X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FTreePanel.java;h=b561ac2bec38e05b048a56083c20ab9dc4933e76;hb=6be89aad9f2003c1b2bb4a9e6581ac3537d556c2;hp=6ce838e058b818da8046d9d5b9b3eae3e01fa68f;hpb=cc09a4de53fe2c95d71a0c93d6f894db2c845491;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/TreePanel.java b/forester/java/src/org/forester/archaeopteryx/TreePanel.java index 6ce838e..b561ac2 100644 --- a/forester/java/src/org/forester/archaeopteryx/TreePanel.java +++ b/forester/java/src/org/forester/archaeopteryx/TreePanel.java @@ -105,7 +105,11 @@ 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 +146,6 @@ 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 final 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 +207,11 @@ 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 +219,8 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee private boolean _edited = false; private Popup _node_desc_popup; private JTextArea _rollover_popup; - private final int _box_size; - private final 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(), @@ -265,10 +268,7 @@ 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 ); @@ -409,7 +409,7 @@ 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 ); @@ -446,12 +446,12 @@ 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() ); } } @@ -576,6 +576,9 @@ 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() ); @@ -662,7 +665,7 @@ 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; @@ -691,11 +694,13 @@ 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(); @@ -708,11 +713,12 @@ 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(); @@ -763,7 +769,8 @@ 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 ); @@ -772,12 +779,57 @@ 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() ); @@ -809,7 +861,7 @@ 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 ); @@ -864,7 +916,7 @@ 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; @@ -943,7 +995,6 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee g.fill( _rectangle ); } - //TODO FIXME final private void drawRectGradient( final double x, final double y, final double width, @@ -967,7 +1018,6 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } } - //TODO FIXME final private void drawOvalGradient( final double x, final double y, final double width, @@ -1009,13 +1059,14 @@ 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; } } @@ -1266,6 +1317,9 @@ 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 ); } @@ -1293,7 +1347,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee return; } setWaitCursor(); - Util.inferCommonPartOfScientificNames( _phylogeny ); + AptxUtil.inferCommonPartOfScientificNames( _phylogeny ); setArrowCursor(); repaint(); } @@ -1755,7 +1809,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee JOptionPane.WARNING_MESSAGE ); return; } - _nodes_in_preorder = null; + setNodeInPreorderToNull(); setWaitCursor(); PhylogenyMethods.midpointRoot( _phylogeny ); resetNodeIdToDistToLeafMap(); @@ -2068,7 +2122,7 @@ 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 ) ) { @@ -2077,14 +2131,14 @@ 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(); } } @@ -2108,7 +2162,7 @@ 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(); } } @@ -2118,7 +2172,7 @@ 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(); } @@ -2129,7 +2183,7 @@ 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(); } } @@ -2139,7 +2193,7 @@ 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(); } } @@ -2149,7 +2203,7 @@ 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(); } } @@ -2159,14 +2213,14 @@ 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(); } } @@ -2305,7 +2359,7 @@ 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, @@ -2326,87 +2380,45 @@ 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 @@ -2415,42 +2427,40 @@ 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 ); - } - } - else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) { - final float x1c = x1a + EURO_D; - if ( x1c < x2a ) { - drawLine( x1c, y2, x2a, y2, g ); - } + if ( !getControlPanel().isWidthBranches() || ( PhylogenyMethods.getBranchWidthValue( node ) == 1 ) ) { + if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) { + x1_r = x1a + ROUNDED_D; + if ( x1_r < x2a ) { + drawLine( x1_r, y2, x2a, y2, g ); } - else { - drawLine( x1a, y2, x2a, y2, g ); + } + else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) { + final float x1c = x1a + EURO_D; + if ( x1c < x2a ) { + drawLine( x1c, y2, x2a, y2, g ); } } else { - final double w = PhylogenyMethods.getBranchWidthValue( node ); - if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) { - x1_r = x1a + ROUNDED_D; - if ( x1_r < x2a ) { - drawRectFilled( x1_r, y2 - ( w / 2 ), x2a - x1_r, w, g ); - } - } - else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) { - final float x1c = x1a + EURO_D; - if ( x1c < x2a ) { - drawRectFilled( x1c, y2 - ( w / 2 ), x2a - x1c, w, g ); - } + drawLine( x1a, y2, x2a, y2, g ); + } + } + else { + final double w = PhylogenyMethods.getBranchWidthValue( node ); + if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) { + x1_r = x1a + ROUNDED_D; + if ( x1_r < x2a ) { + drawRectFilled( x1_r, y2 - ( w / 2 ), x2a - x1_r, w, g ); } - else { - drawRectFilled( x1a, y2 - ( w / 2 ), x2a - x1a, w, g ); + } + else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) { + final float x1c = x1a + EURO_D; + if ( x1c < x2a ) { + drawRectFilled( x1c, y2 - ( w / 2 ), x2a - x1c, w, g ); } } + else { + drawRectFilled( x1a, y2 - ( w / 2 ), x2a - x1a, w, g ); + } } if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) { if ( x1_r > x2a ) { @@ -2466,9 +2476,7 @@ 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 ) ); } } @@ -2481,7 +2489,8 @@ 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 ); @@ -2490,23 +2499,44 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee 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, final double starting_angle, final int center_x, 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 ); @@ -2516,7 +2546,7 @@ 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 ); } @@ -2530,9 +2560,9 @@ 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() ); } @@ -2597,21 +2627,22 @@ 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 ) { @@ -2620,17 +2651,34 @@ 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 ); } @@ -2661,36 +2709,45 @@ 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(); } @@ -2721,8 +2778,10 @@ 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, @@ -2779,51 +2838,93 @@ 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 if ( getOptions().isTaxonomyColorizeNodeShapes() ) { + outline_color = getTaxonomyBasedColor( node ); + } else { - assignGraphicsForNodeBoxWithColorForParentBranch( node, g ); - } - 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() ) { - //TODO FIXME - //drawOvalFilled( 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, + 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, - Color.BLACK, - g.getColor(), - g.getColor() ); + 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 ); + } } } } @@ -2840,20 +2941,21 @@ 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() ) { @@ -2914,6 +3016,12 @@ 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 ) ); @@ -2922,7 +3030,7 @@ 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 ______________ @@ -2947,7 +3055,7 @@ 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() + ")"; @@ -3005,7 +3113,7 @@ 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 ); @@ -3026,7 +3134,7 @@ 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() @@ -3045,12 +3153,12 @@ 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 ); @@ -3063,6 +3171,36 @@ 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() ) { @@ -3310,7 +3448,7 @@ 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 ) @@ -3381,9 +3519,7 @@ 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 ***** } if ( dynamically_hide && !is_in_found_nodes @@ -3415,28 +3551,34 @@ 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 ); } } ////////////// @@ -3445,18 +3587,20 @@ 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 ); } ////////////// } @@ -3793,7 +3937,7 @@ 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 ); @@ -4068,7 +4212,7 @@ 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 ); @@ -4144,7 +4288,7 @@ 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(); @@ -4283,7 +4427,7 @@ 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(); @@ -4404,10 +4548,14 @@ 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; } @@ -4615,6 +4763,26 @@ 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 ) { @@ -4694,7 +4862,7 @@ 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; @@ -4731,7 +4899,7 @@ 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 ); @@ -4745,11 +4913,21 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee final void swap( final PhylogenyNode node ) { if ( !node.isExternal() ) { _phylogeny.swapChildren( node ); - _nodes_in_preorder = null; + setNodeInPreorderToNull(); } repaint(); } - + + + final void sortDescendants( final PhylogenyNode node ) { + if ( !node.isExternal() ) { + PhylogenyMethods.sortNodeDescendents( node ); + setNodeInPreorderToNull(); + } + repaint(); + } + + final private void switchDisplaygetPhylogenyGraphicsType() { switch ( getPhylogenyGraphicsType() ) { case RECTANGULAR: @@ -4816,7 +4994,7 @@ 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 );