X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FTreePanel.java;h=befe375f2e7154c8fae8c99fa7063e257fe23c8e;hb=b1a74bd076c917d428002284a53a2c6f390226fb;hp=96802057de1dee9b694439b51c235dd53ece2a64;hpb=2b4d8edabd858f232899cf045ec0124a079ed8ce;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/TreePanel.java b/forester/java/src/org/forester/archaeopteryx/TreePanel.java index 9680205..befe375 100644 --- a/forester/java/src/org/forester/archaeopteryx/TreePanel.java +++ b/forester/java/src/org/forester/archaeopteryx/TreePanel.java @@ -100,6 +100,7 @@ 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; @@ -109,6 +110,7 @@ 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; @@ -267,7 +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 ); + _phy_has_branch_lengths = AptxUtil.isHasAtLeastOneBranchLengthLargerThanZero( _phylogeny ); init(); // if ( !_phylogeny.isEmpty() ) { _phylogeny.recalculateNumberOfExternalDescendants( true ); @@ -344,10 +346,9 @@ 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 ] ) { @@ -408,9 +409,9 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee else { phy.addAsChild( node ); } - _nodes_in_preorder = null; + setNodeInPreorderToNull(); _phylogeny.externalNodesHaveChanged(); - _phylogeny.hashIDs(); + _phylogeny.clearHashIdToNodeMap(); _phylogeny.recalculateNumberOfExternalDescendants( true ); resetNodeIdToDistToLeafMap(); setEdited( true ); @@ -463,25 +464,37 @@ 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(); + final String query = Blast.obtainQueryForBlast( node ); + boolean nucleotide = false; + if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getType() ) ) { + if ( !node.getNodeData().getSequence().getType().toLowerCase().equals( PhyloXmlUtil.SEQ_TYPE_PROTEIN ) ) { + nucleotide = true; + } } - else if ( node.getNodeData().getSequence().getAccession() != null ) { - name = node.getNodeData().getSequence().getAccession().getValue(); + else if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) { + nucleotide = !ForesterUtil.seqIsLikelyToBeAa( node.getNodeData().getSequence().getMolecularSequence() ); } - if ( !ForesterUtil.isEmpty( name ) ) { + if ( !ForesterUtil.isEmpty( query ) ) { + JApplet applet = null; + if ( isApplet() ) { + applet = obtainApplet(); + } try { - System.out.println( "trying: " + name ); - final Blast s = new Blast(); - s.go( name ); + Blast.openNcbiBlastWeb( query, nucleotide, applet, this ); } catch ( final Exception e ) { e.printStackTrace(); } + if ( Constants.ALLOW_DDBJ_BLAST ) { + try { + System.out.println( "trying: " + query ); + final Blast s = new Blast(); + s.ddbjBlast( query ); + } + catch ( final Exception e ) { + e.printStackTrace(); + } + } } } } @@ -531,7 +544,12 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) { return; } - int longest = 20; + int max_length = ForesterUtil.roundToInt( ( getSize().getWidth() - MOVE ) + * Constants.EXT_NODE_INFO_LENGTH_MAX_RATIO ); + if ( max_length < 40 ) { + max_length = 40; + } + int longest = 30; for( final PhylogenyNode node : _phylogeny.getExternalNodes() ) { int sum = 0; if ( node.isCollapse() ) { @@ -561,6 +579,11 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee .asSimpleText() + " " ); } + if ( getControlPanel().isShowDomainArchitectures() + && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) { + sum += ( ( RenderableDomainArchitecture ) node.getNodeData().getSequence().getDomainArchitecture() ) + .getRenderingSize().getWidth(); + } } if ( node.getNodeData().isHasTaxonomy() ) { final Taxonomy tax = node.getNodeData().getTaxonomy(); @@ -575,25 +598,23 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee sum += getTreeFontSet()._fm_large_italic.stringWidth( tax.getCommonName() + " ()" ); } } + if ( getControlPanel().isShowProperties() && node.getNodeData().isHasProperties() ) { + sum += getTreeFontSet()._fm_large.stringWidth( propertiesToString( node ).toString() ); + } if ( getControlPanel().isShowBinaryCharacters() && node.getNodeData().isHasBinaryCharacters() ) { sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getBinaryCharacters() .getGainedCharactersAsStringBuffer().toString() ); } - if ( getControlPanel().isShowDomainArchitectures() && node.getNodeData().isHasSequence() - && ( node.getNodeData().getSequence().getDomainArchitecture() != null ) ) { - sum += ( ( RenderableDomainArchitecture ) node.getNodeData().getSequence().getDomainArchitecture() ) - .getRenderingSize().getWidth(); - } - if ( sum >= Constants.EXT_NODE_INFO_LENGTH_MAX ) { - setLongestExtNodeInfo( Constants.EXT_NODE_INFO_LENGTH_MAX ); + if ( sum >= max_length ) { + setLongestExtNodeInfo( max_length ); return; } if ( sum > longest ) { longest = sum; } } - if ( longest >= Constants.EXT_NODE_INFO_LENGTH_MAX ) { - setLongestExtNodeInfo( Constants.EXT_NODE_INFO_LENGTH_MAX ); + if ( longest >= max_length ) { + setLongestExtNodeInfo( max_length ); } else { setLongestExtNodeInfo( longest ); @@ -661,7 +682,7 @@ 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; @@ -690,12 +711,13 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } if ( !node.isExternal() && !node.isRoot() ) { final boolean collapse = !node.isCollapse(); - Util.collapseSubtree( node, collapse ); - updateSetOfCollapsedExternalNodes( _phylogeny ); + AptxUtil.collapseSubtree( node, collapse ); + updateSetOfCollapsedExternalNodes(); _phylogeny.recalculateNumberOfExternalDescendants( true ); resetNodeIdToDistToLeafMap(); calculateLongestExtNodeInfo(); - _nodes_in_preorder = null; + setNodeInPreorderToNull(); + _control_panel.displayedPhylogenyMightHaveChanged( true ); resetPreferredSize(); updateOvSizes(); _main_panel.adjustJScrollPane(); @@ -708,12 +730,12 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee return; } setWaitCursor(); - Util.collapseSpeciesSpecificSubtrees( _phylogeny ); - updateSetOfCollapsedExternalNodes( _phylogeny ); + AptxUtil.collapseSpeciesSpecificSubtrees( _phylogeny ); + updateSetOfCollapsedExternalNodes(); _phylogeny.recalculateNumberOfExternalDescendants( true ); resetNodeIdToDistToLeafMap(); calculateLongestExtNodeInfo(); - _nodes_in_preorder = null; + setNodeInPreorderToNull(); resetPreferredSize(); _main_panel.adjustJScrollPane(); setArrowCursor(); @@ -764,7 +786,8 @@ 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 +796,57 @@ 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() ); @@ -810,11 +878,11 @@ 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 ); - _phylogeny.hashIDs(); + _phylogeny.clearHashIdToNodeMap(); _phylogeny.recalculateNumberOfExternalDescendants( true ); resetNodeIdToDistToLeafMap(); setEdited( true ); @@ -865,7 +933,7 @@ 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; @@ -880,7 +948,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee _phylogeny.deleteSubtree( node, true ); } _phylogeny.externalNodesHaveChanged(); - _phylogeny.hashIDs(); + _phylogeny.clearHashIdToNodeMap(); _phylogeny.recalculateNumberOfExternalDescendants( true ); resetNodeIdToDistToLeafMap(); setEdited( true ); @@ -1266,6 +1334,9 @@ 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 +1364,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee return; } setWaitCursor(); - Util.inferCommonPartOfScientificNames( _phylogeny ); + AptxUtil.inferCommonPartOfScientificNames( _phylogeny ); setArrowCursor(); repaint(); } @@ -1386,10 +1457,12 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } final private boolean isCanBlast( final PhylogenyNode node ) { - return ( node.getNodeData().isHasSequence() && ( ( ( node.getNodeData().getSequence().getAccession() != null ) && !ForesterUtil - .isEmpty( node.getNodeData().getSequence().getAccession().getValue() ) ) - || !ForesterUtil.isEmpty( node.getNodeData().getSequence().getName() ) || !ForesterUtil.isEmpty( node - .getNodeData().getSequence().getSymbol() ) ) ); + 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().getMolecularSequence() ) ) && Blast + .isContainsQueryForBlast( node ) ); } final boolean isCanCollapse() { @@ -1688,9 +1761,6 @@ 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 ] ) ) { @@ -1731,7 +1801,7 @@ 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() ); @@ -1739,6 +1809,12 @@ 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 ] ); } @@ -1755,7 +1831,7 @@ 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 +2144,7 @@ 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 +2153,14 @@ 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 +2184,7 @@ 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 +2194,7 @@ 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 +2205,7 @@ 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 +2215,7 @@ 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 +2225,7 @@ 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 +2235,14 @@ 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(); } } @@ -2461,17 +2537,21 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee paintNodeBox( _root.getXcoord(), _root.getYcoord(), _root, g, to_pdf, to_graphics_file, isInFoundNodes( _root ) ); } - private void updateSetOfCollapsedExternalNodes( final Phylogeny phy ) { + void updateSetOfCollapsedExternalNodes() { + final Phylogeny phy = getPhylogeny(); _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; + if ( phy != null ) { + E: for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) { + final PhylogenyNode ext_node = it.next(); + PhylogenyNode n = ext_node; + while ( !n.isRoot() ) { + if ( n.isCollapse() ) { + _collapsed_external_nodeid_set.add( ext_node.getId() ); + ext_node.setCollapse( true ); + continue E; + } + n = n.getParent(); } - n = n.getParent(); } } } @@ -2655,36 +2735,45 @@ 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(); } @@ -2779,7 +2868,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) { 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() ) { outline_color = getTreeColorSet().getDuplicationBoxColor(); @@ -2878,7 +2967,7 @@ 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() ) { @@ -2953,6 +3042,12 @@ 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 ) ); @@ -3102,6 +3197,36 @@ 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() ) { @@ -3349,7 +3474,7 @@ 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 ) @@ -3452,28 +3577,34 @@ 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 ); } } ////////////// @@ -3482,18 +3613,20 @@ 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 ); } ////////////// } @@ -3537,6 +3670,9 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee final int graphics_file_height, final int graphics_file_x, final int graphics_file_y ) { + if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) { + return; + } if ( _control_panel.isShowSequenceRelations() ) { _query_sequence = _control_panel.getSelectedQuerySequence(); } @@ -4105,9 +4241,9 @@ 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.clearHashIdToNodeMap(); _phylogeny.recalculateNumberOfExternalDescendants( true ); resetNodeIdToDistToLeafMap(); setEdited( true ); @@ -4181,7 +4317,7 @@ 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(); @@ -4320,7 +4456,7 @@ 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(); @@ -4410,7 +4546,9 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } } if ( getMainPanel().getOptions().isAntialiasScreen() ) { - if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) { + if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR ) + && !getMainPanel().getOptions().isShowDefaultNodeShapes() + && ( ( getControlPanel() != null ) && !getControlPanel().isShowDomainArchitectures() ) ) { _rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_OFF ); } else { @@ -4441,10 +4579,14 @@ 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; } @@ -4652,6 +4794,26 @@ 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 ) { @@ -4731,7 +4893,7 @@ 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; @@ -4768,7 +4930,7 @@ 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 ); @@ -4780,9 +4942,48 @@ 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.clearHashIdToNodeMap(); + _phylogeny.recalculateNumberOfExternalDescendants( true ); + resetNodeIdToDistToLeafMap(); + setEdited( true ); + } + repaint(); + } + + final void sortDescendants( final PhylogenyNode node ) { + if ( !node.isExternal() ) { + DESCENDANT_SORT_PRIORITY pri = DESCENDANT_SORT_PRIORITY.TAXONOMY; + if ( ( !getControlPanel().isShowTaxonomyScientificNames() && !getControlPanel().isShowTaxonomyCode() && !getControlPanel() + .isShowTaxonomyCommonNames() ) ) { + if ( ( getControlPanel().isShowSequenceAcc() || getControlPanel().isShowGeneNames() || getControlPanel() + .isShowGeneSymbols() ) ) { + pri = DESCENDANT_SORT_PRIORITY.SEQUENCE; + } + else if ( getControlPanel().isShowNodeNames() ) { + pri = DESCENDANT_SORT_PRIORITY.NODE_NAME; + } + } + PhylogenyMethods.sortNodeDescendents( node, pri ); + setNodeInPreorderToNull(); + _phylogeny.externalNodesHaveChanged(); + _phylogeny.clearHashIdToNodeMap(); + _phylogeny.recalculateNumberOfExternalDescendants( true ); + resetNodeIdToDistToLeafMap(); + setEdited( true ); } repaint(); } @@ -4853,7 +5054,7 @@ 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 );