import java.awt.Point;
import java.awt.Rectangle;
import java.awt.RenderingHints;
+import java.awt.Stroke;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.FocusAdapter;
import org.forester.phylogeny.PhylogenyMethods;
import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;
import org.forester.phylogeny.PhylogenyNode;
+import org.forester.phylogeny.data.Accession;
import org.forester.phylogeny.data.Annotation;
import org.forester.phylogeny.data.BranchColor;
import org.forester.phylogeny.data.Confidence;
import org.forester.util.DescriptiveStatistics;
import org.forester.util.ForesterConstants;
import org.forester.util.ForesterUtil;
-import org.forester.util.SequenceIdParser;
+import org.forester.util.SequenceAccessionTools;
+import org.forester.util.TaxonomyUtil;
public final class TreePanel extends JPanel implements ActionListener, MouseWheelListener, Printable {
+ private static final BasicStroke STROKE_2 = new BasicStroke( 2f );
+ private static final BasicStroke STROKE_1 = new BasicStroke( 1f );
+ private static final BasicStroke STROKE_075 = new BasicStroke( 0.75f );
+ private static final BasicStroke STROKE_05 = new BasicStroke( 0.5f );
+ private static final BasicStroke STROKE_025 = new BasicStroke( 0.25f );
+ private static final BasicStroke STROKE_01 = new BasicStroke( 0.1f );
+ private static final BasicStroke STROKE_005 = new BasicStroke( 0.05f );
private static final float PI = ( float ) ( Math.PI );
private static final double TWO_PI = 2 * Math.PI;
private static final float ONEHALF_PI = ( float ) ( 1.5 * Math.PI );
.getValue()
+ " " );
}
- if ( getControlPanel().isShowGeneNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) {
+ if ( getControlPanel().isShowSeqNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) {
sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getName() + " " );
}
- if ( getControlPanel().isShowGeneSymbols()
+ if ( getControlPanel().isShowSeqSymbols()
&& ( node.getNodeData().getSequence().getSymbol().length() > 0 ) ) {
sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getSymbol() + " " );
}
+ if ( getControlPanel().isShowGeneNames()
+ && ( node.getNodeData().getSequence().getGeneName().length() > 0 ) ) {
+ sum += getTreeFontSet()._fm_large
+ .stringWidth( node.getNodeData().getSequence().getGeneName() + " " );
+ }
if ( getControlPanel().isShowAnnotation()
&& ( node.getNodeData().getSequence().getAnnotations() != null )
&& !node.getNodeData().getSequence().getAnnotations().isEmpty() ) {
- sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getAnnotation( 0 )
- .asSimpleText()
+ sum += getTreeFontSet()._fm_large.stringWidth( TreePanelUtil.createAnnotationString( node
+ .getNodeData().getSequence().getAnnotations(), getOptions().isShowAnnotationRefSource() )
+ " " );
}
if ( getControlPanel().isShowDomainArchitectures()
}
final Color calculateTaxonomyBasedColor( final Taxonomy tax ) {
- String species = tax.getTaxonomyCode();
- if ( ForesterUtil.isEmpty( species ) ) {
- species = tax.getScientificName();
- if ( ForesterUtil.isEmpty( species ) ) {
- species = tax.getCommonName();
+ if ( getOptions().isColorByTaxonomicGroup() && !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
+ boolean ex = false;
+ String group = null;
+ try {
+ group = TaxonomyUtil.getTaxGroupByTaxCode( tax.getTaxonomyCode() );
+ }
+ catch ( final Exception e ) {
+ ex = true;
+ }
+ if ( !ex && !ForesterUtil.isEmpty( group ) ) {
+ final Color c = ForesterUtil.obtainColorDependingOnTaxonomyGroup( group );
+ if ( c != null ) {
+ return c;
+ }
}
- }
- if ( ForesterUtil.isEmpty( species ) ) {
return getTreeColorSet().getTaxonomyColor();
}
- // Look in species hash
- Color c = getControlPanel().getSpeciesColors().get( species );
- if ( c == null ) {
- c = AptxUtil.calculateColorFromString( species );
- getControlPanel().getSpeciesColors().put( species, c );
+ else {
+ if ( ForesterUtil.isEmpty( tax.getTaxonomyCode() ) && ForesterUtil.isEmpty( tax.getScientificName() ) ) {
+ return getTreeColorSet().getTaxonomyColor();
+ }
+ Color c = null;
+ if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
+ c = getControlPanel().getSpeciesColors().get( tax.getTaxonomyCode() );
+ }
+ if ( ( c == null ) && !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
+ c = getControlPanel().getSpeciesColors().get( tax.getScientificName() );
+ }
+ if ( c == null ) {
+ if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
+ c = TreePanelUtil.calculateColorFromString( tax.getTaxonomyCode(), true );
+ getControlPanel().getSpeciesColors().put( tax.getTaxonomyCode(), c );
+ }
+ else {
+ c = TreePanelUtil.calculateColorFromString( tax.getScientificName(), true );
+ getControlPanel().getSpeciesColors().put( tax.getScientificName(), c );
+ }
+ }
+ return c;
}
- return c;
}
void checkForVectorProperties( final Phylogeny phy ) {
}
if ( !node.isExternal() && !node.isRoot() ) {
final boolean collapse = !node.isCollapse();
- AptxUtil.collapseSubtree( node, collapse );
+ TreePanelUtil.collapseSubtree( node, collapse );
updateSetOfCollapsedExternalNodes();
_phylogeny.recalculateNumberOfExternalDescendants( true );
resetNodeIdToDistToLeafMap();
return;
}
setWaitCursor();
- AptxUtil.collapseSpeciesSpecificSubtrees( _phylogeny );
+ TreePanelUtil.collapseSpeciesSpecificSubtrees( _phylogeny );
updateSetOfCollapsedExternalNodes();
_phylogeny.recalculateNumberOfExternalDescendants( true );
resetNodeIdToDistToLeafMap();
}
setWaitCursor();
AptxUtil.removeBranchColors( _phylogeny );
- final int colorizations = AptxUtil.colorPhylogenyAccordingToRanks( _phylogeny, rank, this );
+ final int colorizations = TreePanelUtil.colorPhylogenyAccordingToRanks( _phylogeny, rank, this );
if ( colorizations > 0 ) {
_control_panel.setColorBranches( true );
if ( _control_panel.getColorBranchesCb() != null ) {
}
setWaitCursor();
AptxUtil.removeBranchColors( _phylogeny );
- AptxUtil.colorPhylogenyAccordingToConfidenceValues( _phylogeny, this );
+ TreePanelUtil.colorPhylogenyAccordingToConfidenceValues( _phylogeny, this );
_control_panel.setColorBranches( true );
if ( _control_panel.getColorBranchesCb() != null ) {
_control_panel.getColorBranchesCb().setSelected( true );
g.fillRect( graphics_file_x, graphics_file_y, graphics_file_width, graphics_file_height );
}
}
- g.setStroke( new BasicStroke( 1 ) );
+ setupStroke( g );
}
else {
g.setStroke( new BasicStroke( getOptions().getPrintLineWidth() ) );
DESCENDANT_SORT_PRIORITY pri = DESCENDANT_SORT_PRIORITY.TAXONOMY;
if ( ( !getControlPanel().isShowTaxonomyScientificNames() && !getControlPanel().isShowTaxonomyCode() && !getControlPanel()
.isShowTaxonomyCommonNames() ) ) {
- if ( ( getControlPanel().isShowSequenceAcc() || getControlPanel().isShowGeneNames() || getControlPanel()
- .isShowGeneSymbols() ) ) {
+ if ( ( getControlPanel().isShowSequenceAcc() || getControlPanel().isShowSeqNames() || getControlPanel()
+ .isShowSeqSymbols() ) ) {
pri = DESCENDANT_SORT_PRIORITY.SEQUENCE;
}
else if ( getControlPanel().isShowNodeNames() ) {
_sub_phylogenies[ _subtree_index ] = _phylogeny;
_sub_phylogenies_temp_roots[ _subtree_index ] = node;
++_subtree_index;
- _phylogeny = subTree( node, _phylogeny );
+ _phylogeny = TreePanelUtil.subTree( node, _phylogeny );
updateSubSuperTreeButton();
}
else if ( node.isRoot() && isCurrentTreeIsSubtree() ) {
return;
}
setWaitCursor();
- AptxUtil.colorPhylogenyAccordingToExternalTaxonomy( _phylogeny, this );
+ TreePanelUtil.colorPhylogenyAccordingToExternalTaxonomy( _phylogeny, this );
_control_panel.setColorBranches( true );
if ( _control_panel.getColorBranchesCb() != null ) {
_control_panel.getColorBranchesCb().setSelected( true );
}
}
if ( type == '?' ) {
- if ( SequenceIdParser.isProtein( query ) ) {
+ if ( SequenceAccessionTools.isProteinDbQuery( query ) ) {
type = 'p';
}
else {
if ( getControlPanel().isColorAccordingToAnnotation() && ( getControlPanel().getAnnotationColors() != null ) ) {
final StringBuilder sb = new StringBuilder();
for( final Annotation a : ann ) {
- sb.append( !ForesterUtil.isEmpty( a.getRef() ) ? a.getRef() : a.getDesc() );
+ sb.append( !ForesterUtil.isEmpty( a.getRefValue() ) ? a.getRefValue() : a.getDesc() );
}
final String ann_str = sb.toString();
if ( !ForesterUtil.isEmpty( ann_str ) ) {
c = getControlPanel().getAnnotationColors().get( ann_str );
if ( c == null ) {
- c = AptxUtil.calculateColorFromString( ann_str );
+ c = TreePanelUtil.calculateColorFromString( ann_str, false );
getControlPanel().getAnnotationColors().put( ann_str, c );
}
if ( c == null ) {
JOptionPane.WARNING_MESSAGE );
}
- final private void colorizeSubtree( final Color c, final PhylogenyNode node ) {
- if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
- JOptionPane.showMessageDialog( this,
- "Cannot colorize subtree in unrooted display type",
- "Attempt to colorize subtree in unrooted display",
- JOptionPane.WARNING_MESSAGE );
- return;
- }
+ final private void colorizeSubtree( final Color c,
+ final PhylogenyNode node,
+ final List<PhylogenyNode> additional_nodes ) {
_control_panel.setColorBranches( true );
if ( _control_panel.getColorBranchesCb() != null ) {
_control_panel.getColorBranchesCb().setSelected( true );
}
- for( final PreorderTreeIterator it = new PreorderTreeIterator( node ); it.hasNext(); ) {
- it.next().getBranchData().setBranchColor( new BranchColor( c ) );
+ if ( node != null ) {
+ for( final PreorderTreeIterator it = new PreorderTreeIterator( node ); it.hasNext(); ) {
+ it.next().getBranchData().setBranchColor( new BranchColor( c ) );
+ }
+ }
+ if ( additional_nodes != null ) {
+ for( final PhylogenyNode n : additional_nodes ) {
+ n.getBranchData().setBranchColor( new BranchColor( c ) );
+ }
}
repaint();
}
final private void colorSubtree( final PhylogenyNode node ) {
- Color intitial_color = null;
- if ( getControlPanel().isColorBranches() && ( PhylogenyMethods.getBranchColorValue( node ) != null )
- && ( ( ( !node.isRoot() && ( node.getParent().getNumberOfDescendants() < 3 ) ) ) || ( node.isRoot() ) ) ) {
- intitial_color = PhylogenyMethods.getBranchColorValue( node );
+ if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
+ JOptionPane.showMessageDialog( this,
+ "Cannot colorize subtree in unrooted display type",
+ "Attempt to colorize subtree in unrooted display",
+ JOptionPane.WARNING_MESSAGE );
+ return;
+ }
+ _color_chooser.setPreviewPanel( new JPanel() );
+ SubtreeColorizationActionListener al;
+ if ( ( getFoundNodes() != null ) && !getFoundNodes().isEmpty() ) {
+ final List<PhylogenyNode> additional_nodes = getFoundNodesAsListOfPhylogenyNodes();
+ al = new SubtreeColorizationActionListener( _color_chooser, node, additional_nodes );
}
else {
- intitial_color = getTreeColorSet().getBranchColor();
+ al = new SubtreeColorizationActionListener( _color_chooser, node );
}
- _color_chooser.setColor( intitial_color );
- _color_chooser.setPreviewPanel( new JPanel() );
final JDialog dialog = JColorChooser
- .createDialog( this,
- "Subtree colorization",
- true,
- _color_chooser,
- new SubtreeColorizationActionListener( _color_chooser, node ),
- null );
+ .createDialog( this, "Subtree colorization", true, _color_chooser, al, null );
dialog.setVisible( true );
}
+ private List<PhylogenyNode> getFoundNodesAsListOfPhylogenyNodes() {
+ final List<PhylogenyNode> additional_nodes = new ArrayList<PhylogenyNode>();
+ for( final Long id : getFoundNodes() ) {
+ additional_nodes.add( _phylogeny.getNode( id ) );
+ }
+ return additional_nodes;
+ }
+
final private void copySubtree( final PhylogenyNode node ) {
if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
errorMessageNoCutCopyPasteInUnrootedDisplay();
repaint();
}
- private String createAnnotationString( final SortedSet<Annotation> ann ) {
- final StringBuilder sb = new StringBuilder();
- boolean first = true;
- for( final Annotation a : ann ) {
- if ( !first ) {
- sb.append( "+" );
- }
- else {
- first = false;
- }
- sb.append( a.asSimpleText() );
- }
- final String ann_str = sb.toString();
- return ann_str;
- }
-
final private String createASimpleTextRepresentationOfANode( final PhylogenyNode node ) {
final String tax = PhylogenyMethods.getSpecies( node );
String label = node.getName();
case OPEN_TAX_WEB:
openTaxWeb( node );
break;
+ case OPEN_PDB_WEB:
+ openPdbWeb( node );
+ break;
case CUT_SUBTREE:
cutSubtree( node );
break;
return Blast.isContainsQueryForBlast( node );
}
+ final private String isCanOpenSeqWeb( final PhylogenyNode node ) {
+ final Accession a = SequenceAccessionTools.obtainAccessorFromDataFields( node );
+ if ( a != null ) {
+ return a.getValue();
+ }
+ return null;
+ }
+
+ final private List<Accession> getPdbAccs( final PhylogenyNode node ) {
+ final List<Accession> pdb_ids = new ArrayList<Accession>();
+ if ( node.getNodeData().isHasSequence() ) {
+ final Sequence seq = node.getNodeData().getSequence();
+ if ( !ForesterUtil.isEmpty( seq.getCrossReferences() ) ) {
+ final SortedSet<Accession> cross_refs = seq.getCrossReferences();
+ for( final Accession acc : cross_refs ) {
+ if ( acc.getSource().equalsIgnoreCase( "pdb" ) ) {
+ pdb_ids.add( acc );
+ }
+ }
+ }
+ }
+ return pdb_ids;
+ }
+
final private boolean isCanOpenTaxWeb( final PhylogenyNode node ) {
if ( node.getNodeData().isHasTaxonomy()
&& ( ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getScientificName() ) )
_node_popup_menu_items[ i ].setEnabled( false );
}
}
+ else if ( title.equals( Configuration.clickto_options[ Configuration.open_pdb_web ][ 0 ] ) ) {
+ final List<Accession> accs = getPdbAccs( node );
+ _node_popup_menu_items[ i ] = new JMenuItem( title );
+ if ( !ForesterUtil.isEmpty( accs ) ) {
+ if ( accs.size() == 1 ) {
+ _node_popup_menu_items[ i ].setText( _node_popup_menu_items[ i ].getText() + " ["
+ + TreePanelUtil.pdbAccToString( accs, 0 ) + "]" );
+ _node_popup_menu_items[ i ].setEnabled( true );
+ }
+ else if ( accs.size() == 2 ) {
+ _node_popup_menu_items[ i ].setText( _node_popup_menu_items[ i ].getText() + " ["
+ + TreePanelUtil.pdbAccToString( accs, 0 ) + ", "
+ + TreePanelUtil.pdbAccToString( accs, 1 ) + "]" );
+ _node_popup_menu_items[ i ].setEnabled( true );
+ }
+ else if ( accs.size() == 3 ) {
+ _node_popup_menu_items[ i ].setText( _node_popup_menu_items[ i ].getText() + " ["
+ + TreePanelUtil.pdbAccToString( accs, 0 ) + ", "
+ + TreePanelUtil.pdbAccToString( accs, 1 ) + ", "
+ + TreePanelUtil.pdbAccToString( accs, 2 ) + "]" );
+ _node_popup_menu_items[ i ].setEnabled( true );
+ }
+ else {
+ _node_popup_menu_items[ i ].setText( _node_popup_menu_items[ i ].getText() + " ["
+ + TreePanelUtil.pdbAccToString( accs, 0 ) + ", "
+ + TreePanelUtil.pdbAccToString( accs, 1 ) + ", "
+ + TreePanelUtil.pdbAccToString( accs, 2 ) + ", + " + ( accs.size() - 3 ) + " more]" );
+ _node_popup_menu_items[ i ].setEnabled( true );
+ }
+ }
+ else {
+ _node_popup_menu_items[ i ].setEnabled( false );
+ }
+ //
+ }
else if ( title.equals( Configuration.clickto_options[ Configuration.open_tax_web ][ 0 ] ) ) {
_node_popup_menu_items[ i ].setEnabled( isCanOpenTaxWeb( node ) );
}
switch ( getOptions().getExtDescNodeDataToReturn() ) {
case NODE_NAME:
return "Node Names";
+ case GENE_NAME:
+ return "Gene Names";
case SEQUENCE_NAME:
return "Sequence Names";
case SEQUENCE_SYMBOL:
return "Scientific Names";
case TAXONOMY_CODE:
return "Taxonomy Codes";
+ case TAXONOMY_COMM0N_NAME:
+ return "Taxonomy Common Names";
case UNKNOWN:
return "User Selected Data";
default:
}
}
- final private String isCanOpenSeqWeb( final PhylogenyNode node ) {
- String v = ForesterUtil.extractUniProtKbProteinSeqIdentifier( node );
- if ( ForesterUtil.isEmpty( v ) ) {
- v = ForesterUtil.extractGenbankAccessor( node );
- }
- if ( ForesterUtil.isEmpty( v ) ) {
- v = ForesterUtil.extractRefSeqAccessorAccessor( node );
- }
- if ( ForesterUtil.isEmpty( v ) ) {
- v = ForesterUtil.extractGInumber( node );
- }
- return v;
- }
-
final private void openSeqWeb( final PhylogenyNode node ) {
if ( ForesterUtil.isEmpty( isCanOpenSeqWeb( node ) ) ) {
cannotOpenBrowserWarningMessage( "sequence" );
return;
}
- final String uri_str = AptxUtil.createUriForSeqWeb( node, getConfiguration(), this );
+ final String uri_str = TreePanelUtil.createUriForSeqWeb( node, getConfiguration(), this );
if ( !ForesterUtil.isEmpty( uri_str ) ) {
try {
AptxUtil.launchWebBrowser( new URI( uri_str ),
}
}
+ final private void openPdbWeb( final PhylogenyNode node ) {
+ final List<Accession> pdb_ids = getPdbAccs( node );
+ if ( ForesterUtil.isEmpty( pdb_ids ) ) {
+ cannotOpenBrowserWarningMessage( "PDB" );
+ return;
+ }
+ final List<String> uri_strs = TreePanelUtil.createUrisForPdbWeb( node, pdb_ids, getConfiguration(), this );
+ if ( !ForesterUtil.isEmpty( uri_strs ) ) {
+ for( final String uri_str : uri_strs ) {
+ try {
+ AptxUtil.launchWebBrowser( new URI( uri_str ),
+ isApplet(),
+ isApplet() ? obtainApplet() : null,
+ "_aptx_seq" );
+ }
+ catch ( final IOException e ) {
+ AptxUtil.showErrorMessage( this, e.toString() );
+ e.printStackTrace();
+ }
+ catch ( final URISyntaxException e ) {
+ AptxUtil.showErrorMessage( this, e.toString() );
+ e.printStackTrace();
+ }
+ }
+ }
+ else {
+ cannotOpenBrowserWarningMessage( "PDB" );
+ }
+ }
+
final private void openTaxWeb( final PhylogenyNode node ) {
if ( !isCanOpenTaxWeb( node ) ) {
cannotOpenBrowserWarningMessage( "taxonomic" );
if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
outline_color = Color.BLACK;
}
- else if ( getControlPanel().isEvents() && AptxUtil.isHasAssignedEvent( node ) ) {
+ else if ( getControlPanel().isEvents() && TreePanelUtil.isHasAssignedEvent( node ) ) {
final Event event = node.getNodeData().getEvent();
if ( event.isDuplication() ) {
outline_color = getTreeColorSet().getDuplicationBoxColor();
_sb.append( node.getName() );
}
if ( node.getNodeData().isHasSequence() ) {
- if ( getControlPanel().isShowGeneSymbols() && ( node.getNodeData().getSequence().getSymbol().length() > 0 ) ) {
+ if ( getControlPanel().isShowSeqSymbols() && ( node.getNodeData().getSequence().getSymbol().length() > 0 ) ) {
if ( _sb.length() > 0 ) {
_sb.append( " " );
}
_sb.append( node.getNodeData().getSequence().getSymbol() );
}
- if ( getControlPanel().isShowGeneNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) {
+ if ( getControlPanel().isShowGeneNames() && ( node.getNodeData().getSequence().getGeneName().length() > 0 ) ) {
+ if ( _sb.length() > 0 ) {
+ _sb.append( " " );
+ }
+ _sb.append( node.getNodeData().getSequence().getGeneName() );
+ }
+ if ( getControlPanel().isShowSeqNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) {
if ( _sb.length() > 0 ) {
_sb.append( " " );
}
else if ( getControlPanel().isColorAccordingToAnnotation() ) {
g.setColor( calculateColorForAnnotation( ann ) );
}
- final String ann_str = createAnnotationString( ann );
+ final String ann_str = TreePanelUtil.createAnnotationString( ann, getOptions().isShowAnnotationRefSource() );
TreePanel.drawString( ann_str, node.getXcoord() + x + 3 + half_box_size, node.getYcoord()
+ ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g );
_sb.setLength( 0 );
}
_sb.append( node.getNodeData().getSequence().getAccession().getValue() );
}
- if ( getControlPanel().isShowGeneNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) {
+ if ( getControlPanel().isShowSeqNames() && ( node.getNodeData().getSequence().getName().length() > 0 ) ) {
if ( _sb.length() > 0 ) {
_sb.append( " " );
}
}
}
if ( node.getNodeData().isHasSequence() ) {
- if ( getControlPanel().isShowGeneNames()
+ if ( getControlPanel().isShowSeqNames()
&& ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getName() ) ) ) {
x += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getName()
+ " " );
}
- if ( getControlPanel().isShowGeneSymbols()
+ if ( getControlPanel().isShowSeqSymbols()
&& ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getSymbol() ) ) ) {
x += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getSymbol()
+ " " );
}
+ if ( getControlPanel().isShowGeneNames()
+ && ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getGeneName() ) ) ) {
+ x += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence().getGeneName()
+ + " " );
+ }
if ( getControlPanel().isShowSequenceAcc()
&& ( node.getNodeData().getSequence().getAccession() != null ) ) {
x += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getSequence()
.getAccession().toString()
+ " " );
}
+ if ( getControlPanel().isShowAnnotation()
+ && ( node.getNodeData().getSequence().getAnnotations() != null )
+ && ( !node.getNodeData().getSequence().getAnnotations().isEmpty() ) ) {
+ x += getTreeFontSet()._fm_large.stringWidth( TreePanelUtil.createAnnotationString( node
+ .getNodeData().getSequence().getAnnotations(), getOptions()
+ .isShowAnnotationRefSource() )
+ + " " );
+ }
}
if ( getControlPanel().isShowNodeNames() && !ForesterUtil.isEmpty( node.getName() ) ) {
x += getTreeFontSet()._fm_large.stringWidth( node.getName() + " " );
final float y = getVisibleRect().y + getOvYPosition() + ( getOvMaxHeight() / y_ratio );
g.setColor( getTreeColorSet().getFoundColor() );
getOvRectangle().setRect( x, y, width, height );
+ final Stroke s = g.getStroke();
+ g.setStroke( STROKE_1 );
if ( ( width < 6 ) && ( height < 6 ) ) {
drawRectFilled( x, y, 6, 6, g );
getOvVirtualRectangle().setRect( x, y, 6, 6 );
}
getOvVirtualRectangle().setRect( x, y, width, height );
}
+ g.setStroke( s );
}
final private void paintPhylogenyLite( final Graphics2D g ) {
.setXSecondary( ( float ) ( getVisibleRect().x + getOvXPosition() + ( MOVE / ( getVisibleRect().width / getOvRectangle()
.getWidth() ) ) ) );
_phylogeny.getRoot().setYSecondary( ( getVisibleRect().y + getOvYStart() ) );
- g.setStroke( new BasicStroke( 0.5f ) ); //TODO
+ final Stroke s = g.getStroke();
+ g.setStroke( STROKE_05 );
for( final PhylogenyNode element : _nodes_in_preorder ) {
paintNodeLite( g, element );
}
- g.setStroke( new BasicStroke( 1 ) ); //TODO
+ g.setStroke( s );
paintOvRectangle( g );
}
else {
g.setColor( getTreeColorSet().getBranchLengthColor() );
}
+ final Stroke s = g.getStroke();
+ g.setStroke( STROKE_1 );
drawLine( x1, y1, x1, y2, g );
drawLine( x2, y1, x2, y2, g );
drawLine( x1, y3, x2, y3, g );
if ( getScaleLabel() != null ) {
g.drawString( getScaleLabel(), ( x1 + 2 ), y3 - 2 );
}
+ g.setStroke( s );
}
final private int paintTaxonomy( final Graphics2D g,
sb.append( " " );
}
final Property p = properties.getProperty( ref );
- sb.append( getPartAfterColon( p.getRef() ) );
+ sb.append( TreePanelUtil.getPartAfterColon( p.getRef() ) );
sb.append( "=" );
sb.append( p.getValue() );
if ( !ForesterUtil.isEmpty( p.getUnit() ) ) {
- sb.append( getPartAfterColon( p.getUnit() ) );
+ sb.append( TreePanelUtil.getPartAfterColon( p.getUnit() ) );
}
}
return sb;
_scale_label = scale_label;
}
+ private final void setupStroke( final Graphics2D g ) {
+ if ( getYdistance() < 0.001 ) {
+ g.setStroke( STROKE_005 );
+ }
+ else if ( getYdistance() < 0.01 ) {
+ g.setStroke( STROKE_01 );
+ }
+ else if ( getYdistance() < 0.5 ) {
+ g.setStroke( STROKE_025 );
+ }
+ else if ( getYdistance() < 1 ) {
+ g.setStroke( STROKE_05 );
+ }
+ else if ( getYdistance() < 2 ) {
+ g.setStroke( STROKE_075 );
+ }
+ else if ( getYdistance() < 20 ) {
+ g.setStroke( STROKE_1 );
+ }
+ else {
+ g.setStroke( STROKE_2 );
+ }
+ }
+
final private void setUpUrtFactor() {
final int d = getVisibleRect().width < getVisibleRect().height ? getVisibleRect().width
: getVisibleRect().height;
private void showExtDescNodeData( final PhylogenyNode node ) {
final List<String> data = new ArrayList<String>();
- for( final PhylogenyNode n : node.getAllExternalDescendants() ) {
+ final List<PhylogenyNode> nodes = node.getAllExternalDescendants();
+ if ( ( getFoundNodes() != null ) && !getFoundNodes().isEmpty() ) {
+ for( final PhylogenyNode n : getFoundNodesAsListOfPhylogenyNodes() ) {
+ if ( !nodes.contains( n ) ) {
+ nodes.add( n );
+ }
+ }
+ }
+ for( final PhylogenyNode n : nodes ) {
switch ( getOptions().getExtDescNodeDataToReturn() ) {
case NODE_NAME:
if ( !ForesterUtil.isEmpty( n.getName() ) ) {
data.add( n.getNodeData().getSequence().getName() );
}
break;
+ case GENE_NAME:
+ if ( n.getNodeData().isHasSequence()
+ && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getGeneName() ) ) {
+ data.add( n.getNodeData().getSequence().getGeneName() );
+ }
+ break;
case SEQUENCE_SYMBOL:
if ( n.getNodeData().isHasSequence()
&& !ForesterUtil.isEmpty( n.getNodeData().getSequence().getSymbol() ) ) {
final StringBuilder sb = new StringBuilder();
if ( n.getNodeData().isHasSequence()
&& !ForesterUtil.isEmpty( n.getNodeData().getSequence().getMolecularSequence() ) ) {
+ final StringBuilder ann = new StringBuilder();
+ if ( !ForesterUtil.isEmpty( n.getName() ) ) {
+ ann.append( n.getName() );
+ ann.append( "|" );
+ }
+ if ( !ForesterUtil.isEmpty( n.getNodeData().getSequence().getSymbol() ) ) {
+ ann.append( "SYM=" );
+ ann.append( n.getNodeData().getSequence().getSymbol() );
+ ann.append( "|" );
+ }
if ( !ForesterUtil.isEmpty( n.getNodeData().getSequence().getName() ) ) {
- sb.append( SequenceWriter.toFasta( n.getNodeData().getSequence().getName(), n.getNodeData()
- .getSequence().getMolecularSequence(), 60 ) );
+ ann.append( "NAME=" );
+ ann.append( n.getNodeData().getSequence().getName() );
+ ann.append( "|" );
+ }
+ if ( !ForesterUtil.isEmpty( n.getNodeData().getSequence().getGeneName() ) ) {
+ ann.append( "GN=" );
+ ann.append( n.getNodeData().getSequence().getGeneName() );
+ ann.append( "|" );
+ }
+ if ( n.getNodeData().getSequence().getAccession() != null ) {
+ ann.append( "ACC=" );
+ ann.append( n.getNodeData().getSequence().getAccession().asText() );
+ ann.append( "|" );
+ }
+ if ( n.getNodeData().isHasTaxonomy() ) {
+ if ( !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) {
+ ann.append( "TAXID=" );
+ ann.append( n.getNodeData().getTaxonomy().getTaxonomyCode() );
+ ann.append( "|" );
+ }
+ if ( !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) {
+ ann.append( "SN=" );
+ ann.append( n.getNodeData().getTaxonomy().getScientificName() );
+ ann.append( "|" );
+ }
+ }
+ String ann_str;
+ if ( ann.charAt( ann.length() - 1 ) == '|' ) {
+ ann_str = ann.substring( 0, ann.length() - 1 );
}
else {
- sb.append( SequenceWriter.toFasta( n.getName(), n.getNodeData().getSequence()
- .getMolecularSequence(), 60 ) );
+ ann_str = ann.toString();
}
+ sb.append( SequenceWriter.toFasta( ann_str, n.getNodeData().getSequence()
+ .getMolecularSequence(), 60 ) );
data.add( sb.toString() );
}
break;
data.add( n.getNodeData().getTaxonomy().getScientificName() );
}
break;
+ case TAXONOMY_COMM0N_NAME:
+ if ( n.getNodeData().isHasTaxonomy()
+ && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getCommonName() ) ) {
+ data.add( n.getNodeData().getTaxonomy().getCommonName() );
+ }
+ break;
case TAXONOMY_CODE:
if ( n.getNodeData().isHasTaxonomy()
&& !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) {
}
break;
case UNKNOWN:
- AptxUtil.showExtDescNodeDataUserSelectedHelper( getControlPanel(), n, data );
+ TreePanelUtil.showExtDescNodeDataUserSelectedHelper( getControlPanel(), n, data );
break;
default:
throw new IllegalArgumentException( "unknown data element: "
+ getOptions().getExtDescNodeDataToReturn() );
}
} // for loop
+ final StringBuilder sb = new StringBuilder();
+ final int size = TreePanelUtil.makeSB( data, getOptions(), sb );
if ( ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.CONSOLE )
|| ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.BUFFER_ONLY ) ) {
- final StringBuilder sb = new StringBuilder();
- for( final String d : data ) {
- if ( !ForesterUtil.isEmpty( d ) ) {
- if ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.CONSOLE ) {
- System.out.println( d );
- }
- sb.append( d );
- sb.append( ForesterUtil.LINE_SEPARATOR );
- }
+ if ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.CONSOLE ) {
+ System.out.println( sb );
}
if ( sb.length() < 1 ) {
clearCurrentExternalNodesDataBuffer();
}
}
else if ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.WINODW ) {
- final StringBuilder sb = new StringBuilder();
- for( final String d : data ) {
- if ( !ForesterUtil.isEmpty( d ) ) {
- sb.append( d );
- sb.append( ForesterUtil.LINE_SEPARATOR );
- }
- }
if ( sb.length() < 1 ) {
- AptxUtil.showInformationMessage( this,
- "No Appropriate Data (" + obtainTitleForExtDescNodeData() + ")",
- "Descendants of selected node do not contain selected data" );
+ TreePanelUtil.showInformationMessage( this, "No Appropriate Data (" + obtainTitleForExtDescNodeData()
+ + ")", "Descendants of selected node do not contain selected data" );
clearCurrentExternalNodesDataBuffer();
}
else {
setCurrentExternalNodesDataBuffer( sb );
- final String title = "External Descendants "
- + ( getOptions().getExtDescNodeDataToReturn() == NODE_DATA.UNKNOWN ? "Data"
- : obtainTitleForExtDescNodeData() ) + " (" + data.size() + "/"
- + node.getNumberOfExternalNodes() + ") For Node " + node;
+ String title;
+ if ( ( getFoundNodes() != null ) && !getFoundNodes().isEmpty() ) {
+ title = ( getOptions().getExtDescNodeDataToReturn() == NODE_DATA.UNKNOWN ? "Data"
+ : obtainTitleForExtDescNodeData() )
+ + " for "
+ + data.size()
+ + " nodes, unique entries: "
+ + size;
+ }
+ else {
+ title = ( getOptions().getExtDescNodeDataToReturn() == NODE_DATA.UNKNOWN ? "Data"
+ : obtainTitleForExtDescNodeData() )
+ + " for "
+ + data.size()
+ + "/"
+ + node.getNumberOfExternalNodes()
+ + " external descendats of node "
+ + node
+ + ", unique entries: " + size;
+ }
final String s = sb.toString().trim();
if ( getMainPanel().getMainFrame() == null ) {
// Must be "E" applet version.
final private void showNodeDataPopup( final MouseEvent e, final PhylogenyNode node ) {
try {
if ( ( node.getName().length() > 0 )
- || ( node.getNodeData().isHasTaxonomy() && !isTaxonomyEmpty( node.getNodeData().getTaxonomy() ) )
- || ( node.getNodeData().isHasSequence() && !isSequenceEmpty( node.getNodeData().getSequence() ) )
- || ( node.getNodeData().isHasDate() ) || ( node.getNodeData().isHasDistribution() )
- || node.getBranchData().isHasConfidences() ) {
+ || ( node.getNodeData().isHasTaxonomy() && !TreePanelUtil.isTaxonomyEmpty( node.getNodeData()
+ .getTaxonomy() ) )
+ || ( node.getNodeData().isHasSequence() && !TreePanelUtil.isSequenceEmpty( node.getNodeData()
+ .getSequence() ) ) || ( node.getNodeData().isHasDate() )
+ || ( node.getNodeData().isHasDistribution() ) || node.getBranchData().isHasConfidences() ) {
_popup_buffer.setLength( 0 );
short lines = 0;
if ( node.getName().length() > 0 ) {
lines++;
_popup_buffer.append( node.getName() );
}
- if ( node.getNodeData().isHasTaxonomy() && !isTaxonomyEmpty( node.getNodeData().getTaxonomy() ) ) {
+ if ( node.getNodeData().isHasTaxonomy()
+ && !TreePanelUtil.isTaxonomyEmpty( node.getNodeData().getTaxonomy() ) ) {
lines++;
boolean enc_data = false;
final Taxonomy tax = node.getNodeData().getTaxonomy();
}
}
}
- if ( node.getNodeData().isHasSequence() && !isSequenceEmpty( node.getNodeData().getSequence() ) ) {
+ if ( node.getNodeData().isHasSequence()
+ && !TreePanelUtil.isSequenceEmpty( node.getNodeData().getSequence() ) ) {
lines++;
boolean enc_data = false;
if ( _popup_buffer.length() > 0 ) {
_popup_buffer.append( "]" );
enc_data = true;
}
+ if ( !ForesterUtil.isEmpty( seq.getGeneName() ) ) {
+ if ( enc_data ) {
+ _popup_buffer.append( " [" );
+ }
+ else {
+ _popup_buffer.append( "[" );
+ }
+ _popup_buffer.append( seq.getGeneName() );
+ _popup_buffer.append( "]" );
+ enc_data = true;
+ }
if ( !ForesterUtil.isEmpty( seq.getName() ) ) {
if ( enc_data ) {
_popup_buffer.append( " " );
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( TreePanelUtil.getPartAfterColon( p.getRef() ) );
_popup_buffer.append( "=" );
_popup_buffer.append( p.getValue() );
if ( !ForesterUtil.isEmpty( p.getUnit() ) ) {
- _popup_buffer.append( getPartAfterColon( p.getUnit() ) );
+ _popup_buffer.append( TreePanelUtil.getPartAfterColon( p.getUnit() ) );
}
}
}
}
}
- final private static void drawString( final int i, final double x, final double y, final Graphics2D g ) {
- g.drawString( String.valueOf( i ), ( int ) ( x + 0.5 ), ( int ) ( y + 0.5 ) );
- }
-
final private static void drawString( final String str, final double x, final double y, final Graphics2D g ) {
g.drawString( str, ( int ) ( x + 0.5 ), ( int ) ( y + 0.5 ) );
}
- 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() );
- }
-
- final private static boolean isSequenceEmpty( final Sequence seq ) {
- return ( seq.getAccession() == null ) && ForesterUtil.isEmpty( seq.getName() )
- && ForesterUtil.isEmpty( seq.getSymbol() );
- }
-
- final private static boolean isTaxonomyEmpty( final Taxonomy tax ) {
- return ( ( tax.getIdentifier() == null ) && ForesterUtil.isEmpty( tax.getTaxonomyCode() )
- && ForesterUtil.isEmpty( tax.getCommonName() ) && ForesterUtil.isEmpty( tax.getScientificName() ) && tax
- .getSynonyms().isEmpty() );
- }
-
final private static boolean plusPressed( final int key_code ) {
return ( ( key_code == KeyEvent.VK_ADD ) || ( key_code == KeyEvent.VK_PLUS )
|| ( key_code == KeyEvent.VK_EQUALS ) || ( key_code == KeyEvent.VK_SEMICOLON ) || ( key_code == KeyEvent.VK_1 ) );
}
- final private static Phylogeny subTree( final PhylogenyNode new_root, final Phylogeny source_phy ) {
- final Phylogeny new_phy = new Phylogeny();
- new_phy.setRooted( true );
- new_phy.setName( source_phy.getName() );
- new_phy.setDescription( source_phy.getDescription() );
- new_phy.setType( source_phy.getType() );
- new_phy.setDistanceUnit( source_phy.getDistanceUnit() );
- new_phy.setConfidence( source_phy.getConfidence() );
- new_phy.setIdentifier( source_phy.getIdentifier() );
- new_phy.setRoot( new_root.copyNodeDataShallow() );
- int i = 0;
- for( final PhylogenyNode n : new_root.getDescendants() ) {
- new_phy.getRoot().setChildNode( i++, n );
- }
- return new_phy;
- }
-
final private class SubtreeColorizationActionListener implements ActionListener {
- JColorChooser _chooser;
- PhylogenyNode _node;
+ JColorChooser _chooser = null;
+ PhylogenyNode _node = null;
+ List<PhylogenyNode> _additional_nodes = null;
SubtreeColorizationActionListener( final JColorChooser chooser, final PhylogenyNode node ) {
_chooser = chooser;
_node = node;
}
+ SubtreeColorizationActionListener( final JColorChooser chooser,
+ final PhylogenyNode node,
+ final List<PhylogenyNode> additional_nodes ) {
+ _chooser = chooser;
+ _node = node;
+ _additional_nodes = additional_nodes;
+ }
+
@Override
public void actionPerformed( final ActionEvent e ) {
final Color c = _chooser.getColor();
if ( c != null ) {
- colorizeSubtree( c, _node );
+ colorizeSubtree( c, _node, _additional_nodes );
}
}
}
git://source.jalview.org / jalview.git / blobdiff