}
final public void actionPerformed( final ActionEvent e ) {
-
boolean done = false;
final JMenuItem node_popup_menu_item = ( JMenuItem ) e.getSource();
for( int index = 0; ( index < _node_popup_menu_items.length ) && !done; index++ ) {
return;
}
if ( node.getNodeData().isHasSequence() ) {
- String query = Blast.obtainQueryForBlast( node );
+ 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 ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) {
+ nucleotide = !ForesterUtil.seqIsLikelyToBeAa( node.getNodeData().getSequence().getMolecularSequence() );
+ }
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: " + query );
- final Blast s = new Blast();
- s.ddbjBlast( query );
+ 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();
+ }
}
}
}
}
-
-
final void calcMaxDepth() {
if ( _phylogeny != null ) {
_circ_max_depth = PhylogenyMethods.calculateMaxDepth( _phylogeny );
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();
}
setWaitCursor();
AptxUtil.collapseSpeciesSpecificSubtrees( _phylogeny );
- updateSetOfCollapsedExternalNodes( _phylogeny );
+ updateSetOfCollapsedExternalNodes();
_phylogeny.recalculateNumberOfExternalDescendants( true );
resetNodeIdToDistToLeafMap();
calculateLongestExtNodeInfo();
}
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() ) || !ForesterUtil.isEmpty( node
- .getNodeData().getSequence().getMolecularSequence() )) );
+ 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 ] ) ) {
-
_node_popup_menu_items[ i ].setEnabled( isCanBlast( node ) );
}
else if ( title.equals( Configuration.clickto_options[ Configuration.delete_subtree_or_node ][ 0 ] ) ) {
paintNodeBox( _root.getXcoord(), _root.getYcoord(), _root, g, to_pdf, to_graphics_file, isInFoundNodes( _root ) );
}
- 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();
}
}
}
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();
}