import java.awt.Graphics;
import java.awt.Graphics2D;
import java.awt.Point;
-import java.awt.Polygon;
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 java.awt.geom.CubicCurve2D;
import java.awt.geom.Ellipse2D;
import java.awt.geom.Line2D;
+import java.awt.geom.Path2D;
import java.awt.geom.QuadCurve2D;
import java.awt.geom.Rectangle2D;
import java.awt.image.BufferedImage;
import java.util.HashSet;
import java.util.Hashtable;
import java.util.List;
+import java.util.Map.Entry;
import java.util.Set;
+import java.util.SortedMap;
import java.util.SortedSet;
+import java.util.TreeMap;
import javax.swing.BorderFactory;
import javax.swing.JApplet;
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 );
private final static NumberFormat FORMATTER_CONFIDENCE;
private final static NumberFormat FORMATTER_BRANCH_LENGTH;
private final static int WIGGLE = 2;
- private final static int LIMIT_FOR_HQ_RENDERING = 1000;
+ private final static int LIMIT_FOR_HQ_RENDERING = 2000;
private final static int CONFIDENCE_LEFT_MARGIN = 4;
private final RenderingHints _rendering_hints = new RenderingHints( RenderingHints.KEY_RENDERING,
RenderingHints.VALUE_RENDER_DEFAULT );
private float _last_drag_point_y = 0;
private ControlPanel _control_panel = null;
private int _external_node_index = 0;
- private final Polygon _polygon = new Polygon();
+ private final Path2D.Float _polygon = new Path2D.Float();
private final StringBuilder _sb = new StringBuilder();
private JColorChooser _color_chooser = null;
private double _scale_distance = 0.0;
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 ( ForesterUtil.isEmpty( species ) ) {
+ if ( ForesterUtil.isEmpty( tax.getTaxonomyCode() ) && ForesterUtil.isEmpty( tax.getScientificName() ) ) {
return getTreeColorSet().getTaxonomyColor();
}
- // Look in species hash
- Color c = getControlPanel().getSpeciesColors().get( species );
+ 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 ) {
- c = AptxUtil.calculateColorFromString( species );
- getControlPanel().getSpeciesColors().put( species, c );
+ 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;
}
}
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() ) );
}
}
if ( getMainPanel().getOptions().isAntialiasScreen() ) {
- if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR )
- && !getMainPanel().getOptions().isShowDefaultNodeShapesInternal()
- && !getMainPanel().getOptions().isShowDefaultNodeShapesExternal()
- && ( ( getControlPanel() != null ) && !getControlPanel().isShowDomainArchitectures() ) ) {
- _rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_OFF );
- }
- else {
- _rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON );
- }
- try {
- _rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING,
- RenderingHints.VALUE_TEXT_ANTIALIAS_LCD_HRGB );
- }
- catch ( final Throwable e ) {
- _rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_ON );
- }
+ _rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON );
+ // try {
+ _rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_LCD_HRGB );
+ // }
+ // catch ( final Throwable e ) {
+ // _rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_ON );
+ //}
}
else {
_rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_OFF );
_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 ( 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 = new ArrayList<PhylogenyNode>();
+ for( final Long id : getFoundNodes() ) {
+ additional_nodes.add( _phylogeny.getNode( id ) );
+ }
+ 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 );
}
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();
return Blast.isContainsQueryForBlast( node );
}
- final private boolean isCanOpenSeqWeb( final PhylogenyNode node ) {
- if ( node.getNodeData().isHasSequence()
- && ( node.getNodeData().getSequence().getAccession() != null )
- && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() )
- && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getValue() )
- && getConfiguration().isHasWebLink( node.getNodeData().getSequence().getAccession().getSource()
- .toLowerCase() ) ) {
- return true;
+ 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 false;
+ return v;
}
final private boolean isCanOpenTaxWeb( final PhylogenyNode node ) {
if ( node.getNodeData().isHasTaxonomy()
- && ( ( ( node.getNodeData().getTaxonomy().getIdentifier() != null )
- && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getIdentifier().getProvider() )
- && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getIdentifier().getValue() ) && getConfiguration()
- .isHasWebLink( node.getNodeData().getTaxonomy().getIdentifier().getProvider().toLowerCase() ) )
- || ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getScientificName() ) )
+ && ( ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getScientificName() ) )
|| ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getTaxonomyCode() ) )
|| ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getCommonName() ) ) || ( ( node
- .getNodeData().getTaxonomy().getIdentifier() != null )
- && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getIdentifier().getValue() ) && node
- .getNodeData().getTaxonomy().getIdentifier().getValue().startsWith( "http://" ) ) ) ) {
+ .getNodeData().getTaxonomy().getIdentifier() != null ) && !ForesterUtil.isEmpty( node
+ .getNodeData().getTaxonomy().getIdentifier().getValue() ) ) ) ) {
return true;
}
else {
final String title = clickto_names.get( i );
_node_popup_menu_items[ i ] = new JMenuItem( title );
if ( title.equals( Configuration.clickto_options[ Configuration.open_seq_web ][ 0 ] ) ) {
- _node_popup_menu_items[ i ].setEnabled( isCanOpenSeqWeb( node ) );
+ final String id = isCanOpenSeqWeb( node );
+ if ( !ForesterUtil.isEmpty( id ) ) {
+ _node_popup_menu_items[ i ].setText( _node_popup_menu_items[ i ].getText() + " [" + id + "]" );
+ _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 ) );
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 void openSeqWeb( final PhylogenyNode node ) {
- if ( !isCanOpenSeqWeb( node ) ) {
+ if ( ForesterUtil.isEmpty( isCanOpenSeqWeb( node ) ) ) {
cannotOpenBrowserWarningMessage( "sequence" );
return;
}
- String uri_str = null;
- final Sequence seq = node.getNodeData().getSequence();
- final String source = seq.getAccession().getSource().toLowerCase();
- String url;
- if ( source.toLowerCase().equals( "ncbi" ) ) {
- url = Constants.NCBI_ALL_DATABASE_SEARCH;
- }
- else {
- final WebLink weblink = getConfiguration().getWebLink( source );
- url = weblink.getUrl().toString();
- }
- try {
- uri_str = url + URLEncoder.encode( seq.getAccession().getValue(), ForesterConstants.UTF8 );
- }
- catch ( final UnsupportedEncodingException e ) {
- AptxUtil.showErrorMessage( this, e.toString() );
- e.printStackTrace();
- }
+ final String uri_str = TreePanelUtil.createUriForSeqWeb( node, getConfiguration(), this );
if ( !ForesterUtil.isEmpty( uri_str ) ) {
try {
- JApplet applet = null;
- if ( isApplet() ) {
- applet = obtainApplet();
- }
- AptxUtil.launchWebBrowser( new URI( uri_str ), isApplet(), applet, "_aptx_seq" );
+ AptxUtil.launchWebBrowser( new URI( uri_str ),
+ isApplet(),
+ isApplet() ? obtainApplet() : null,
+ "_aptx_seq" );
}
catch ( final IOException e ) {
AptxUtil.showErrorMessage( this, e.toString() );
}
String uri_str = null;
final Taxonomy tax = node.getNodeData().getTaxonomy();
- if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getProvider() )
- && getConfiguration().isHasWebLink( tax.getIdentifier().getProvider().toLowerCase() ) ) {
- final String type = tax.getIdentifier().getProvider().toLowerCase();
- final WebLink weblink = getConfiguration().getWebLink( type );
+ if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getValue() )
+ && tax.getIdentifier().getValue().startsWith( "http://" ) ) {
try {
- uri_str = weblink.getUrl() + URLEncoder.encode( tax.getIdentifier().getValue(), ForesterConstants.UTF8 );
+ uri_str = new URI( tax.getIdentifier().getValue() ).toString();
}
- catch ( final UnsupportedEncodingException e ) {
+ catch ( final URISyntaxException e ) {
AptxUtil.showErrorMessage( this, e.toString() );
+ uri_str = null;
e.printStackTrace();
}
}
- else if ( ( tax.getIdentifier() != null ) && !ForesterUtil.isEmpty( tax.getIdentifier().getValue() )
- && tax.getIdentifier().getValue().startsWith( "http://" ) ) {
+ else if ( ( tax.getIdentifier() != null )
+ && !ForesterUtil.isEmpty( tax.getIdentifier().getValue() )
+ && !ForesterUtil.isEmpty( tax.getIdentifier().getProvider() )
+ && ( tax.getIdentifier().getProvider().equalsIgnoreCase( "ncbi" ) || tax.getIdentifier().getProvider()
+ .equalsIgnoreCase( "uniprot" ) ) ) {
try {
- uri_str = new URI( tax.getIdentifier().getValue() ).toString();
+ uri_str = "http://www.uniprot.org/taxonomy/"
+ + URLEncoder.encode( tax.getIdentifier().getValue(), ForesterConstants.UTF8 );
}
- catch ( final URISyntaxException e ) {
+ catch ( final UnsupportedEncodingException e ) {
AptxUtil.showErrorMessage( this, e.toString() );
- uri_str = null;
e.printStackTrace();
}
}
else if ( !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
try {
- uri_str = "http://www.eol.org/search?q="
+ uri_str = "http://www.uniprot.org/taxonomy/?query="
+ URLEncoder.encode( tax.getScientificName(), ForesterConstants.UTF8 );
}
catch ( final UnsupportedEncodingException e ) {
}
else if ( !ForesterUtil.isEmpty( tax.getCommonName() ) ) {
try {
- uri_str = "http://www.eol.org/search?q="
+ uri_str = "http://www.uniprot.org/taxonomy/?query="
+ URLEncoder.encode( tax.getCommonName(), ForesterConstants.UTF8 );
}
catch ( final UnsupportedEncodingException e ) {
}
if ( !ForesterUtil.isEmpty( uri_str ) ) {
try {
- JApplet applet = null;
- if ( isApplet() ) {
- applet = obtainApplet();
- }
- AptxUtil.launchWebBrowser( new URI( uri_str ), isApplet(), applet, "_aptx_tax" );
+ AptxUtil.launchWebBrowser( new URI( uri_str ),
+ isApplet(),
+ isApplet() ? obtainApplet() : null,
+ "_aptx_tax" );
}
catch ( final IOException e ) {
AptxUtil.showErrorMessage( this, e.toString() );
else {
d = ( Math.log10( d ) * _y_distance ) / 2.5;
}
- final int box_size = getOptions().getDefaultNodeShapeSize();
+ final int box_size = getOptions().getDefaultNodeShapeSize() + 1;
if ( d < box_size ) {
d = box_size;
}
+ final float xx = node.getXcoord() - ( 2 * box_size );
+ final float xxx = xx > node.getParent().getXcoord() + 1 ? xx : node.getParent().getXcoord() + 1;
_polygon.reset();
- _polygon.addPoint( ForesterUtil.roundToInt( node.getXcoord() - box_size ),
- ForesterUtil.roundToInt( node.getYcoord() ) );
- _polygon.addPoint( ForesterUtil.roundToInt( node.getXcoord() + box_size ),
- ForesterUtil.roundToInt( node.getYcoord() - d ) );
- _polygon.addPoint( ForesterUtil.roundToInt( node.getXcoord() + box_size ),
- ForesterUtil.roundToInt( node.getYcoord() + d ) );
+ _polygon.moveTo( xxx, node.getYcoord() );
+ _polygon.lineTo( node.getXcoord() + 1, node.getYcoord() - d );
+ _polygon.lineTo( node.getXcoord() + 1, node.getYcoord() + d );
+ _polygon.closePath();
if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.SOLID ) {
g.setColor( c );
- g.fillPolygon( _polygon );
+ g.fill( _polygon );
}
else if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.NONE ) {
g.setColor( getBackground() );
- g.fillPolygon( _polygon );
+ g.fill( _polygon );
g.setColor( c );
- g.drawPolygon( _polygon );
+ g.draw( _polygon );
}
else if ( getOptions().getDefaultNodeFill() == NodeFill.GRADIENT ) {
- g.setPaint( new GradientPaint( node.getXcoord() - box_size, node.getYcoord(), getBackground(), ( node
- .getXcoord() + box_size ), ( float ) ( node.getYcoord() - d ), c, false ) );
+ g.setPaint( new GradientPaint( xxx, node.getYcoord(), getBackground(), node.getXcoord(), ( float ) ( node
+ .getYcoord() - d ), c, false ) );
g.fill( _polygon );
g.setPaint( c );
g.draw( _polygon );
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();
if ( !getControlPanel().isShowInternalData() && !node.isExternal() && !node.isCollapse() ) {
return;
}
+ _sb.setLength( 0 );
int x = 0;
final int half_box_size = getOptions().getDefaultNodeShapeSize() / 2;
if ( getControlPanel().isShowTaxonomyImages()
else {
g.setColor( getTreeColorSet().getSequenceColor() );
}
- _sb.setLength( 0 );
if ( node.isCollapse() && ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) ) {
- _sb.append( " [" );
- _sb.append( node.getAllExternalDescendants().size() );
- _sb.append( "]" );
+ if ( _sb.length() > 0 ) {
+ _sb.setLength( 0 );
+ _sb.append( "(" );
+ _sb.append( node.getAllExternalDescendants().size() );
+ _sb.append( ")" );
+ }
+ }
+ else {
+ _sb.setLength( 0 );
}
if ( getControlPanel().isShowNodeNames() && ( node.getName().length() > 0 ) ) {
if ( _sb.length() > 0 ) {
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 );
final private void paintNodeLite( final Graphics2D g, final PhylogenyNode node ) {
if ( node.isCollapse() ) {
- if ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) {
+ if ( !node.isRoot() && !node.getParent().isCollapse() ) {
paintCollapsedNode( g, node, false, false, false );
}
return;
final boolean to_graphics_file ) {
final boolean is_in_found_nodes = isInFoundNodes( node ) || isInCurrentExternalNodes( node );
if ( node.isCollapse() ) {
- if ( ( !node.isRoot() && !node.getParent().isCollapse() ) || node.isRoot() ) {
+ if ( ( !node.isRoot() && !node.getParent().isCollapse() ) ) {
paintCollapsedNode( g, node, to_graphics_file, to_pdf, is_in_found_nodes );
}
return;
.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 private void paintOvRectangle( final Graphics2D g ) {
- final float w_ratio = ( float ) getWidth() / getVisibleRect().width;
- final float h_ratio = ( float ) getHeight() / getVisibleRect().height;
- final float x_ratio = ( float ) getWidth() / getVisibleRect().x;
- final float y_ratio = ( float ) getHeight() / getVisibleRect().y;
+ final float w_ratio = ( ( float ) getWidth() ) / getVisibleRect().width;
+ final float h_ratio = ( ( float ) getHeight() ) / getVisibleRect().height;
+ final float x_ratio = ( ( float ) getWidth() ) / getVisibleRect().x;
+ final float y_ratio = ( ( float ) getHeight() ) / getVisibleRect().y;
final float width = getOvMaxWidth() / w_ratio;
final float height = getOvMaxHeight() / h_ratio;
final float x = getVisibleRect().x + getOvXPosition() + ( getOvMaxWidth() / x_ratio );
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() ) );
+ final Stroke s = g.getStroke();
+ g.setStroke( STROKE_05 );
for( final PhylogenyNode element : _nodes_in_preorder ) {
paintNodeLite( g, element );
}
+ 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;
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( "|" );
}
- else {
- sb.append( SequenceWriter.toFasta( n.getName(), n.getNodeData().getSequence()
- .getMolecularSequence(), 60 ) );
+ 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 = ann.toString().trim();
+ if ( ann_str.endsWith( "|" ) ) {
+ ann_str = ann_str.substring( 0, ann_str.length() - 1 );
}
+ 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 = 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;
+ final String 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.
}
}
+ private int makeSB( final List<String> data, final Options optz, final StringBuilder sb ) {
+ final SortedMap<String, Integer> map = new TreeMap<String, Integer>();
+ if ( ( optz.getExtDescNodeDataToReturn() != NODE_DATA.SEQUENCE_MOL_SEQ )
+ && ( optz.getExtDescNodeDataToReturn() != NODE_DATA.SEQUENCE_MOL_SEQ_FASTA ) ) {
+ for( final String d : data ) {
+ if ( !ForesterUtil.isEmpty( d ) ) {
+ if ( map.containsKey( d ) ) {
+ map.put( d, map.get( d ) + 1 );
+ }
+ else {
+ map.put( d, 1 );
+ }
+ }
+ }
+ }
+ int size = 0;
+ if ( ( optz.getExtDescNodeDataToReturn() != NODE_DATA.SEQUENCE_MOL_SEQ )
+ && ( optz.getExtDescNodeDataToReturn() != NODE_DATA.SEQUENCE_MOL_SEQ_FASTA ) ) {
+ for( final Entry<String, Integer> e : map.entrySet() ) {
+ final String v = e.getKey();
+ final Object c = e.getValue();
+ sb.append( v );
+ sb.append( "\t" );
+ sb.append( c );
+ sb.append( ForesterUtil.LINE_SEPARATOR );
+ }
+ size = map.size();
+ }
+ else {
+ for( final String d : data ) {
+ if ( !ForesterUtil.isEmpty( d ) ) {
+ sb.append( d );
+ sb.append( ForesterUtil.LINE_SEPARATOR );
+ }
+ }
+ size = data.size();
+ }
+ return size;
+ }
+
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 ) {
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