X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FTreePanel.java;h=36afa049aa673e6c8399cdc73ebc689a2c60f039;hb=0794f6835ef636577d1bb581f423ac937246586b;hp=a2936fcfb6dc5b54d6b29a9cced26d9aaa73648c;hpb=d83c580c4105be2b7ae25357e067d4b7ea42c5e3;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/TreePanel.java b/forester/java/src/org/forester/archaeopteryx/TreePanel.java index a2936fc..36afa04 100644 --- a/forester/java/src/org/forester/archaeopteryx/TreePanel.java +++ b/forester/java/src/org/forester/archaeopteryx/TreePanel.java @@ -100,12 +100,17 @@ import org.forester.archaeopteryx.tools.ImageLoader; import org.forester.io.parsers.phyloxml.PhyloXmlUtil; import org.forester.phylogeny.Phylogeny; import org.forester.phylogeny.PhylogenyMethods; +import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY; import org.forester.phylogeny.PhylogenyNode; import org.forester.phylogeny.data.Annotation; import org.forester.phylogeny.data.BranchColor; import org.forester.phylogeny.data.Confidence; import org.forester.phylogeny.data.Event; +import org.forester.phylogeny.data.NodeVisualization; +import org.forester.phylogeny.data.NodeVisualization.NodeFill; +import org.forester.phylogeny.data.NodeVisualization.NodeShape; import org.forester.phylogeny.data.PhylogenyData; +import org.forester.phylogeny.data.PhylogenyDataUtil; import org.forester.phylogeny.data.PropertiesMap; import org.forester.phylogeny.data.Property; import org.forester.phylogeny.data.Sequence; @@ -142,7 +147,6 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee private final static NumberFormat FORMATTER_CONFIDENCE; private final static NumberFormat FORMATTER_BRANCH_LENGTH; private final static int WIGGLE = 2; - private int _half_box_size_plus_wiggle; private final static int LIMIT_FOR_HQ_RENDERING = 1000; private final static int CONFIDENCE_LEFT_MARGIN = 4; // TODO "rendering_hints" was static before. Need to make sure everything is OK with it not @@ -204,11 +208,11 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee final private static double _180_OVER_PI = 180.0 / Math.PI; private static final float ROUNDED_D = 8; private int _circ_max_depth; - private int _circ_num_ext_nodes; private PhylogenyNode _root; final private Arc2D _arc = new Arc2D.Double(); final private HashMap _urt_nodeid_angle_map = new HashMap(); final private HashMap _urt_nodeid_index_map = new HashMap(); + final private Set _collapsed_external_nodeid_set = new HashSet(); HashMap _nodeid_dist_to_leaf = new HashMap(); private AffineTransform _at; private double _max_distance_to_root = -1; @@ -216,8 +220,8 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee private boolean _edited = false; private Popup _node_desc_popup; private JTextArea _rollover_popup; - private int _box_size ; - private int _half_box_size; + // private final int _box_size; + // private final int _half_box_size; //private final short _skip_counter = 0; private final StringBuffer _popup_buffer = new StringBuffer(); final private static Font POPUP_FONT = new Font( Configuration.getDefaultFontFamilyName(), @@ -265,11 +269,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee _main_panel = tjp; _configuration = configuration; _phylogeny = t; - _phy_has_branch_lengths = ForesterUtil.isHasAtLeastOneBranchLengthLargerThanZero( _phylogeny ); - _box_size = tjp.getOptions().getDefaultNodeBoxSize(); - _half_box_size = tjp.getOptions().getDefaultNodeBoxSize() / 2; - - _half_box_size_plus_wiggle = _half_box_size + WIGGLE; + _phy_has_branch_lengths = AptxUtil.isHasAtLeastOneBranchLengthLargerThanZero( _phylogeny ); init(); // if ( !_phylogeny.isEmpty() ) { _phylogeny.recalculateNumberOfExternalDescendants( true ); @@ -346,10 +346,10 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } final public void actionPerformed( final ActionEvent e ) { - int index; + boolean done = false; final JMenuItem node_popup_menu_item = ( JMenuItem ) e.getSource(); - for( index = 0; ( index < _node_popup_menu_items.length ) && !done; index++ ) { + for( int index = 0; ( index < _node_popup_menu_items.length ) && !done; index++ ) { // NOTE: index corresponds to the indices of click-to options // in the control panel. if ( node_popup_menu_item == _node_popup_menu_items[ index ] ) { @@ -410,7 +410,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee else { phy.addAsChild( node ); } - _nodes_in_preorder = null; + setNodeInPreorderToNull(); _phylogeny.externalNodesHaveChanged(); _phylogeny.hashIDs(); _phylogeny.recalculateNumberOfExternalDescendants( true ); @@ -447,12 +447,12 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } } - final void assignGraphicsForNodeBoxWithColorForParentBranch( final PhylogenyNode node, final Graphics g ) { + final Color getGraphicsForNodeBoxWithColorForParentBranch( final PhylogenyNode node ) { if ( getControlPanel().isColorBranches() && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) { - g.setColor( PhylogenyMethods.getBranchColorValue( node ) ); + return ( PhylogenyMethods.getBranchColorValue( node ) ); } else { - g.setColor( getTreeColorSet().getBranchColor() ); + return ( getTreeColorSet().getBranchColor() ); } } @@ -465,29 +465,34 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee return; } if ( node.getNodeData().isHasSequence() ) { - String name = ""; - if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getName() ) ) { - name = node.getNodeData().getSequence().getName(); - } - else if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getSymbol() ) ) { - name = node.getNodeData().getSequence().getSymbol(); - } - else if ( node.getNodeData().getSequence().getAccession() != null ) { - name = node.getNodeData().getSequence().getAccession().getValue(); - } - if ( !ForesterUtil.isEmpty( name ) ) { + String query = Blast.obtainQueryForBlast( node ); + if ( !ForesterUtil.isEmpty( query ) ) { + + JApplet applet = null; + if ( isApplet() ) { + applet = obtainApplet(); + } + Blast.NcbiBlastWeb( query, applet, this ); + + + + + if ( Constants.ALLOW_DDBJ_BLAST ) { try { - System.out.println( "trying: " + name ); + System.out.println( "trying: " + query ); final Blast s = new Blast(); - s.go( name ); + s.ddbjBlast( query ); } catch ( final Exception e ) { e.printStackTrace(); } + } } } } + + final void calcMaxDepth() { if ( _phylogeny != null ) { _circ_max_depth = PhylogenyMethods.calculateMaxDepth( _phylogeny ); @@ -577,6 +582,9 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee sum += getTreeFontSet()._fm_large_italic.stringWidth( tax.getCommonName() + " ()" ); } } + if ( getControlPanel().isShowProperties() && node.getNodeData().isHasProperties() ) { + sum += getTreeFontSet()._fm_large.stringWidth( propertiesToString( node ).toString() ); + } if ( getControlPanel().isShowBinaryCharacters() && node.getNodeData().isHasBinaryCharacters() ) { sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getBinaryCharacters() .getGainedCharactersAsStringBuffer().toString() ); @@ -663,7 +671,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee // Look in species hash Color c = getControlPanel().getSpeciesColors().get( species ); if ( c == null ) { - c = Util.calculateColorFromString( species ); + c = AptxUtil.calculateColorFromString( species ); getControlPanel().getSpeciesColors().put( species, c ); } return c; @@ -692,11 +700,13 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } if ( !node.isExternal() && !node.isRoot() ) { final boolean collapse = !node.isCollapse(); - Util.collapseSubtree( node, collapse ); + AptxUtil.collapseSubtree( node, collapse ); + updateSetOfCollapsedExternalNodes( _phylogeny ); _phylogeny.recalculateNumberOfExternalDescendants( true ); resetNodeIdToDistToLeafMap(); calculateLongestExtNodeInfo(); - _nodes_in_preorder = null; + setNodeInPreorderToNull(); + _control_panel.displayedPhylogenyMightHaveChanged( true ); resetPreferredSize(); updateOvSizes(); _main_panel.adjustJScrollPane(); @@ -709,11 +719,12 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee return; } setWaitCursor(); - Util.collapseSpeciesSpecificSubtrees( _phylogeny ); + AptxUtil.collapseSpeciesSpecificSubtrees( _phylogeny ); + updateSetOfCollapsedExternalNodes( _phylogeny ); _phylogeny.recalculateNumberOfExternalDescendants( true ); resetNodeIdToDistToLeafMap(); calculateLongestExtNodeInfo(); - _nodes_in_preorder = null; + setNodeInPreorderToNull(); resetPreferredSize(); _main_panel.adjustJScrollPane(); setArrowCursor(); @@ -764,7 +775,8 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee return; } setWaitCursor(); - Util.colorPhylogenyAccordingToConfidenceValues( _phylogeny, this ); + AptxUtil.removeBranchColors( _phylogeny ); + AptxUtil.colorPhylogenyAccordingToConfidenceValues( _phylogeny, this ); _control_panel.setColorBranches( true ); if ( _control_panel.getColorBranchesCb() != null ) { _control_panel.getColorBranchesCb().setSelected( true ); @@ -773,12 +785,57 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee repaint(); } + final void colorRank( final String rank ) { + if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) { + return; + } + setWaitCursor(); + AptxUtil.removeBranchColors( _phylogeny ); + final int colorizations = AptxUtil.colorPhylogenyAccordingToRanks( _phylogeny, rank, this ); + if ( colorizations > 0 ) { + _control_panel.setColorBranches( true ); + if ( _control_panel.getColorBranchesCb() != null ) { + _control_panel.getColorBranchesCb().setSelected( true ); + } + if ( _control_panel.getColorAccSpeciesCb() != null ) { + _control_panel.getColorAccSpeciesCb().setSelected( false ); + } + _options.setColorLabelsSameAsParentBranch( true ); + _control_panel.repaint(); + } + setArrowCursor(); + repaint(); + if ( colorizations > 0 ) { + String msg = "Taxonomy colorization via " + rank + " completed:\n"; + if ( colorizations > 1 ) { + msg += "colorized " + colorizations + " subtrees"; + } + else { + msg += "colorized one subtree"; + } + JOptionPane.showMessageDialog( this, + msg, + "Taxonomy Colorization Completed (" + rank + ")", + JOptionPane.INFORMATION_MESSAGE ); + } + else { + String msg = "Could not taxonomy colorize any subtree via " + rank + ".\n"; + msg += "Possible solutions (given that suitable taxonomic information is present):\n"; + msg += "select a different rank (e.g. phylum, genus, ...)\n"; + msg += " and/or\n"; + msg += "execute:\n"; + msg += "1. \"" + MainFrameApplication.OBTAIN_DETAILED_TAXONOMIC_INFORMATION + "\" (Tools)\n"; + msg += "2. \"" + MainFrameApplication.INFER_ANCESTOR_TAXONOMIES + "\" (Analysis)"; + JOptionPane.showMessageDialog( this, msg, "Taxonomy Colorization Failed", JOptionPane.WARNING_MESSAGE ); + } + } + final private void copySubtree( final PhylogenyNode node ) { if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) { errorMessageNoCutCopyPasteInUnrootedDisplay(); return; } - _nodes_in_preorder = null; + setNodeInPreorderToNull(); setCutOrCopiedTree( _phylogeny.copy( node ) ); final List nodes = PhylogenyMethods.getAllDescendants( node ); final Set node_ids = new HashSet( nodes.size() ); @@ -810,7 +867,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee if ( r != JOptionPane.OK_OPTION ) { return; } - _nodes_in_preorder = null; + setNodeInPreorderToNull(); setCopiedAndPastedNodes( null ); setCutOrCopiedTree( _phylogeny.copy( node ) ); _phylogeny.deleteSubtree( node, true ); @@ -865,7 +922,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee null, options, options[ 2 ] ); - _nodes_in_preorder = null; + setNodeInPreorderToNull(); boolean node_only = true; if ( r == 1 ) { node_only = false; @@ -943,8 +1000,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee _rectangle.setFrame( x, y, width, heigth ); g.fill( _rectangle ); } - - //TODO FIXME + final private void drawRectGradient( final double x, final double y, final double width, @@ -954,16 +1010,20 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee 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.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 ); } } - - //TODO FIXME + final private void drawOvalGradient( final double x, final double y, final double width, @@ -973,8 +1033,13 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee 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.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 ); @@ -1000,13 +1065,14 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) { return null; } + final int half_box_size_plus_wiggle = getOptions().getDefaultNodeShapeSize() / 2 + WIGGLE; for( final PhylogenyNodeIterator iter = _phylogeny.iteratorPostorder(); iter.hasNext(); ) { final PhylogenyNode node = iter.next(); if ( ( _phylogeny.isRooted() || !node.isRoot() || ( node.getNumberOfDescendants() > 2 ) ) - && ( ( node.getXcoord() - _half_box_size_plus_wiggle ) <= x ) - && ( ( node.getXcoord() + _half_box_size_plus_wiggle ) >= x ) - && ( ( node.getYcoord() - _half_box_size_plus_wiggle ) <= y ) - && ( ( node.getYcoord() + _half_box_size_plus_wiggle ) >= y ) ) { + && ( ( node.getXcoord() - half_box_size_plus_wiggle ) <= x ) + && ( ( node.getXcoord() + half_box_size_plus_wiggle ) >= x ) + && ( ( node.getYcoord() - half_box_size_plus_wiggle ) <= y ) + && ( ( node.getYcoord() + half_box_size_plus_wiggle ) >= y ) ) { return node; } } @@ -1257,6 +1323,9 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee case EDIT_NODE_DATA: showNodeEditFrame( node ); break; + case SORT_DESCENDENTS: + sortDescendants( node ); + break; default: throw new IllegalArgumentException( "unknown action: " + action ); } @@ -1284,7 +1353,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee return; } setWaitCursor(); - Util.inferCommonPartOfScientificNames( _phylogeny ); + AptxUtil.inferCommonPartOfScientificNames( _phylogeny ); setArrowCursor(); repaint(); } @@ -1380,7 +1449,8 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee return ( node.getNodeData().isHasSequence() && ( ( ( node.getNodeData().getSequence().getAccession() != null ) && !ForesterUtil .isEmpty( node.getNodeData().getSequence().getAccession().getValue() ) ) || !ForesterUtil.isEmpty( node.getNodeData().getSequence().getName() ) || !ForesterUtil.isEmpty( node - .getNodeData().getSequence().getSymbol() ) ) ); + .getNodeData().getSequence().getSymbol() ) || !ForesterUtil.isEmpty( node + .getNodeData().getSequence().getMolecularSequence() )) ); } final boolean isCanCollapse() { @@ -1679,9 +1749,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee _node_popup_menu_items[ i ].setEnabled( isCanOpenTaxWeb( node ) ); } else if ( title.equals( Configuration.clickto_options[ Configuration.blast ][ 0 ] ) ) { - if ( Constants.__RELEASE || Constants.__SNAPSHOT_RELEASE ) { - continue; - } + _node_popup_menu_items[ i ].setEnabled( isCanBlast( node ) ); } else if ( title.equals( Configuration.clickto_options[ Configuration.delete_subtree_or_node ][ 0 ] ) ) { @@ -1722,7 +1790,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee _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_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() ); @@ -1730,6 +1798,12 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee 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 ] ); } @@ -1746,7 +1820,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee JOptionPane.WARNING_MESSAGE ); return; } - _nodes_in_preorder = null; + setNodeInPreorderToNull(); setWaitCursor(); PhylogenyMethods.midpointRoot( _phylogeny ); resetNodeIdToDistToLeafMap(); @@ -2059,7 +2133,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee uri_str = url + URLEncoder.encode( seq.getAccession().getValue(), ForesterConstants.UTF8 ); } catch ( final UnsupportedEncodingException e ) { - Util.showErrorMessage( this, e.toString() ); + AptxUtil.showErrorMessage( this, e.toString() ); e.printStackTrace(); } if ( !ForesterUtil.isEmpty( uri_str ) ) { @@ -2068,14 +2142,14 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee if ( isApplet() ) { applet = obtainApplet(); } - Util.launchWebBrowser( new URI( uri_str ), isApplet(), applet, "_aptx_seq" ); + AptxUtil.launchWebBrowser( new URI( uri_str ), isApplet(), applet, "_aptx_seq" ); } catch ( final IOException e ) { - Util.showErrorMessage( this, e.toString() ); + AptxUtil.showErrorMessage( this, e.toString() ); e.printStackTrace(); } catch ( final URISyntaxException e ) { - Util.showErrorMessage( this, e.toString() ); + AptxUtil.showErrorMessage( this, e.toString() ); e.printStackTrace(); } } @@ -2099,7 +2173,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee uri_str = weblink.getUrl() + URLEncoder.encode( tax.getIdentifier().getValue(), ForesterConstants.UTF8 ); } catch ( final UnsupportedEncodingException e ) { - Util.showErrorMessage( this, e.toString() ); + AptxUtil.showErrorMessage( this, e.toString() ); e.printStackTrace(); } } @@ -2109,7 +2183,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee uri_str = new URI( tax.getIdentifier().getValue() ).toString(); } catch ( final URISyntaxException e ) { - Util.showErrorMessage( this, e.toString() ); + AptxUtil.showErrorMessage( this, e.toString() ); uri_str = null; e.printStackTrace(); } @@ -2120,7 +2194,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee + URLEncoder.encode( tax.getScientificName(), ForesterConstants.UTF8 ); } catch ( final UnsupportedEncodingException e ) { - Util.showErrorMessage( this, e.toString() ); + AptxUtil.showErrorMessage( this, e.toString() ); e.printStackTrace(); } } @@ -2130,7 +2204,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee + URLEncoder.encode( tax.getTaxonomyCode(), ForesterConstants.UTF8 ); } catch ( final UnsupportedEncodingException e ) { - Util.showErrorMessage( this, e.toString() ); + AptxUtil.showErrorMessage( this, e.toString() ); e.printStackTrace(); } } @@ -2140,7 +2214,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee + URLEncoder.encode( tax.getCommonName(), ForesterConstants.UTF8 ); } catch ( final UnsupportedEncodingException e ) { - Util.showErrorMessage( this, e.toString() ); + AptxUtil.showErrorMessage( this, e.toString() ); e.printStackTrace(); } } @@ -2150,14 +2224,14 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee if ( isApplet() ) { applet = obtainApplet(); } - Util.launchWebBrowser( new URI( uri_str ), isApplet(), applet, "_aptx_tax" ); + AptxUtil.launchWebBrowser( new URI( uri_str ), isApplet(), applet, "_aptx_tax" ); } catch ( final IOException e ) { - Util.showErrorMessage( this, e.toString() ); + AptxUtil.showErrorMessage( this, e.toString() ); e.printStackTrace(); } catch ( final URISyntaxException e ) { - Util.showErrorMessage( this, e.toString() ); + AptxUtil.showErrorMessage( this, e.toString() ); e.printStackTrace(); } } @@ -2296,7 +2370,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee final private void paintBranchRectangular( final Graphics2D g, final float x1, final float x2, - float y1, + final float y1, final float y2, final PhylogenyNode node, final boolean to_pdf, @@ -2317,87 +2391,45 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee g.draw( _cubic_curve ); } else { - float x2a = x2; - float x1a = x1; - // draw the vertical line - boolean draw_horizontal = true; + final float x2a = x2; + final float x1a = x1; float y2_r = 0; if ( node.isFirstChildNode() || node.isLastChildNode() || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) { - boolean draw_vertical = true; - final PhylogenyNode parent = node.getParent(); - if ( ( ( getOptions().getDefaultNodeShape() != Options.NodeShape.NONE && !to_pdf && !to_graphics_file ) || ( ( getControlPanel() - .isEvents() ) && ( parent != null ) && parent.isHasAssignedEvent() ) ) - && ( _phylogeny.isRooted() || !( ( parent != null ) && parent.isRoot() ) ) - && !( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() && !parent - .isDuplication() ) ) { - if ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) - && ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) { - if ( Math.abs( y2 - y1 ) <= _half_box_size ) { - draw_vertical = false; - } - else { - if ( y1 < y2 ) { - y1 += _half_box_size; - } - else { - if ( !to_pdf ) { - y1 -= _half_box_size + 1; - } - else { - y1 -= _half_box_size; - } - } - } - } - if ( ( x2 - x1 ) <= _half_box_size ) { - draw_horizontal = false; - } - else if ( !draw_vertical ) { - x1a += _half_box_size; - } - if ( ( ( x2 - x1a ) > _half_box_size ) - && !( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() && !node - .isDuplication() ) ) { - x2a -= _half_box_size; - } + if ( !to_graphics_file + && !to_pdf + && ( ( ( y2 < getVisibleRect().getMinY() - 20 ) && ( y1 < getVisibleRect().getMinY() - 20 ) ) || ( ( y2 > getVisibleRect() + .getMaxY() + 20 ) && ( y1 > getVisibleRect().getMaxY() + 20 ) ) ) ) { + // Do nothing. } - if ( draw_vertical ) { - if ( !to_graphics_file - && !to_pdf - && ( ( ( y2 < getVisibleRect().getMinY() - 20 ) && ( y1 < getVisibleRect().getMinY() - 20 ) ) || ( ( y2 > getVisibleRect() - .getMaxY() + 20 ) && ( y1 > getVisibleRect().getMaxY() + 20 ) ) ) ) { - // Do nothing. - } - else { - if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) { - float x2c = x1 + EURO_D; - if ( x2c > x2a ) { - x2c = x2a; - } - drawLine( x1, y1, x2c, y2, g ); + else { + if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) { + float x2c = x1 + EURO_D; + if ( x2c > x2a ) { + x2c = x2a; } - else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) { - if ( y2 > y1 ) { - y2_r = y2 - ROUNDED_D; - if ( y2_r < y1 ) { - y2_r = y1; - } - drawLine( x1, y1, x1, y2_r, g ); - } - else { - y2_r = y2 + ROUNDED_D; - if ( y2_r > y1 ) { - y2_r = y1; - } - drawLine( x1, y1, x1, y2_r, g ); + drawLine( x1, y1, x2c, y2, g ); + } + else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) { + if ( y2 > y1 ) { + y2_r = y2 - ROUNDED_D; + if ( y2_r < y1 ) { + y2_r = y1; } + drawLine( x1, y1, x1, y2_r, g ); } else { - drawLine( x1, y1, x1, y2, g ); + y2_r = y2 + ROUNDED_D; + if ( y2_r > y1 ) { + y2_r = y1; + } + drawLine( x1, y1, x1, y2_r, g ); } } + else { + drawLine( x1, y1, x1, y2, g ); + } } } // draw the horizontal line @@ -2406,42 +2438,40 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee return; } float x1_r = 0; - if ( draw_horizontal ) { - if ( !getControlPanel().isWidthBranches() || ( PhylogenyMethods.getBranchWidthValue( node ) == 1 ) ) { - if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) { - x1_r = x1a + ROUNDED_D; - if ( x1_r < x2a ) { - drawLine( x1_r, y2, x2a, y2, g ); - } + if ( !getControlPanel().isWidthBranches() || ( PhylogenyMethods.getBranchWidthValue( node ) == 1 ) ) { + if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) { + x1_r = x1a + ROUNDED_D; + if ( x1_r < x2a ) { + drawLine( x1_r, y2, x2a, y2, g ); } - else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) { - final float x1c = x1a + EURO_D; - if ( x1c < x2a ) { - drawLine( x1c, y2, x2a, y2, g ); - } - } - else { - drawLine( x1a, y2, x2a, y2, g ); + } + else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) { + final float x1c = x1a + EURO_D; + if ( x1c < x2a ) { + drawLine( x1c, y2, x2a, y2, g ); } } else { - final double w = PhylogenyMethods.getBranchWidthValue( node ); - if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) { - x1_r = x1a + ROUNDED_D; - if ( x1_r < x2a ) { - drawRectFilled( x1_r, y2 - ( w / 2 ), x2a - x1_r, w, g ); - } - } - else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) { - final float x1c = x1a + EURO_D; - if ( x1c < x2a ) { - drawRectFilled( x1c, y2 - ( w / 2 ), x2a - x1c, w, g ); - } + drawLine( x1a, y2, x2a, y2, g ); + } + } + else { + final double w = PhylogenyMethods.getBranchWidthValue( node ); + if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) { + x1_r = x1a + ROUNDED_D; + if ( x1_r < x2a ) { + drawRectFilled( x1_r, y2 - ( w / 2 ), x2a - x1_r, w, g ); } - else { - drawRectFilled( x1a, y2 - ( w / 2 ), x2a - x1a, w, g ); + } + else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) { + final float x1c = x1a + EURO_D; + if ( x1c < x2a ) { + drawRectFilled( x1c, y2 - ( w / 2 ), x2a - x1c, w, g ); } } + else { + drawRectFilled( x1a, y2 - ( w / 2 ), x2a - x1a, w, g ); + } } if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) { if ( x1_r > x2a ) { @@ -2457,9 +2487,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee g.draw( _arc ); } } - //TODO new ***** if ( node.isExternal() ) { - //TODO new ***** paintNodeBox( x2, y2, node, g, to_pdf, to_graphics_file, isInFoundNodes( node ) ); } } @@ -2472,24 +2500,45 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee final Graphics2D g, final boolean to_pdf, final boolean to_graphics_file ) { - _circ_num_ext_nodes = phy.getNumberOfExternalNodes(); + 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; + final boolean radial_labels = getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL; double current_angle = starting_angle; int i = 0; for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) { final PhylogenyNode n = it.next(); - n.setXcoord( ( float ) ( center_x + ( radius * Math.cos( current_angle ) ) ) ); - n.setYcoord( ( float ) ( center_y + ( radius * Math.sin( current_angle ) ) ) ); - _urt_nodeid_angle_map.put( n.getId(), current_angle ); - _urt_nodeid_index_map.put( n.getId(), i++ ); - current_angle += ( TWO_PI / _circ_num_ext_nodes ); + 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 ) { + _collapsed_external_nodeid_set.clear(); + 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() ); + continue E; + } + n = n.getParent(); + } + } } final void paintCircularLite( final Phylogeny phy, @@ -2498,7 +2547,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee final int center_y, final int radius, final Graphics2D g ) { - _circ_num_ext_nodes = phy.getNumberOfExternalNodes(); + final int circ_num_ext_nodes = phy.getNumberOfExternalNodes(); _root = phy.getRoot(); _root.setXSecondary( center_x ); _root.setYSecondary( center_y ); @@ -2508,7 +2557,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee 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 ); + current_angle += ( TWO_PI / circ_num_ext_nodes ); } paintCircularsLite( phy.getRoot(), phy, center_x, center_y, radius, g ); } @@ -2522,9 +2571,9 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee final Graphics2D g, final boolean to_pdf, final boolean to_graphics_file ) { - if ( n.isExternal() ) { + if ( n.isExternal() || n.isCollapse() ) { //~~circ collapse if ( !_urt_nodeid_angle_map.containsKey( n.getId() ) ) { - System.out.println( "no " + n + ", ERROR!" );//TODO + System.out.println( "no " + n + " =====>>>>>>> ERROR!" );//TODO } return _urt_nodeid_angle_map.get( n.getId() ); } @@ -2589,21 +2638,22 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee final boolean to_graphics_file, final boolean to_pdf, final boolean is_in_found_nodes ) { + Color c = null; if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) { - g.setColor( Color.BLACK ); + c = Color.BLACK; } else if ( is_in_found_nodes ) { - g.setColor( getTreeColorSet().getFoundColor() ); + c = getTreeColorSet().getFoundColor(); } else if ( getControlPanel().isColorAccordingToTaxonomy() ) { - g.setColor( getTaxonomyBasedColor( node ) ); + c = getTaxonomyBasedColor( node ); } else if ( getOptions().isColorLabelsSameAsParentBranch() && getControlPanel().isColorBranches() && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) { - g.setColor( PhylogenyMethods.getBranchColorValue( node ) ); + c = PhylogenyMethods.getBranchColorValue( node ); } else { - g.setColor( getTreeColorSet().getCollapseFillColor() ); + c = getTreeColorSet().getCollapseFillColor(); } double d = node.getAllExternalDescendants().size(); if ( d > 1000 ) { @@ -2612,17 +2662,34 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee else { d = ( Math.log10( d ) * _y_distance ) / 2.5; } - if ( d < _box_size ) { - d = _box_size; + final int box_size = getOptions().getDefaultNodeShapeSize(); + if ( d < box_size ) { + d = box_size; } _polygon.reset(); - _polygon.addPoint( ForesterUtil.roundToInt( node.getXcoord() - _box_size ), + _polygon.addPoint( ForesterUtil.roundToInt( node.getXcoord() - box_size ), ForesterUtil.roundToInt( node.getYcoord() ) ); - _polygon.addPoint( ForesterUtil.roundToInt( node.getXcoord() + _box_size ), + _polygon.addPoint( ForesterUtil.roundToInt( node.getXcoord() + box_size ), ForesterUtil.roundToInt( node.getYcoord() - d ) ); - _polygon.addPoint( ForesterUtil.roundToInt( node.getXcoord() + _box_size ), + _polygon.addPoint( ForesterUtil.roundToInt( node.getXcoord() + box_size ), ForesterUtil.roundToInt( node.getYcoord() + d ) ); - g.fillPolygon( _polygon ); + if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.SOLID ) { + g.setColor( c ); + g.fillPolygon( _polygon ); + } + else if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.NONE ) { + g.setColor( getBackground() ); + g.fillPolygon( _polygon ); + g.setColor( c ); + g.drawPolygon( _polygon ); + } + else if ( getOptions().getDefaultNodeFill() == NodeFill.GRADIENT ) { + g.setPaint( new GradientPaint( node.getXcoord() - box_size, node.getYcoord(), getBackground(), ( node + .getXcoord() + box_size ), ( float ) ( node.getYcoord() - d ), c, false ) ); + g.fill( _polygon ); + g.setPaint( c ); + g.draw( _polygon ); + } paintNodeData( g, node, to_graphics_file, to_pdf, is_in_found_nodes ); } @@ -2653,36 +2720,45 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee final PhylogenyNode node, final boolean to_pdf, final boolean to_graphics_file ) { - String conf_str = ""; final List confidences = node.getBranchData().getConfidences(); - if ( confidences.size() == 1 ) { - final double value = node.getBranchData().getConfidence( 0 ).getValue(); - if ( ( value == Confidence.CONFIDENCE_DEFAULT_VALUE ) || ( value < getOptions().getMinConfidenceValue() ) ) { - return; - } - conf_str = FORMATTER_CONFIDENCE.format( value ); - } - else if ( confidences.size() > 1 ) { - boolean one_ok = false; - boolean not_first = false; - Collections.sort( confidences ); - final StringBuilder sb = new StringBuilder(); - for( final Confidence confidence : confidences ) { - final double value = confidence.getValue(); - if ( value != Confidence.CONFIDENCE_DEFAULT_VALUE ) { - if ( value >= getOptions().getMinConfidenceValue() ) { - one_ok = true; - } - if ( not_first ) { - sb.append( "/" ); - } - else { - not_first = true; + // if ( confidences.size() == 1 ) { + // final double value = node.getBranchData().getConfidence( 0 ).getValue(); + // if ( ( value == Confidence.CONFIDENCE_DEFAULT_VALUE ) || ( value < getOptions().getMinConfidenceValue() ) ) { + // return; + // } + // conf_str = FORMATTER_CONFIDENCE.format( value ); + // } + // else if ( confidences.size() > 1 ) { + boolean one_ok = false; + boolean not_first = false; + Collections.sort( confidences ); + final StringBuilder sb = new StringBuilder(); + String conf_str = ""; + for( final Confidence confidence : confidences ) { + final double value = confidence.getValue(); + if ( value != Confidence.CONFIDENCE_DEFAULT_VALUE ) { + if ( value >= getOptions().getMinConfidenceValue() ) { + one_ok = true; + } + if ( not_first ) { + sb.append( "/" ); + } + else { + not_first = true; + } + sb.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( value, getOptions() + .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) ); + if ( getOptions().isShowConfidenceStddev() ) { + if ( confidence.getStandardDeviation() != Confidence.CONFIDENCE_DEFAULT_VALUE ) { + sb.append( "(" ); + sb.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence.getStandardDeviation(), + getOptions() + .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) ); + sb.append( ")" ); } - sb.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( value, getOptions() - .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) ); } } + //} if ( one_ok ) { conf_str = sb.toString(); } @@ -2713,8 +2789,10 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } final private void paintFoundNode( final int x, final int y, final Graphics2D g ) { + final int box_size = getOptions().getDefaultNodeShapeSize(); + final int half_box_size = getOptions().getDefaultNodeShapeSize() / 2; g.setColor( getTreeColorSet().getFoundColor() ); - g.fillRect( x - _half_box_size, y - _half_box_size, _box_size, _box_size ); + g.fillRect( x - half_box_size, y - half_box_size, box_size, box_size ); } final private void paintGainedAndLostCharacters( final Graphics2D g, @@ -2771,37 +2849,93 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee paintFoundNode( ForesterUtil.roundToInt( x ), ForesterUtil.roundToInt( y ), g ); } else { + Color outline_color = null; if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) { - g.setColor( Color.BLACK ); + outline_color = Color.BLACK; } - else if ( getControlPanel().isEvents() && Util.isHasAssignedEvent( node ) ) { + else if ( getControlPanel().isEvents() && AptxUtil.isHasAssignedEvent( node ) ) { final Event event = node.getNodeData().getEvent(); if ( event.isDuplication() ) { - g.setColor( getTreeColorSet().getDuplicationBoxColor() ); + outline_color = getTreeColorSet().getDuplicationBoxColor(); } else if ( event.isSpeciation() ) { - g.setColor( getTreeColorSet().getSpecBoxColor() ); + outline_color = getTreeColorSet().getSpecBoxColor(); } else if ( event.isSpeciationOrDuplication() ) { - g.setColor( getTreeColorSet().getDuplicationOrSpeciationColor() ); + outline_color = getTreeColorSet().getDuplicationOrSpeciationColor(); } } - else { - assignGraphicsForNodeBoxWithColorForParentBranch( node, g ); + else if ( getOptions().isTaxonomyColorizeNodeShapes() ) { + outline_color = getTaxonomyBasedColor( node ); } - if ( ( getOptions().getDefaultNodeShape() != Options.NodeShape.NONE && !to_pdf && !to_graphics_file ) - || ( getControlPanel().isEvents() && node.isHasAssignedEvent() ) ) { - if ( to_pdf || to_graphics_file ) { - if ( node.isDuplication() || !getOptions().isPrintBlackAndWhite() ) { - drawOvalFilled( x - _half_box_size, y - _half_box_size, _box_size, _box_size, g ); + else { + outline_color = getGraphicsForNodeBoxWithColorForParentBranch( node ); + if ( to_pdf && ( outline_color == getTreeColorSet().getBranchColor() ) ) { + outline_color = getTreeColorSet().getBranchColorForPdf(); + } + } + final int box_size = getOptions().getDefaultNodeShapeSize(); + final int half_box_size = box_size / 2; + if ( getOptions().isShowDefaultNodeShapes() || ( getControlPanel().isEvents() && node.isHasAssignedEvent() ) ) { + if ( getOptions().getDefaultNodeShape() == NodeShape.CIRCLE ) { + if ( getOptions().getDefaultNodeFill() == NodeFill.GRADIENT ) { + drawOvalGradient( x - half_box_size, + y - half_box_size, + box_size, + box_size, + g, + to_pdf ? Color.WHITE : outline_color, + to_pdf ? outline_color : getBackground(), + outline_color ); + } + else if ( getOptions().getDefaultNodeFill() == NodeFill.NONE ) { + Color background = getBackground(); + if ( to_pdf ) { + background = Color.WHITE; + } + drawOvalGradient( x - half_box_size, + y - half_box_size, + box_size, + box_size, + g, + background, + background, + outline_color ); + } + else if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.SOLID ) { + g.setColor( outline_color ); + drawOvalFilled( x - half_box_size, y - half_box_size, box_size, box_size, g ); } } - else { - //TODO FIXME - //drawRectFilled( x - HALF_BOX_SIZE, y - HALF_BOX_SIZE, BOX_SIZE, BOX_SIZE, g ); - drawOvalGradient( x - _half_box_size, y - _half_box_size, _box_size, _box_size, g - ,Color.BLACK, - g.getColor(), g.getColor()); + else if ( getOptions().getDefaultNodeShape() == NodeVisualization.NodeShape.RECTANGLE ) { + if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.GRADIENT ) { + drawRectGradient( x - half_box_size, + y - half_box_size, + box_size, + box_size, + g, + to_pdf ? Color.WHITE : outline_color, + to_pdf ? outline_color : getBackground(), + outline_color ); + } + else if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.NONE ) { + Color background = getBackground(); + if ( to_pdf ) { + background = Color.WHITE; + } + drawRectGradient( x - half_box_size, + y - half_box_size, + box_size, + box_size, + g, + background, + background, + outline_color ); + } + else if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.SOLID ) { + g.setColor( outline_color ); + drawRectFilled( x - half_box_size, y - half_box_size, box_size, box_size, g ); + } } } } @@ -2818,20 +2952,21 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee if ( getOptions().isShowBranchLengthValues() && ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) ) - && ( !node.isRoot() ) && ( node.getDistanceToParent() != PhylogenyNode.DISTANCE_DEFAULT ) ) { + && ( !node.isRoot() ) && ( node.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) ) { paintBranchLength( g, node, to_pdf, to_graphics_file ); } if ( !getControlPanel().isShowInternalData() && !node.isExternal() && !node.isCollapse() ) { return; } int x = 0; + final int half_box_size = getOptions().getDefaultNodeShapeSize() / 2; if ( getControlPanel().isShowTaxonomyImages() && ( getImageMap() != null ) && !getImageMap().isEmpty() && node.getNodeData().isHasTaxonomy() && ( ( node.getNodeData().getTaxonomy().getUris() != null ) && !node.getNodeData().getTaxonomy() .getUris().isEmpty() ) ) { - x += drawTaxonomyImage( node.getXcoord() + 2 + _half_box_size, node.getYcoord(), node, g ); + x += drawTaxonomyImage( node.getXcoord() + 2 + half_box_size, node.getYcoord(), node, g ); } if ( ( getControlPanel().isShowTaxonomyCode() || getControlPanel().isShowTaxonomyScientificNames() || getControlPanel() .isShowTaxonomyCommonNames() ) && node.getNodeData().isHasTaxonomy() ) { @@ -2892,6 +3027,12 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee _sb.append( node.getNodeData().getSequence().getAccession().getValue() ); } } + if ( getControlPanel().isShowProperties() && node.getNodeData().isHasProperties() ) { + if ( _sb.length() > 0 ) { + _sb.append( " " ); + } + _sb.append( propertiesToString( node ) ); + } g.setFont( getTreeFontSet().getLargeFont() ); if ( is_in_found_nodes ) { g.setFont( getTreeFontSet().getLargeFont().deriveFont( Font.BOLD ) ); @@ -2900,7 +3041,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee if ( !node.isExternal() && ( node.getNumberOfDescendants() == 1 ) ) { down_shift_factor = 1; } - final double pos_x = node.getXcoord() + x + 2 + _half_box_size; + final double pos_x = node.getXcoord() + x + 2 + half_box_size; final double pos_y = ( node.getYcoord() + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ) ); final String sb_str = _sb.toString(); // GUILHEM_BEG ______________ @@ -2925,7 +3066,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee && seqRelation.getType().equals( getControlPanel().getSequenceRelationTypeBox() .getSelectedItem() ); if ( fGotRelationWithQuery ) { // we will underline the text to show that this sequence is ortholog to the query - final double linePosX = node.getXcoord() + 2 + _half_box_size; + final double linePosX = node.getXcoord() + 2 + half_box_size; final String sConfidence = ( !getControlPanel().isShowSequenceRelationConfidence() || ( seqRelation .getConfidence() == null ) ) ? null : " (" + seqRelation.getConfidence().getValue() + ")"; @@ -2983,7 +3124,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee g.setColor( calculateColorForAnnotation( ann ) ); } final String ann_str = ann.asSimpleText().toString(); - TreePanel.drawString( ann_str, node.getXcoord() + x + 3 + _half_box_size, node.getYcoord() + 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 ); @@ -3004,7 +3145,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } if ( getControlPanel().isShowBinaryCharacters() ) { TreePanel.drawString( node.getNodeData().getBinaryCharacters().getPresentCharactersAsStringBuffer() - .toString(), node.getXcoord() + x + 1 + _half_box_size, node.getYcoord() + .toString(), node.getXcoord() + x + 1 + half_box_size, node.getYcoord() + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g ); paintGainedAndLostCharacters( g, node, node.getNodeData().getBinaryCharacters() .getGainedCharactersAsStringBuffer().toString(), node.getNodeData().getBinaryCharacters() @@ -3023,12 +3164,12 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } final double mean = ForesterUtil.round( sum / count, 1 ); TreePanel.drawString( " " + node.getNodeData().getBinaryCharacters().getPresentCount() + " [" - + mean + "]", node.getXcoord() + x + 4 + _half_box_size, node.getYcoord() + + mean + "]", node.getXcoord() + x + 4 + half_box_size, node.getYcoord() + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g ); } else { TreePanel.drawString( " " + node.getNodeData().getBinaryCharacters().getPresentCount(), - node.getXcoord() + x + 4 + _half_box_size, + node.getXcoord() + x + 4 + half_box_size, node.getYcoord() + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g ); @@ -3041,6 +3182,36 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } } + private StringBuffer propertiesToString( final PhylogenyNode node ) { + final PropertiesMap properties = node.getNodeData().getProperties(); + final StringBuffer sb = new StringBuffer(); + boolean first = true; + for( final String ref : properties.getPropertyRefs() ) { + if ( first ) { + first = false; + } + else { + sb.append( " " ); + } + final Property p = properties.getProperty( ref ); + sb.append( getPartAfterColon( p.getRef() ) ); + sb.append( "=" ); + sb.append( p.getValue() ); + if ( !ForesterUtil.isEmpty( p.getUnit() ) ) { + sb.append( getPartAfterColon( p.getUnit() ) ); + } + } + return sb; + } + + final private static String getPartAfterColon( final String s ) { + final int i = s.indexOf( ':' ); + if ( ( i < 1 ) || ( i == ( s.length() - 1 ) ) ) { + return s; + } + return s.substring( i + 1, s.length() ); + } + private double drawTaxonomyImage( final double x, final double y, final PhylogenyNode node, final Graphics2D g ) { final List us = new ArrayList(); for( final Taxonomy t : node.getNodeData().getTaxonomies() ) { @@ -3288,7 +3459,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee ++_external_node_index; } // Confidence values - if ( getControlPanel().isShowBootstrapValues() + if ( getControlPanel().isShowConfidenceValues() && !node.isExternal() && !node.isRoot() && ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) @@ -3359,9 +3530,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee child_node.setYcoord( y2 ); y2 += _y_distance * child_node.getNumberOfExternalNodes(); } - //TODO new ***** - paintNodeBox( node.getXcoord(), node.getYcoord(), node, g, to_pdf, to_graphics_file, isInFoundNodes( node ) ); - //TODO new ***** + paintNodeBox( node.getXcoord(), node.getYcoord(), node, g, to_pdf, to_graphics_file, isInFoundNodes( node ) ); } if ( dynamically_hide && !is_in_found_nodes @@ -3393,28 +3562,34 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } catch ( final ClassCastException cce ) { cce.printStackTrace(); - return; - } - rds.setRenderingHeight( 6 ); - int x = 0; - if ( getControlPanel().isShowTaxonomyCode() && ( PhylogenyMethods.getSpecies( node ).length() > 0 ) ) { - x += getTreeFontSet()._fm_large_italic.stringWidth( PhylogenyMethods.getSpecies( node ) + " " ); - } - if ( getControlPanel().isShowGeneNames() ) { - x += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getName() + " " ); - } - if ( getControlPanel().isShowGeneSymbols() ) { - x += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getSymbol() + " " ); } - if ( getControlPanel().isShowSequenceAcc() ) { - x += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getAccession() - .toString() - + " " ); - } - if ( getControlPanel().isShowNodeNames() && ( node.getName().length() > 0 ) ) { - x += getTreeFontSet()._fm_large.stringWidth( node.getName() + " " ); + if ( rds != null ) { + rds.setRenderingHeight( 6 ); + int x = 0; + if ( getControlPanel().isShowTaxonomyCode() + && ( !ForesterUtil.isEmpty( PhylogenyMethods.getSpecies( node ) ) ) ) { + x += getTreeFontSet()._fm_large_italic.stringWidth( PhylogenyMethods.getSpecies( node ) + " " ); + } + if ( getControlPanel().isShowGeneNames() + && ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getName() ) ) ) { + x += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getName() + " " ); + } + if ( getControlPanel().isShowGeneSymbols() + && ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getSymbol() ) ) ) { + x += getTreeFontSet()._fm_large + .stringWidth( node.getNodeData().getSequence().getSymbol() + " " ); + } + if ( getControlPanel().isShowSequenceAcc() + && ( node.getNodeData().getSequence().getAccession() != null ) ) { + x += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getAccession() + .toString() + + " " ); + } + if ( getControlPanel().isShowNodeNames() && ( node.getName().length() > 0 ) ) { + x += getTreeFontSet()._fm_large.stringWidth( node.getName() + " " ); + } + rds.render( node.getXcoord() + x, node.getYcoord() - 3, g, this, to_pdf ); } - rds.render( node.getXcoord() + x, node.getYcoord() - 3, g, this, to_pdf ); } } ////////////// @@ -3423,18 +3598,20 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee final RenderableVector rv = RenderableVector.createInstance( node.getNodeData().getVector(), getStatisticsForExpressionValues(), getConfiguration() ); - int x = 0; - PhylogenyNode my_node = node; - if ( !getControlPanel().isDrawPhylogram() ) { - my_node = getPhylogeny().getFirstExternalNode(); - } - if ( getControlPanel().isShowTaxonomyCode() && ( PhylogenyMethods.getSpecies( my_node ).length() > 0 ) ) { - x += getTreeFontSet()._fm_large_italic.stringWidth( PhylogenyMethods.getSpecies( my_node ) + " " ); - } - if ( getControlPanel().isShowNodeNames() && ( my_node.getName().length() > 0 ) ) { - x += getTreeFontSet()._fm_large.stringWidth( my_node.getName() + " " ); + 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 ); } - rv.render( my_node.getXcoord() + x, node.getYcoord() - 5, g, this, to_pdf ); } ////////////// } @@ -3771,7 +3948,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee else { g.setColor( getTreeColorSet().getTaxonomyColor() ); } - final double start_x = node.getXcoord() + 3 + _half_box_size + x_shift; + final double start_x = node.getXcoord() + 3 + ( getOptions().getDefaultNodeShapeSize() / 2 ) + x_shift; final double start_y = node.getYcoord() + ( getTreeFontSet()._fm_large.getAscent() / ( node.getNumberOfDescendants() == 1 ? 1 : 3.0 ) ); _sb.setLength( 0 ); @@ -3870,7 +4047,6 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee if ( n.isRoot() ) { n.setXcoord( getWidth() / 2 ); n.setYcoord( getHeight() / 2 ); - paintNodeBox( n.getXcoord(), n.getYcoord(), n, g, to_pdf, to_graphics_file, isInFoundNodes( n ) ); } if ( n.isExternal() ) { paintNodeDataUnrootedCirc( g, @@ -3923,11 +4099,14 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee final float new_y = ( float ) ( y + Math.sin( mid_angle ) * length ); desc.setXcoord( new_x ); desc.setYcoord( new_y ); - paintNodeBox( new_x, new_y, desc, g, to_pdf, to_graphics_file, isInFoundNodes( desc ) ); paintUnrooted( desc, current_angle, current_angle + arc_size, radial_labels, g, to_pdf, to_graphics_file ); current_angle += arc_size; assignGraphicsForBranchWithColorForParentBranch( desc, false, g, to_pdf, to_graphics_file ); drawLine( x, y, new_x, new_y, g ); + paintNodeBox( new_x, new_y, desc, g, to_pdf, to_graphics_file, isInFoundNodes( desc ) ); + } + if ( n.isRoot() ) { + paintNodeBox( n.getXcoord(), n.getYcoord(), n, g, to_pdf, to_graphics_file, isInFoundNodes( n ) ); } } @@ -4044,7 +4223,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } node_ids.add( node.getId() ); getCopiedAndPastedNodes().addAll( node_ids ); - _nodes_in_preorder = null; + setNodeInPreorderToNull(); _phylogeny.externalNodesHaveChanged(); _phylogeny.hashIDs(); _phylogeny.recalculateNumberOfExternalDescendants( true ); @@ -4120,7 +4299,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee getPhylogeny().reRoot( node ); getPhylogeny().recalculateNumberOfExternalDescendants( true ); resetNodeIdToDistToLeafMap(); - _nodes_in_preorder = null; + setNodeInPreorderToNull(); resetPreferredSize(); getMainPanel().adjustJScrollPane(); repaint(); @@ -4259,7 +4438,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee * @param x * @param y */ - final void setParametersForPainting( final int x, final int y, final boolean recalc_longest_ext_node_info ) { + 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(); @@ -4380,10 +4559,14 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee * an instance of a Phylogeny */ public final void setTree( final Phylogeny t ) { - _nodes_in_preorder = null; + setNodeInPreorderToNull(); _phylogeny = t; } + final void setNodeInPreorderToNull() { + _nodes_in_preorder = null; + } + final void setTreeFile( final File treefile ) { _treefile = treefile; } @@ -4591,6 +4774,26 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee .append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence.getValue(), getOptions() .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) ); + if ( confidence.getStandardDeviation() != Confidence.CONFIDENCE_DEFAULT_VALUE ) { + _popup_buffer.append( " (sd=" ); + _popup_buffer.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence + .getStandardDeviation(), getOptions() + .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) ); + _popup_buffer.append( ")" ); + } + } + } + if ( node.getNodeData().isHasProperties() ) { + final PropertiesMap properties = node.getNodeData().getProperties(); + for( final String ref : properties.getPropertyRefs() ) { + _popup_buffer.append( "\n" ); + final Property p = properties.getProperty( ref ); + _popup_buffer.append( getPartAfterColon( p.getRef() ) ); + _popup_buffer.append( "=" ); + _popup_buffer.append( p.getValue() ); + if ( !ForesterUtil.isEmpty( p.getUnit() ) ) { + _popup_buffer.append( getPartAfterColon( p.getUnit() ) ); + } } } if ( _popup_buffer.length() > 0 ) { @@ -4670,7 +4873,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee JOptionPane.WARNING_MESSAGE ); return; } - _nodes_in_preorder = null; + setNodeInPreorderToNull(); if ( !node.isExternal() && !node.isRoot() && ( _subtree_index <= ( TreePanel.MAX_SUBTREES - 1 ) ) ) { _sub_phylogenies[ _subtree_index ] = _phylogeny; _sub_phylogenies_temp_roots[ _subtree_index ] = node; @@ -4690,7 +4893,6 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } 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() ); @@ -4708,7 +4910,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } final void superTree() { - _nodes_in_preorder = null; + setNodeInPreorderToNull(); final PhylogenyNode temp_root = _sub_phylogenies_temp_roots[ _subtree_index - 1 ]; for( final PhylogenyNode n : temp_root.getDescendants() ) { n.setParent( temp_root ); @@ -4720,9 +4922,48 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } 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() ) { - _phylogeny.swapChildren( node ); - _nodes_in_preorder = null; + node.swapChildren(); + setNodeInPreorderToNull(); + _phylogeny.externalNodesHaveChanged(); + _phylogeny.hashIDs(); + _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.hashIDs(); + _phylogeny.recalculateNumberOfExternalDescendants( true ); + resetNodeIdToDistToLeafMap(); + setEdited( true ); } repaint(); } @@ -4793,7 +5034,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee return; } setWaitCursor(); - Util.colorPhylogenyAccordingToExternalTaxonomy( _phylogeny, this ); + AptxUtil.colorPhylogenyAccordingToExternalTaxonomy( _phylogeny, this ); _control_panel.setColorBranches( true ); if ( _control_panel.getColorBranchesCb() != null ) { _control_panel.getColorBranchesCb().setSelected( true );