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;
}
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();
+ 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();
+ }
+ }
}
}
}
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() ) {
.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();
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 );
if ( !node.isExternal() && !node.isRoot() ) {
final boolean collapse = !node.isCollapse();
AptxUtil.collapseSubtree( node, collapse );
- updateSetOfCollapsedExternalNodes( _phylogeny );
+ updateSetOfCollapsedExternalNodes();
_phylogeny.recalculateNumberOfExternalDescendants( true );
resetNodeIdToDistToLeafMap();
calculateLongestExtNodeInfo();
- _nodes_in_preorder = null;
+ setNodeInPreorderToNull();
+ _control_panel.displayedPhylogenyMightHaveChanged( true );
resetPreferredSize();
updateOvSizes();
_main_panel.adjustJScrollPane();
}
setWaitCursor();
AptxUtil.collapseSpeciesSpecificSubtrees( _phylogeny );
- updateSetOfCollapsedExternalNodes( _phylogeny );
+ updateSetOfCollapsedExternalNodes();
_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;
case EDIT_NODE_DATA:
showNodeEditFrame( node );
break;
+ case SORT_DESCENDENTS:
+ sortDescendants( node );
+ break;
default:
throw new IllegalArgumentException( "unknown action: " + action );
}
}
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() {
_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();
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();
}
}
}
}
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;
}
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();
}