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;
import org.forester.phylogeny.data.Confidence;
import org.forester.phylogeny.data.Event;
+import org.forester.phylogeny.data.NodeVisualization;
+import org.forester.phylogeny.data.NodeVisualization.NodeFill;
+import org.forester.phylogeny.data.NodeVisualization.NodeShape;
import org.forester.phylogeny.data.PhylogenyData;
+import org.forester.phylogeny.data.PhylogenyDataUtil;
import org.forester.phylogeny.data.PropertiesMap;
import org.forester.phylogeny.data.Property;
import org.forester.phylogeny.data.Sequence;
private final static NumberFormat FORMATTER_CONFIDENCE;
private final static NumberFormat FORMATTER_BRANCH_LENGTH;
private final static int WIGGLE = 2;
- private int _half_box_size_plus_wiggle;
private final static int LIMIT_FOR_HQ_RENDERING = 1000;
private final static int CONFIDENCE_LEFT_MARGIN = 4;
// TODO "rendering_hints" was static before. Need to make sure everything is OK with it not
final private static double _180_OVER_PI = 180.0 / Math.PI;
private static final float ROUNDED_D = 8;
private int _circ_max_depth;
- private int _circ_num_ext_nodes;
private PhylogenyNode _root;
final private Arc2D _arc = new Arc2D.Double();
final private HashMap<Integer, Double> _urt_nodeid_angle_map = new HashMap<Integer, Double>();
final private HashMap<Integer, Integer> _urt_nodeid_index_map = new HashMap<Integer, Integer>();
+ final private Set<Integer> _collapsed_external_nodeid_set = new HashSet<Integer>();
HashMap<Integer, Short> _nodeid_dist_to_leaf = new HashMap<Integer, Short>();
private AffineTransform _at;
private double _max_distance_to_root = -1;
private boolean _edited = false;
private Popup _node_desc_popup;
private JTextArea _rollover_popup;
- private int _box_size ;
- private int _half_box_size;
+ // private final int _box_size;
+ // private final int _half_box_size;
//private final short _skip_counter = 0;
private final StringBuffer _popup_buffer = new StringBuffer();
final private static Font POPUP_FONT = new Font( Configuration.getDefaultFontFamilyName(),
_main_panel = tjp;
_configuration = configuration;
_phylogeny = t;
- _phy_has_branch_lengths = ForesterUtil.isHasAtLeastOneBranchLengthLargerThanZero( _phylogeny );
- _box_size = tjp.getOptions().getDefaultNodeBoxSize();
- _half_box_size = tjp.getOptions().getDefaultNodeBoxSize() / 2;
-
- _half_box_size_plus_wiggle = _half_box_size + WIGGLE;
+ _phy_has_branch_lengths = AptxUtil.isHasAtLeastOneBranchLengthLargerThanZero( _phylogeny );
init();
// if ( !_phylogeny.isEmpty() ) {
_phylogeny.recalculateNumberOfExternalDescendants( true );
}
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 );
}
}
- final void assignGraphicsForNodeBoxWithColorForParentBranch( final PhylogenyNode node, final Graphics g ) {
+ final Color getGraphicsForNodeBoxWithColorForParentBranch( final PhylogenyNode node ) {
if ( getControlPanel().isColorBranches() && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
- g.setColor( PhylogenyMethods.getBranchColorValue( node ) );
+ return ( PhylogenyMethods.getBranchColorValue( node ) );
}
else {
- g.setColor( getTreeColorSet().getBranchColor() );
+ return ( getTreeColorSet().getBranchColor() );
}
}
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();
- }
- else if ( node.getNodeData().getSequence().getAccession() != null ) {
- name = node.getNodeData().getSequence().getAccession().getValue();
- }
- if ( !ForesterUtil.isEmpty( name ) ) {
+ String query = Blast.obtainQueryForBlast( node );
+ 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: " + name );
+ System.out.println( "trying: " + query );
final Blast s = new Blast();
- s.go( name );
+ s.ddbjBlast( query );
}
catch ( final Exception e ) {
e.printStackTrace();
}
+ }
}
}
}
+
+
final void calcMaxDepth() {
if ( _phylogeny != null ) {
_circ_max_depth = PhylogenyMethods.calculateMaxDepth( _phylogeny );
sum += getTreeFontSet()._fm_large_italic.stringWidth( tax.getCommonName() + " ()" );
}
}
+ if ( getControlPanel().isShowProperties() && node.getNodeData().isHasProperties() ) {
+ sum += getTreeFontSet()._fm_large.stringWidth( propertiesToString( node ).toString() );
+ }
if ( getControlPanel().isShowBinaryCharacters() && node.getNodeData().isHasBinaryCharacters() ) {
sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getBinaryCharacters()
.getGainedCharactersAsStringBuffer().toString() );
// Look in species hash
Color c = getControlPanel().getSpeciesColors().get( species );
if ( c == null ) {
- c = Util.calculateColorFromString( species );
+ c = AptxUtil.calculateColorFromString( species );
getControlPanel().getSpeciesColors().put( species, c );
}
return c;
}
if ( !node.isExternal() && !node.isRoot() ) {
final boolean collapse = !node.isCollapse();
- Util.collapseSubtree( node, collapse );
+ AptxUtil.collapseSubtree( node, collapse );
+ updateSetOfCollapsedExternalNodes( _phylogeny );
_phylogeny.recalculateNumberOfExternalDescendants( true );
resetNodeIdToDistToLeafMap();
calculateLongestExtNodeInfo();
- _nodes_in_preorder = null;
+ setNodeInPreorderToNull();
+ _control_panel.displayedPhylogenyMightHaveChanged( true );
resetPreferredSize();
updateOvSizes();
_main_panel.adjustJScrollPane();
return;
}
setWaitCursor();
- Util.collapseSpeciesSpecificSubtrees( _phylogeny );
+ AptxUtil.collapseSpeciesSpecificSubtrees( _phylogeny );
+ updateSetOfCollapsedExternalNodes( _phylogeny );
_phylogeny.recalculateNumberOfExternalDescendants( true );
resetNodeIdToDistToLeafMap();
calculateLongestExtNodeInfo();
- _nodes_in_preorder = null;
+ setNodeInPreorderToNull();
resetPreferredSize();
_main_panel.adjustJScrollPane();
setArrowCursor();
return;
}
setWaitCursor();
- Util.colorPhylogenyAccordingToConfidenceValues( _phylogeny, this );
+ AptxUtil.removeBranchColors( _phylogeny );
+ AptxUtil.colorPhylogenyAccordingToConfidenceValues( _phylogeny, this );
_control_panel.setColorBranches( true );
if ( _control_panel.getColorBranchesCb() != null ) {
_control_panel.getColorBranchesCb().setSelected( true );
repaint();
}
+ final void colorRank( final String rank ) {
+ if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
+ return;
+ }
+ setWaitCursor();
+ AptxUtil.removeBranchColors( _phylogeny );
+ final int colorizations = AptxUtil.colorPhylogenyAccordingToRanks( _phylogeny, rank, this );
+ if ( colorizations > 0 ) {
+ _control_panel.setColorBranches( true );
+ if ( _control_panel.getColorBranchesCb() != null ) {
+ _control_panel.getColorBranchesCb().setSelected( true );
+ }
+ if ( _control_panel.getColorAccSpeciesCb() != null ) {
+ _control_panel.getColorAccSpeciesCb().setSelected( false );
+ }
+ _options.setColorLabelsSameAsParentBranch( true );
+ _control_panel.repaint();
+ }
+ setArrowCursor();
+ repaint();
+ if ( colorizations > 0 ) {
+ String msg = "Taxonomy colorization via " + rank + " completed:\n";
+ if ( colorizations > 1 ) {
+ msg += "colorized " + colorizations + " subtrees";
+ }
+ else {
+ msg += "colorized one subtree";
+ }
+ JOptionPane.showMessageDialog( this,
+ msg,
+ "Taxonomy Colorization Completed (" + rank + ")",
+ JOptionPane.INFORMATION_MESSAGE );
+ }
+ else {
+ String msg = "Could not taxonomy colorize any subtree via " + rank + ".\n";
+ msg += "Possible solutions (given that suitable taxonomic information is present):\n";
+ msg += "select a different rank (e.g. phylum, genus, ...)\n";
+ msg += " and/or\n";
+ msg += "execute:\n";
+ msg += "1. \"" + MainFrameApplication.OBTAIN_DETAILED_TAXONOMIC_INFORMATION + "\" (Tools)\n";
+ msg += "2. \"" + MainFrameApplication.INFER_ANCESTOR_TAXONOMIES + "\" (Analysis)";
+ JOptionPane.showMessageDialog( this, msg, "Taxonomy Colorization Failed", JOptionPane.WARNING_MESSAGE );
+ }
+ }
+
final private void copySubtree( final PhylogenyNode node ) {
if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.UNROOTED ) {
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;
_rectangle.setFrame( x, y, width, heigth );
g.fill( _rectangle );
}
-
- //TODO FIXME
+
final private void drawRectGradient( final double x,
final double y,
final double width,
final Color color_2,
final Color color_border ) {
_rectangle.setFrame( x, y, width, heigth );
- g.setPaint( new GradientPaint(( float )x, ( float )y, color_1, ( float ) (x +width), ( float )( y+heigth), color_2,
- false) );
+ g.setPaint( new GradientPaint( ( float ) x,
+ ( float ) y,
+ color_1,
+ ( float ) ( x + width ),
+ ( float ) ( y + heigth ),
+ color_2,
+ false ) );
g.fill( _rectangle );
if ( color_border != null ) {
g.setPaint( color_border );
g.draw( _rectangle );
}
}
-
- //TODO FIXME
+
final private void drawOvalGradient( final double x,
final double y,
final double width,
final Color color_2,
final Color color_border ) {
_ellipse.setFrame( x, y, width, heigth );
- g.setPaint( new GradientPaint(( float )x, ( float )y, color_1, ( float ) (x +width), ( float )( y+heigth), color_2,
- false) );
+ g.setPaint( new GradientPaint( ( float ) x,
+ ( float ) y,
+ color_1,
+ ( float ) ( x + width ),
+ ( float ) ( y + heigth ),
+ color_2,
+ false ) );
g.fill( _ellipse );
if ( color_border != null ) {
g.setPaint( color_border );
if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) {
return null;
}
+ final int half_box_size_plus_wiggle = getOptions().getDefaultNodeShapeSize() / 2 + WIGGLE;
for( final PhylogenyNodeIterator iter = _phylogeny.iteratorPostorder(); iter.hasNext(); ) {
final PhylogenyNode node = iter.next();
if ( ( _phylogeny.isRooted() || !node.isRoot() || ( node.getNumberOfDescendants() > 2 ) )
- && ( ( node.getXcoord() - _half_box_size_plus_wiggle ) <= x )
- && ( ( node.getXcoord() + _half_box_size_plus_wiggle ) >= x )
- && ( ( node.getYcoord() - _half_box_size_plus_wiggle ) <= y )
- && ( ( node.getYcoord() + _half_box_size_plus_wiggle ) >= y ) ) {
+ && ( ( node.getXcoord() - half_box_size_plus_wiggle ) <= x )
+ && ( ( node.getXcoord() + half_box_size_plus_wiggle ) >= x )
+ && ( ( node.getYcoord() - half_box_size_plus_wiggle ) <= y )
+ && ( ( node.getYcoord() + half_box_size_plus_wiggle ) >= y ) ) {
return node;
}
}
case EDIT_NODE_DATA:
showNodeEditFrame( node );
break;
+ case SORT_DESCENDENTS:
+ sortDescendants( node );
+ break;
default:
throw new IllegalArgumentException( "unknown action: " + action );
}
return;
}
setWaitCursor();
- Util.inferCommonPartOfScientificNames( _phylogeny );
+ AptxUtil.inferCommonPartOfScientificNames( _phylogeny );
setArrowCursor();
repaint();
}
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() ) ) );
+ .getNodeData().getSequence().getSymbol() ) || !ForesterUtil.isEmpty( node
+ .getNodeData().getSequence().getMolecularSequence() )) );
}
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();
uri_str = url + URLEncoder.encode( seq.getAccession().getValue(), ForesterConstants.UTF8 );
}
catch ( final UnsupportedEncodingException e ) {
- Util.showErrorMessage( this, e.toString() );
+ AptxUtil.showErrorMessage( this, e.toString() );
e.printStackTrace();
}
if ( !ForesterUtil.isEmpty( uri_str ) ) {
if ( isApplet() ) {
applet = obtainApplet();
}
- Util.launchWebBrowser( new URI( uri_str ), isApplet(), applet, "_aptx_seq" );
+ AptxUtil.launchWebBrowser( new URI( uri_str ), isApplet(), applet, "_aptx_seq" );
}
catch ( final IOException e ) {
- Util.showErrorMessage( this, e.toString() );
+ AptxUtil.showErrorMessage( this, e.toString() );
e.printStackTrace();
}
catch ( final URISyntaxException e ) {
- Util.showErrorMessage( this, e.toString() );
+ AptxUtil.showErrorMessage( this, e.toString() );
e.printStackTrace();
}
}
uri_str = weblink.getUrl() + URLEncoder.encode( tax.getIdentifier().getValue(), ForesterConstants.UTF8 );
}
catch ( final UnsupportedEncodingException e ) {
- Util.showErrorMessage( this, e.toString() );
+ AptxUtil.showErrorMessage( this, e.toString() );
e.printStackTrace();
}
}
uri_str = new URI( tax.getIdentifier().getValue() ).toString();
}
catch ( final URISyntaxException e ) {
- Util.showErrorMessage( this, e.toString() );
+ AptxUtil.showErrorMessage( this, e.toString() );
uri_str = null;
e.printStackTrace();
}
+ URLEncoder.encode( tax.getScientificName(), ForesterConstants.UTF8 );
}
catch ( final UnsupportedEncodingException e ) {
- Util.showErrorMessage( this, e.toString() );
+ AptxUtil.showErrorMessage( this, e.toString() );
e.printStackTrace();
}
}
+ URLEncoder.encode( tax.getTaxonomyCode(), ForesterConstants.UTF8 );
}
catch ( final UnsupportedEncodingException e ) {
- Util.showErrorMessage( this, e.toString() );
+ AptxUtil.showErrorMessage( this, e.toString() );
e.printStackTrace();
}
}
+ URLEncoder.encode( tax.getCommonName(), ForesterConstants.UTF8 );
}
catch ( final UnsupportedEncodingException e ) {
- Util.showErrorMessage( this, e.toString() );
+ AptxUtil.showErrorMessage( this, e.toString() );
e.printStackTrace();
}
}
if ( isApplet() ) {
applet = obtainApplet();
}
- Util.launchWebBrowser( new URI( uri_str ), isApplet(), applet, "_aptx_tax" );
+ AptxUtil.launchWebBrowser( new URI( uri_str ), isApplet(), applet, "_aptx_tax" );
}
catch ( final IOException e ) {
- Util.showErrorMessage( this, e.toString() );
+ AptxUtil.showErrorMessage( this, e.toString() );
e.printStackTrace();
}
catch ( final URISyntaxException e ) {
- Util.showErrorMessage( this, e.toString() );
+ AptxUtil.showErrorMessage( this, e.toString() );
e.printStackTrace();
}
}
final private void paintBranchRectangular( final Graphics2D g,
final float x1,
final float x2,
- float y1,
+ final float y1,
final float y2,
final PhylogenyNode node,
final boolean to_pdf,
g.draw( _cubic_curve );
}
else {
- float x2a = x2;
- float x1a = x1;
- // draw the vertical line
- boolean draw_horizontal = true;
+ final float x2a = x2;
+ final float x1a = x1;
float y2_r = 0;
if ( node.isFirstChildNode() || node.isLastChildNode()
|| ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE )
|| ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) {
- boolean draw_vertical = true;
- final PhylogenyNode parent = node.getParent();
- if ( ( ( getOptions().getDefaultNodeShape() != Options.NodeShape.NONE && !to_pdf && !to_graphics_file ) || ( ( getControlPanel()
- .isEvents() ) && ( parent != null ) && parent.isHasAssignedEvent() ) )
- && ( _phylogeny.isRooted() || !( ( parent != null ) && parent.isRoot() ) )
- && !( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() && !parent
- .isDuplication() ) ) {
- if ( ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE )
- && ( getPhylogenyGraphicsType() != PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) {
- if ( Math.abs( y2 - y1 ) <= _half_box_size ) {
- draw_vertical = false;
- }
- else {
- if ( y1 < y2 ) {
- y1 += _half_box_size;
- }
- else {
- if ( !to_pdf ) {
- y1 -= _half_box_size + 1;
- }
- else {
- y1 -= _half_box_size;
- }
- }
- }
- }
- if ( ( x2 - x1 ) <= _half_box_size ) {
- draw_horizontal = false;
- }
- else if ( !draw_vertical ) {
- x1a += _half_box_size;
- }
- if ( ( ( x2 - x1a ) > _half_box_size )
- && !( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() && !node
- .isDuplication() ) ) {
- x2a -= _half_box_size;
- }
+ if ( !to_graphics_file
+ && !to_pdf
+ && ( ( ( y2 < getVisibleRect().getMinY() - 20 ) && ( y1 < getVisibleRect().getMinY() - 20 ) ) || ( ( y2 > getVisibleRect()
+ .getMaxY() + 20 ) && ( y1 > getVisibleRect().getMaxY() + 20 ) ) ) ) {
+ // Do nothing.
}
- if ( draw_vertical ) {
- if ( !to_graphics_file
- && !to_pdf
- && ( ( ( y2 < getVisibleRect().getMinY() - 20 ) && ( y1 < getVisibleRect().getMinY() - 20 ) ) || ( ( y2 > getVisibleRect()
- .getMaxY() + 20 ) && ( y1 > getVisibleRect().getMaxY() + 20 ) ) ) ) {
- // Do nothing.
- }
- else {
- if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
- float x2c = x1 + EURO_D;
- if ( x2c > x2a ) {
- x2c = x2a;
- }
- drawLine( x1, y1, x2c, y2, g );
+ else {
+ if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
+ float x2c = x1 + EURO_D;
+ if ( x2c > x2a ) {
+ x2c = x2a;
}
- else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
- if ( y2 > y1 ) {
- y2_r = y2 - ROUNDED_D;
- if ( y2_r < y1 ) {
- y2_r = y1;
- }
- drawLine( x1, y1, x1, y2_r, g );
- }
- else {
- y2_r = y2 + ROUNDED_D;
- if ( y2_r > y1 ) {
- y2_r = y1;
- }
- drawLine( x1, y1, x1, y2_r, g );
+ drawLine( x1, y1, x2c, y2, g );
+ }
+ else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
+ if ( y2 > y1 ) {
+ y2_r = y2 - ROUNDED_D;
+ if ( y2_r < y1 ) {
+ y2_r = y1;
}
+ drawLine( x1, y1, x1, y2_r, g );
}
else {
- drawLine( x1, y1, x1, y2, g );
+ y2_r = y2 + ROUNDED_D;
+ if ( y2_r > y1 ) {
+ y2_r = y1;
+ }
+ drawLine( x1, y1, x1, y2_r, g );
}
}
+ else {
+ drawLine( x1, y1, x1, y2, g );
+ }
}
}
// draw the horizontal line
return;
}
float x1_r = 0;
- if ( draw_horizontal ) {
- if ( !getControlPanel().isWidthBranches() || ( PhylogenyMethods.getBranchWidthValue( node ) == 1 ) ) {
- if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
- x1_r = x1a + ROUNDED_D;
- if ( x1_r < x2a ) {
- drawLine( x1_r, y2, x2a, y2, g );
- }
+ if ( !getControlPanel().isWidthBranches() || ( PhylogenyMethods.getBranchWidthValue( node ) == 1 ) ) {
+ if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
+ x1_r = x1a + ROUNDED_D;
+ if ( x1_r < x2a ) {
+ drawLine( x1_r, y2, x2a, y2, g );
}
- else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
- final float x1c = x1a + EURO_D;
- if ( x1c < x2a ) {
- drawLine( x1c, y2, x2a, y2, g );
- }
- }
- else {
- drawLine( x1a, y2, x2a, y2, g );
+ }
+ else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
+ final float x1c = x1a + EURO_D;
+ if ( x1c < x2a ) {
+ drawLine( x1c, y2, x2a, y2, g );
}
}
else {
- final double w = PhylogenyMethods.getBranchWidthValue( node );
- if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
- x1_r = x1a + ROUNDED_D;
- if ( x1_r < x2a ) {
- drawRectFilled( x1_r, y2 - ( w / 2 ), x2a - x1_r, w, g );
- }
- }
- else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
- final float x1c = x1a + EURO_D;
- if ( x1c < x2a ) {
- drawRectFilled( x1c, y2 - ( w / 2 ), x2a - x1c, w, g );
- }
+ drawLine( x1a, y2, x2a, y2, g );
+ }
+ }
+ else {
+ final double w = PhylogenyMethods.getBranchWidthValue( node );
+ if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) {
+ x1_r = x1a + ROUNDED_D;
+ if ( x1_r < x2a ) {
+ drawRectFilled( x1_r, y2 - ( w / 2 ), x2a - x1_r, w, g );
}
- else {
- drawRectFilled( x1a, y2 - ( w / 2 ), x2a - x1a, w, g );
+ }
+ else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) {
+ final float x1c = x1a + EURO_D;
+ if ( x1c < x2a ) {
+ drawRectFilled( x1c, y2 - ( w / 2 ), x2a - x1c, w, g );
}
}
+ else {
+ drawRectFilled( x1a, y2 - ( w / 2 ), x2a - x1a, w, g );
+ }
}
if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) {
if ( x1_r > x2a ) {
g.draw( _arc );
}
}
- //TODO new *****
if ( node.isExternal() ) {
- //TODO new *****
paintNodeBox( x2, y2, node, g, to_pdf, to_graphics_file, isInFoundNodes( node ) );
}
}
final Graphics2D g,
final boolean to_pdf,
final boolean to_graphics_file ) {
- _circ_num_ext_nodes = phy.getNumberOfExternalNodes();
+ final int circ_num_ext_nodes = phy.getNumberOfExternalNodes() - _collapsed_external_nodeid_set.size();
+ System.out.println( "# collapsed external = " + _collapsed_external_nodeid_set.size() );
_root = phy.getRoot();
_root.setXcoord( center_x );
_root.setYcoord( center_y );
- final boolean radial_labels = getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL;
+ final boolean radial_labels = getOptions().getNodeLabelDirection() == NODE_LABEL_DIRECTION.RADIAL;
double current_angle = starting_angle;
int i = 0;
for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
final PhylogenyNode n = it.next();
- n.setXcoord( ( float ) ( center_x + ( radius * Math.cos( current_angle ) ) ) );
- n.setYcoord( ( float ) ( center_y + ( radius * Math.sin( current_angle ) ) ) );
- _urt_nodeid_angle_map.put( n.getId(), current_angle );
- _urt_nodeid_index_map.put( n.getId(), i++ );
- current_angle += ( TWO_PI / _circ_num_ext_nodes );
+ if ( !n.isCollapse() ) {
+ n.setXcoord( ( float ) ( center_x + ( radius * Math.cos( current_angle ) ) ) );
+ n.setYcoord( ( float ) ( center_y + ( radius * Math.sin( current_angle ) ) ) );
+ _urt_nodeid_angle_map.put( n.getId(), current_angle );
+ _urt_nodeid_index_map.put( n.getId(), i++ );
+ current_angle += ( TWO_PI / circ_num_ext_nodes );
+ }
+ else {
+ //TODO remove me
+ System.out.println( "is collapse" + n.getName() );
+ }
}
paintCirculars( phy.getRoot(), phy, center_x, center_y, radius, radial_labels, g, to_pdf, to_graphics_file );
paintNodeBox( _root.getXcoord(), _root.getYcoord(), _root, g, to_pdf, to_graphics_file, isInFoundNodes( _root ) );
-
+ }
+
+ void updateSetOfCollapsedExternalNodes( final Phylogeny phy ) {
+ _collapsed_external_nodeid_set.clear();
+ E: for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
+ final PhylogenyNode ext_node = it.next();
+ PhylogenyNode n = ext_node;
+ while ( !n.isRoot() ) {
+ if ( n.isCollapse() ) {
+ _collapsed_external_nodeid_set.add( ext_node.getId() );
+ continue E;
+ }
+ n = n.getParent();
+ }
+ }
}
final void paintCircularLite( final Phylogeny phy,
final int center_y,
final int radius,
final Graphics2D g ) {
- _circ_num_ext_nodes = phy.getNumberOfExternalNodes();
+ final int circ_num_ext_nodes = phy.getNumberOfExternalNodes();
_root = phy.getRoot();
_root.setXSecondary( center_x );
_root.setYSecondary( center_y );
n.setXSecondary( ( float ) ( center_x + radius * Math.cos( current_angle ) ) );
n.setYSecondary( ( float ) ( center_y + radius * Math.sin( current_angle ) ) );
_urt_nodeid_angle_map.put( n.getId(), current_angle );
- current_angle += ( TWO_PI / _circ_num_ext_nodes );
+ current_angle += ( TWO_PI / circ_num_ext_nodes );
}
paintCircularsLite( phy.getRoot(), phy, center_x, center_y, radius, g );
}
final Graphics2D g,
final boolean to_pdf,
final boolean to_graphics_file ) {
- if ( n.isExternal() ) {
+ if ( n.isExternal() || n.isCollapse() ) { //~~circ collapse
if ( !_urt_nodeid_angle_map.containsKey( n.getId() ) ) {
- System.out.println( "no " + n + ", ERROR!" );//TODO
+ System.out.println( "no " + n + " =====>>>>>>> ERROR!" );//TODO
}
return _urt_nodeid_angle_map.get( n.getId() );
}
final boolean to_graphics_file,
final boolean to_pdf,
final boolean is_in_found_nodes ) {
+ Color c = null;
if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
- g.setColor( Color.BLACK );
+ c = Color.BLACK;
}
else if ( is_in_found_nodes ) {
- g.setColor( getTreeColorSet().getFoundColor() );
+ c = getTreeColorSet().getFoundColor();
}
else if ( getControlPanel().isColorAccordingToTaxonomy() ) {
- g.setColor( getTaxonomyBasedColor( node ) );
+ c = getTaxonomyBasedColor( node );
}
else if ( getOptions().isColorLabelsSameAsParentBranch() && getControlPanel().isColorBranches()
&& ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) {
- g.setColor( PhylogenyMethods.getBranchColorValue( node ) );
+ c = PhylogenyMethods.getBranchColorValue( node );
}
else {
- g.setColor( getTreeColorSet().getCollapseFillColor() );
+ c = getTreeColorSet().getCollapseFillColor();
}
double d = node.getAllExternalDescendants().size();
if ( d > 1000 ) {
else {
d = ( Math.log10( d ) * _y_distance ) / 2.5;
}
- if ( d < _box_size ) {
- d = _box_size;
+ final int box_size = getOptions().getDefaultNodeShapeSize();
+ if ( d < box_size ) {
+ d = box_size;
}
_polygon.reset();
- _polygon.addPoint( ForesterUtil.roundToInt( node.getXcoord() - _box_size ),
+ _polygon.addPoint( ForesterUtil.roundToInt( node.getXcoord() - box_size ),
ForesterUtil.roundToInt( node.getYcoord() ) );
- _polygon.addPoint( ForesterUtil.roundToInt( node.getXcoord() + _box_size ),
+ _polygon.addPoint( ForesterUtil.roundToInt( node.getXcoord() + box_size ),
ForesterUtil.roundToInt( node.getYcoord() - d ) );
- _polygon.addPoint( ForesterUtil.roundToInt( node.getXcoord() + _box_size ),
+ _polygon.addPoint( ForesterUtil.roundToInt( node.getXcoord() + box_size ),
ForesterUtil.roundToInt( node.getYcoord() + d ) );
- g.fillPolygon( _polygon );
+ if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.SOLID ) {
+ g.setColor( c );
+ g.fillPolygon( _polygon );
+ }
+ else if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.NONE ) {
+ g.setColor( getBackground() );
+ g.fillPolygon( _polygon );
+ g.setColor( c );
+ g.drawPolygon( _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.fill( _polygon );
+ g.setPaint( c );
+ g.draw( _polygon );
+ }
paintNodeData( g, node, to_graphics_file, to_pdf, is_in_found_nodes );
}
final PhylogenyNode node,
final boolean to_pdf,
final boolean to_graphics_file ) {
- String conf_str = "";
final List<Confidence> confidences = node.getBranchData().getConfidences();
- if ( confidences.size() == 1 ) {
- final double value = node.getBranchData().getConfidence( 0 ).getValue();
- if ( ( value == Confidence.CONFIDENCE_DEFAULT_VALUE ) || ( value < getOptions().getMinConfidenceValue() ) ) {
- return;
- }
- conf_str = FORMATTER_CONFIDENCE.format( value );
- }
- else if ( confidences.size() > 1 ) {
- boolean one_ok = false;
- boolean not_first = false;
- Collections.sort( confidences );
- final StringBuilder sb = new StringBuilder();
- for( final Confidence confidence : confidences ) {
- final double value = confidence.getValue();
- if ( value != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
- if ( value >= getOptions().getMinConfidenceValue() ) {
- one_ok = true;
- }
- if ( not_first ) {
- sb.append( "/" );
- }
- else {
- not_first = true;
+ // if ( confidences.size() == 1 ) {
+ // final double value = node.getBranchData().getConfidence( 0 ).getValue();
+ // if ( ( value == Confidence.CONFIDENCE_DEFAULT_VALUE ) || ( value < getOptions().getMinConfidenceValue() ) ) {
+ // return;
+ // }
+ // conf_str = FORMATTER_CONFIDENCE.format( value );
+ // }
+ // else if ( confidences.size() > 1 ) {
+ boolean one_ok = false;
+ boolean not_first = false;
+ Collections.sort( confidences );
+ final StringBuilder sb = new StringBuilder();
+ String conf_str = "";
+ for( final Confidence confidence : confidences ) {
+ final double value = confidence.getValue();
+ if ( value != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
+ if ( value >= getOptions().getMinConfidenceValue() ) {
+ one_ok = true;
+ }
+ if ( not_first ) {
+ sb.append( "/" );
+ }
+ else {
+ not_first = true;
+ }
+ sb.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( value, getOptions()
+ .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
+ if ( getOptions().isShowConfidenceStddev() ) {
+ if ( confidence.getStandardDeviation() != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
+ sb.append( "(" );
+ sb.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence.getStandardDeviation(),
+ getOptions()
+ .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
+ sb.append( ")" );
}
- sb.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( value, getOptions()
- .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
}
}
+ //}
if ( one_ok ) {
conf_str = sb.toString();
}
}
final private void paintFoundNode( final int x, final int y, final Graphics2D g ) {
+ final int box_size = getOptions().getDefaultNodeShapeSize();
+ final int half_box_size = getOptions().getDefaultNodeShapeSize() / 2;
g.setColor( getTreeColorSet().getFoundColor() );
- g.fillRect( x - _half_box_size, y - _half_box_size, _box_size, _box_size );
+ g.fillRect( x - half_box_size, y - half_box_size, box_size, box_size );
}
final private void paintGainedAndLostCharacters( final Graphics2D g,
paintFoundNode( ForesterUtil.roundToInt( x ), ForesterUtil.roundToInt( y ), g );
}
else {
+ Color outline_color = null;
if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) {
- g.setColor( Color.BLACK );
+ outline_color = Color.BLACK;
}
- else if ( getControlPanel().isEvents() && Util.isHasAssignedEvent( node ) ) {
+ else if ( getControlPanel().isEvents() && AptxUtil.isHasAssignedEvent( node ) ) {
final Event event = node.getNodeData().getEvent();
if ( event.isDuplication() ) {
- g.setColor( getTreeColorSet().getDuplicationBoxColor() );
+ outline_color = getTreeColorSet().getDuplicationBoxColor();
}
else if ( event.isSpeciation() ) {
- g.setColor( getTreeColorSet().getSpecBoxColor() );
+ outline_color = getTreeColorSet().getSpecBoxColor();
}
else if ( event.isSpeciationOrDuplication() ) {
- g.setColor( getTreeColorSet().getDuplicationOrSpeciationColor() );
+ outline_color = getTreeColorSet().getDuplicationOrSpeciationColor();
}
}
- else {
- assignGraphicsForNodeBoxWithColorForParentBranch( node, g );
+ else if ( getOptions().isTaxonomyColorizeNodeShapes() ) {
+ outline_color = getTaxonomyBasedColor( node );
}
- if ( ( getOptions().getDefaultNodeShape() != Options.NodeShape.NONE && !to_pdf && !to_graphics_file )
- || ( getControlPanel().isEvents() && node.isHasAssignedEvent() ) ) {
- if ( to_pdf || to_graphics_file ) {
- if ( node.isDuplication() || !getOptions().isPrintBlackAndWhite() ) {
- drawOvalFilled( x - _half_box_size, y - _half_box_size, _box_size, _box_size, g );
+ else {
+ outline_color = getGraphicsForNodeBoxWithColorForParentBranch( node );
+ if ( to_pdf && ( outline_color == getTreeColorSet().getBranchColor() ) ) {
+ outline_color = getTreeColorSet().getBranchColorForPdf();
+ }
+ }
+ final int box_size = getOptions().getDefaultNodeShapeSize();
+ final int half_box_size = box_size / 2;
+ if ( getOptions().isShowDefaultNodeShapes() || ( getControlPanel().isEvents() && node.isHasAssignedEvent() ) ) {
+ if ( getOptions().getDefaultNodeShape() == NodeShape.CIRCLE ) {
+ if ( getOptions().getDefaultNodeFill() == NodeFill.GRADIENT ) {
+ drawOvalGradient( x - half_box_size,
+ y - half_box_size,
+ box_size,
+ box_size,
+ g,
+ to_pdf ? Color.WHITE : outline_color,
+ to_pdf ? outline_color : getBackground(),
+ outline_color );
+ }
+ else if ( getOptions().getDefaultNodeFill() == NodeFill.NONE ) {
+ Color background = getBackground();
+ if ( to_pdf ) {
+ background = Color.WHITE;
+ }
+ drawOvalGradient( x - half_box_size,
+ y - half_box_size,
+ box_size,
+ box_size,
+ g,
+ background,
+ background,
+ outline_color );
+ }
+ else if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.SOLID ) {
+ g.setColor( outline_color );
+ drawOvalFilled( x - half_box_size, y - half_box_size, box_size, box_size, g );
}
}
- else {
- //TODO FIXME
- //drawRectFilled( x - HALF_BOX_SIZE, y - HALF_BOX_SIZE, BOX_SIZE, BOX_SIZE, g );
- drawOvalGradient( x - _half_box_size, y - _half_box_size, _box_size, _box_size, g
- ,Color.BLACK,
- g.getColor(), g.getColor());
+ else if ( getOptions().getDefaultNodeShape() == NodeVisualization.NodeShape.RECTANGLE ) {
+ if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.GRADIENT ) {
+ drawRectGradient( x - half_box_size,
+ y - half_box_size,
+ box_size,
+ box_size,
+ g,
+ to_pdf ? Color.WHITE : outline_color,
+ to_pdf ? outline_color : getBackground(),
+ outline_color );
+ }
+ else if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.NONE ) {
+ Color background = getBackground();
+ if ( to_pdf ) {
+ background = Color.WHITE;
+ }
+ drawRectGradient( x - half_box_size,
+ y - half_box_size,
+ box_size,
+ box_size,
+ g,
+ background,
+ background,
+ outline_color );
+ }
+ else if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.SOLID ) {
+ g.setColor( outline_color );
+ drawRectFilled( x - half_box_size, y - half_box_size, box_size, box_size, g );
+ }
}
}
}
if ( getOptions().isShowBranchLengthValues()
&& ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR )
|| ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) || ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.EURO_STYLE ) )
- && ( !node.isRoot() ) && ( node.getDistanceToParent() != PhylogenyNode.DISTANCE_DEFAULT ) ) {
+ && ( !node.isRoot() ) && ( node.getDistanceToParent() != PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT ) ) {
paintBranchLength( g, node, to_pdf, to_graphics_file );
}
if ( !getControlPanel().isShowInternalData() && !node.isExternal() && !node.isCollapse() ) {
return;
}
int x = 0;
+ final int half_box_size = getOptions().getDefaultNodeShapeSize() / 2;
if ( getControlPanel().isShowTaxonomyImages()
&& ( getImageMap() != null )
&& !getImageMap().isEmpty()
&& node.getNodeData().isHasTaxonomy()
&& ( ( node.getNodeData().getTaxonomy().getUris() != null ) && !node.getNodeData().getTaxonomy()
.getUris().isEmpty() ) ) {
- x += drawTaxonomyImage( node.getXcoord() + 2 + _half_box_size, node.getYcoord(), node, g );
+ x += drawTaxonomyImage( node.getXcoord() + 2 + half_box_size, node.getYcoord(), node, g );
}
if ( ( getControlPanel().isShowTaxonomyCode() || getControlPanel().isShowTaxonomyScientificNames() || getControlPanel()
.isShowTaxonomyCommonNames() ) && node.getNodeData().isHasTaxonomy() ) {
_sb.append( node.getNodeData().getSequence().getAccession().getValue() );
}
}
+ if ( getControlPanel().isShowProperties() && node.getNodeData().isHasProperties() ) {
+ if ( _sb.length() > 0 ) {
+ _sb.append( " " );
+ }
+ _sb.append( propertiesToString( node ) );
+ }
g.setFont( getTreeFontSet().getLargeFont() );
if ( is_in_found_nodes ) {
g.setFont( getTreeFontSet().getLargeFont().deriveFont( Font.BOLD ) );
if ( !node.isExternal() && ( node.getNumberOfDescendants() == 1 ) ) {
down_shift_factor = 1;
}
- final double pos_x = node.getXcoord() + x + 2 + _half_box_size;
+ final double pos_x = node.getXcoord() + x + 2 + half_box_size;
final double pos_y = ( node.getYcoord() + ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ) );
final String sb_str = _sb.toString();
// GUILHEM_BEG ______________
&& seqRelation.getType().equals( getControlPanel().getSequenceRelationTypeBox()
.getSelectedItem() );
if ( fGotRelationWithQuery ) { // we will underline the text to show that this sequence is ortholog to the query
- final double linePosX = node.getXcoord() + 2 + _half_box_size;
+ final double linePosX = node.getXcoord() + 2 + half_box_size;
final String sConfidence = ( !getControlPanel().isShowSequenceRelationConfidence() || ( seqRelation
.getConfidence() == null ) ) ? null : " (" + seqRelation.getConfidence().getValue()
+ ")";
g.setColor( calculateColorForAnnotation( ann ) );
}
final String ann_str = ann.asSimpleText().toString();
- TreePanel.drawString( ann_str, node.getXcoord() + x + 3 + _half_box_size, node.getYcoord()
+ 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( ann_str );
}
if ( getControlPanel().isShowBinaryCharacters() ) {
TreePanel.drawString( node.getNodeData().getBinaryCharacters().getPresentCharactersAsStringBuffer()
- .toString(), node.getXcoord() + x + 1 + _half_box_size, node.getYcoord()
+ .toString(), node.getXcoord() + x + 1 + half_box_size, node.getYcoord()
+ ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g );
paintGainedAndLostCharacters( g, node, node.getNodeData().getBinaryCharacters()
.getGainedCharactersAsStringBuffer().toString(), node.getNodeData().getBinaryCharacters()
}
final double mean = ForesterUtil.round( sum / count, 1 );
TreePanel.drawString( " " + node.getNodeData().getBinaryCharacters().getPresentCount() + " ["
- + mean + "]", node.getXcoord() + x + 4 + _half_box_size, node.getYcoord()
+ + mean + "]", node.getXcoord() + x + 4 + half_box_size, node.getYcoord()
+ ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ), g );
}
else {
TreePanel.drawString( " " + node.getNodeData().getBinaryCharacters().getPresentCount(),
- node.getXcoord() + x + 4 + _half_box_size,
+ node.getXcoord() + x + 4 + half_box_size,
node.getYcoord()
+ ( getTreeFontSet()._fm_large.getAscent() / down_shift_factor ),
g );
}
}
+ private StringBuffer propertiesToString( final PhylogenyNode node ) {
+ final PropertiesMap properties = node.getNodeData().getProperties();
+ final StringBuffer sb = new StringBuffer();
+ boolean first = true;
+ for( final String ref : properties.getPropertyRefs() ) {
+ if ( first ) {
+ first = false;
+ }
+ else {
+ sb.append( " " );
+ }
+ final Property p = properties.getProperty( ref );
+ sb.append( getPartAfterColon( p.getRef() ) );
+ sb.append( "=" );
+ sb.append( p.getValue() );
+ if ( !ForesterUtil.isEmpty( p.getUnit() ) ) {
+ sb.append( getPartAfterColon( p.getUnit() ) );
+ }
+ }
+ return sb;
+ }
+
+ 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() );
+ }
+
private double drawTaxonomyImage( final double x, final double y, final PhylogenyNode node, final Graphics2D g ) {
final List<Uri> us = new ArrayList<Uri>();
for( final Taxonomy t : node.getNodeData().getTaxonomies() ) {
++_external_node_index;
}
// Confidence values
- if ( getControlPanel().isShowBootstrapValues()
+ if ( getControlPanel().isShowConfidenceValues()
&& !node.isExternal()
&& !node.isRoot()
&& ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED )
child_node.setYcoord( y2 );
y2 += _y_distance * child_node.getNumberOfExternalNodes();
}
- //TODO new *****
- paintNodeBox( node.getXcoord(), node.getYcoord(), node, g, to_pdf, to_graphics_file, isInFoundNodes( node ) );
- //TODO new *****
+ paintNodeBox( node.getXcoord(), node.getYcoord(), node, g, to_pdf, to_graphics_file, isInFoundNodes( node ) );
}
if ( dynamically_hide
&& !is_in_found_nodes
}
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 );
}
//////////////
}
else {
g.setColor( getTreeColorSet().getTaxonomyColor() );
}
- final double start_x = node.getXcoord() + 3 + _half_box_size + x_shift;
+ final double start_x = node.getXcoord() + 3 + ( getOptions().getDefaultNodeShapeSize() / 2 ) + x_shift;
final double start_y = node.getYcoord()
+ ( getTreeFontSet()._fm_large.getAscent() / ( node.getNumberOfDescendants() == 1 ? 1 : 3.0 ) );
_sb.setLength( 0 );
if ( n.isRoot() ) {
n.setXcoord( getWidth() / 2 );
n.setYcoord( getHeight() / 2 );
- paintNodeBox( n.getXcoord(), n.getYcoord(), n, g, to_pdf, to_graphics_file, isInFoundNodes( n ) );
}
if ( n.isExternal() ) {
paintNodeDataUnrootedCirc( g,
final float new_y = ( float ) ( y + Math.sin( mid_angle ) * length );
desc.setXcoord( new_x );
desc.setYcoord( new_y );
- paintNodeBox( new_x, new_y, desc, g, to_pdf, to_graphics_file, isInFoundNodes( desc ) );
paintUnrooted( desc, current_angle, current_angle + arc_size, radial_labels, g, to_pdf, to_graphics_file );
current_angle += arc_size;
assignGraphicsForBranchWithColorForParentBranch( desc, false, g, to_pdf, to_graphics_file );
drawLine( x, y, new_x, new_y, g );
+ paintNodeBox( new_x, new_y, desc, g, to_pdf, to_graphics_file, isInFoundNodes( desc ) );
+ }
+ if ( n.isRoot() ) {
+ paintNodeBox( n.getXcoord(), n.getYcoord(), n, g, to_pdf, to_graphics_file, isInFoundNodes( n ) );
}
}
}
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();
* @param x
* @param y
*/
- final void setParametersForPainting( final int x, final int y, final boolean recalc_longest_ext_node_info ) {
+ public final void setParametersForPainting( final int x, final int y, final boolean recalc_longest_ext_node_info ) {
// updateStyle(); not needed?
if ( ( _phylogeny != null ) && !_phylogeny.isEmpty() ) {
initNodeData();
* an instance of a Phylogeny
*/
public final void setTree( final Phylogeny t ) {
- _nodes_in_preorder = null;
+ setNodeInPreorderToNull();
_phylogeny = t;
}
+ final void setNodeInPreorderToNull() {
+ _nodes_in_preorder = null;
+ }
+
final void setTreeFile( final File treefile ) {
_treefile = treefile;
}
.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence.getValue(),
getOptions()
.getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
+ if ( confidence.getStandardDeviation() != Confidence.CONFIDENCE_DEFAULT_VALUE ) {
+ _popup_buffer.append( " (sd=" );
+ _popup_buffer.append( FORMATTER_CONFIDENCE.format( ForesterUtil.round( confidence
+ .getStandardDeviation(), getOptions()
+ .getNumberOfDigitsAfterCommaForConfidenceValues() ) ) );
+ _popup_buffer.append( ")" );
+ }
+ }
+ }
+ if ( node.getNodeData().isHasProperties() ) {
+ final PropertiesMap properties = node.getNodeData().getProperties();
+ 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( "=" );
+ _popup_buffer.append( p.getValue() );
+ if ( !ForesterUtil.isEmpty( p.getUnit() ) ) {
+ _popup_buffer.append( getPartAfterColon( p.getUnit() ) );
+ }
}
}
if ( _popup_buffer.length() > 0 ) {
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 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() );
}
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();
}
return;
}
setWaitCursor();
- Util.colorPhylogenyAccordingToExternalTaxonomy( _phylogeny, this );
+ AptxUtil.colorPhylogenyAccordingToExternalTaxonomy( _phylogeny, this );
_control_panel.setColorBranches( true );
if ( _control_panel.getColorBranchesCb() != null ) {
_control_panel.getColorBranchesCb().setSelected( true );
git://source.jalview.org / jalview.git / blobdiff