( image_map );
- }
-
- public synchronized Hashtable<String, BufferedImage> getImageMap() {
- return getMainPanel().getImageMap();
- }
}
git://source.jalview.org / jalview.git / commitdiff