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;
private double _max_distance_to_root = -1;
private int _dynamic_hiding_factor = 0;
private boolean _edited = false;
- private Popup _node_desc_popup;
+ private Popup _node_desc_popup;
private JTextArea _rollover_popup;
// private final int _box_size;
// private final int _half_box_size;
else {
phy.addAsChild( node );
}
- _nodes_in_preorder = null;
+ setNodeInPreorderToNull();
_phylogeny.externalNodesHaveChanged();
_phylogeny.hashIDs();
_phylogeny.recalculateNumberOfExternalDescendants( true );
_phylogeny.recalculateNumberOfExternalDescendants( true );
resetNodeIdToDistToLeafMap();
calculateLongestExtNodeInfo();
- _nodes_in_preorder = null;
+ setNodeInPreorderToNull();
+ _control_panel.displayedPhylogenyMightHaveChanged( true );
resetPreferredSize();
updateOvSizes();
_main_panel.adjustJScrollPane();
_phylogeny.recalculateNumberOfExternalDescendants( true );
resetNodeIdToDistToLeafMap();
calculateLongestExtNodeInfo();
- _nodes_in_preorder = null;
+ setNodeInPreorderToNull();
resetPreferredSize();
_main_panel.adjustJScrollPane();
setArrowCursor();
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;
JOptionPane.WARNING_MESSAGE );
return;
}
- _nodes_in_preorder = null;
+ setNodeInPreorderToNull();
setWaitCursor();
PhylogenyMethods.midpointRoot( _phylogeny );
resetNodeIdToDistToLeafMap();
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 ( 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() ) {
else {
sb.append( " " );
}
-
-
final Property p = properties.getProperty( ref );
-
sb.append( getPartAfterColon( p.getRef() ) );
sb.append( "=" );
sb.append( p.getValue() );
}
return sb;
}
-
+
final private static String getPartAfterColon( final String s ) {
final int i = s.indexOf( ':' );
- if ( (i < 1) ||( i == ( s.length()-1)) ) {
+ if ( ( i < 1 ) || ( i == ( s.length() - 1 ) ) ) {
return s;
}
return s.substring( i + 1, s.length() );
++_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();
* 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() ) {
}
}
}
-
if ( _popup_buffer.length() > 0 ) {
if ( !getConfiguration().isUseNativeUI() ) {
_rollover_popup
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() ) {
_phylogeny.swapChildren( node );
- _nodes_in_preorder = null;
+ setNodeInPreorderToNull();
}
repaint();
}