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.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;
_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 );
}
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 ] ) {
else {
phy.addAsChild( node );
}
- _nodes_in_preorder = null;
+ setNodeInPreorderToNull();
_phylogeny.externalNodesHaveChanged();
_phylogeny.hashIDs();
_phylogeny.recalculateNumberOfExternalDescendants( true );
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 );
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() );
// 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;
}
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();
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();
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 );
return;
}
setWaitCursor();
- Util.colorPhylogenyAccordingToRanks( _phylogeny, rank, this );
- _control_panel.setColorBranches( true );
- if ( _control_panel.getColorBranchesCb() != null ) {
- _control_panel.getColorBranchesCb().setSelected( true );
+ 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 ) {
errorMessageNoCutCopyPasteInUnrootedDisplay();
return;
}
- _nodes_in_preorder = null;
+ setNodeInPreorderToNull();
setCutOrCopiedTree( _phylogeny.copy( node ) );
final List<PhylogenyNode> nodes = PhylogenyMethods.getAllDescendants( node );
final Set<Integer> node_ids = new HashSet<Integer>( nodes.size() );
if ( r != JOptionPane.OK_OPTION ) {
return;
}
- _nodes_in_preorder = null;
+ setNodeInPreorderToNull();
setCopiedAndPastedNodes( null );
setCutOrCopiedTree( _phylogeny.copy( node ) );
_phylogeny.deleteSubtree( node, true );
null,
options,
options[ 2 ] );
- _nodes_in_preorder = null;
+ setNodeInPreorderToNull();
boolean node_only = true;
if ( r == 1 ) {
node_only = false;
case EDIT_NODE_DATA:
showNodeEditFrame( node );
break;
+ case SORT_DESCENDENTS:
+ sortDescendants( node );
+ break;
default:
throw new IllegalArgumentException( "unknown action: " + action );
}
return;
}
setWaitCursor();
- Util.inferCommonPartOfScientificNames( _phylogeny );
+ AptxUtil.inferCommonPartOfScientificNames( _phylogeny );
setArrowCursor();
repaint();
}
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() {
_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 ] ) ) {
_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() );
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 ] );
}
JOptionPane.WARNING_MESSAGE );
return;
}
- _nodes_in_preorder = null;
+ setNodeInPreorderToNull();
setWaitCursor();
PhylogenyMethods.midpointRoot( _phylogeny );
resetNodeIdToDistToLeafMap();
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 ) ) {
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();
}
}
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();
}
}
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();
}
+ URLEncoder.encode( tax.getScientificName(), ForesterConstants.UTF8 );
}
catch ( final UnsupportedEncodingException e ) {
- Util.showErrorMessage( this, e.toString() );
+ AptxUtil.showErrorMessage( this, e.toString() );
e.printStackTrace();
}
}
+ URLEncoder.encode( tax.getTaxonomyCode(), ForesterConstants.UTF8 );
}
catch ( final UnsupportedEncodingException e ) {
- Util.showErrorMessage( this, e.toString() );
+ AptxUtil.showErrorMessage( this, e.toString() );
e.printStackTrace();
}
}
+ URLEncoder.encode( tax.getCommonName(), ForesterConstants.UTF8 );
}
catch ( final UnsupportedEncodingException e ) {
- Util.showErrorMessage( this, e.toString() );
+ AptxUtil.showErrorMessage( this, e.toString() );
e.printStackTrace();
}
}
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();
}
}
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 ) {
_collapsed_external_nodeid_set.clear();
E: for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
final PhylogenyNode ext_node = it.next();
final PhylogenyNode node,
final boolean to_pdf,
final boolean to_graphics_file ) {
- String conf_str = "";
final List<Confidence> 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();
}
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();
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() ) {
_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 ) );
}
}
+ private StringBuffer propertiesToString( final PhylogenyNode node ) {
+ final PropertiesMap properties = node.getNodeData().getProperties();
+ final StringBuffer sb = new StringBuffer();
+ boolean first = true;
+ for( final String ref : properties.getPropertyRefs() ) {
+ if ( first ) {
+ first = false;
+ }
+ else {
+ sb.append( " " );
+ }
+ final Property p = properties.getProperty( ref );
+ sb.append( getPartAfterColon( p.getRef() ) );
+ sb.append( "=" );
+ sb.append( p.getValue() );
+ if ( !ForesterUtil.isEmpty( p.getUnit() ) ) {
+ sb.append( getPartAfterColon( p.getUnit() ) );
+ }
+ }
+ return sb;
+ }
+
+ final private static String getPartAfterColon( final String s ) {
+ final int i = s.indexOf( ':' );
+ if ( ( i < 1 ) || ( i == ( s.length() - 1 ) ) ) {
+ return s;
+ }
+ return s.substring( i + 1, s.length() );
+ }
+
private double drawTaxonomyImage( final double x, final double y, final PhylogenyNode node, final Graphics2D g ) {
final List<Uri> us = new ArrayList<Uri>();
for( final Taxonomy t : node.getNodeData().getTaxonomies() ) {
++_external_node_index;
}
// Confidence values
- if ( getControlPanel().isShowBootstrapValues()
+ if ( getControlPanel().isShowConfidenceValues()
&& !node.isExternal()
&& !node.isRoot()
&& ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED )
}
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 );
}
}
//////////////
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 );
}
//////////////
}
}
node_ids.add( node.getId() );
getCopiedAndPastedNodes().addAll( node_ids );
- _nodes_in_preorder = null;
+ setNodeInPreorderToNull();
_phylogeny.externalNodesHaveChanged();
_phylogeny.hashIDs();
_phylogeny.recalculateNumberOfExternalDescendants( true );
getPhylogeny().reRoot( node );
getPhylogeny().recalculateNumberOfExternalDescendants( true );
resetNodeIdToDistToLeafMap();
- _nodes_in_preorder = null;
+ setNodeInPreorderToNull();
resetPreferredSize();
getMainPanel().adjustJScrollPane();
repaint();
* @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();
* 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;
}
.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 ) {
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;
}
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 );
}
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();
}
return;
}
setWaitCursor();
- Util.colorPhylogenyAccordingToExternalTaxonomy( _phylogeny, this );
+ AptxUtil.colorPhylogenyAccordingToExternalTaxonomy( _phylogeny, this );
_control_panel.setColorBranches( true );
if ( _control_panel.getColorBranchesCb() != null ) {
_control_panel.getColorBranchesCb().setSelected( true );
git://source.jalview.org / jalview.git / blobdiff