import org.forester.archaeopteryx.ControlPanel.NodeClickAction;
import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
-import org.forester.archaeopteryx.Options.NodeFill;
-import org.forester.archaeopteryx.Options.NodeShape;
import org.forester.archaeopteryx.Options.PHYLOGENY_GRAPHICS_TYPE;
import org.forester.archaeopteryx.phylogeny.data.RenderableDomainArchitecture;
import org.forester.archaeopteryx.phylogeny.data.RenderableVector;
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.PropertiesMap;
import org.forester.phylogeny.data.Property;
private final static NumberFormat FORMATTER_CONFIDENCE;
private final static NumberFormat FORMATTER_BRANCH_LENGTH;
private final static int WIGGLE = 2;
- //private final 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;
_main_panel = tjp;
_configuration = configuration;
_phylogeny = t;
- _phy_has_branch_lengths = ForesterUtil.isHasAtLeastOneBranchLengthLargerThanZero( _phylogeny );
+ _phy_has_branch_lengths = Util.isHasAtLeastOneBranchLengthLargerThanZero( _phylogeny );
init();
// if ( !_phylogeny.isEmpty() ) {
_phylogeny.recalculateNumberOfExternalDescendants( true );
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() );
if ( !node.isExternal() && !node.isRoot() ) {
final boolean collapse = !node.isCollapse();
Util.collapseSubtree( node, collapse );
+ updateSetOfCollapsedExternalNodes( _phylogeny );
_phylogeny.recalculateNumberOfExternalDescendants( true );
resetNodeIdToDistToLeafMap();
calculateLongestExtNodeInfo();
}
setWaitCursor();
Util.collapseSpeciesSpecificSubtrees( _phylogeny );
+ updateSetOfCollapsedExternalNodes( _phylogeny );
_phylogeny.recalculateNumberOfExternalDescendants( true );
resetNodeIdToDistToLeafMap();
calculateLongestExtNodeInfo();
return;
}
setWaitCursor();
+ Util.removeBranchColors( _phylogeny );
Util.colorPhylogenyAccordingToConfidenceValues( _phylogeny, this );
_control_panel.setColorBranches( true );
if ( _control_panel.getColorBranchesCb() != null ) {
repaint();
}
+ final void colorRank( final String rank ) {
+ if ( ( _phylogeny == null ) || ( _phylogeny.getNumberOfExternalNodes() < 2 ) ) {
+ return;
+ }
+ setWaitCursor();
+ Util.removeBranchColors( _phylogeny );
+ final int colorizations = Util.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();
else {
final float x2a = x2;
final float x1a = x1;
- // draw the vertical line
- // boolean draw_horizontal = true;
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();
- //TODO fix below -- actually this might not be necessay anymore? test pdf, though!
- // if ( ( ( ( getOptions().isShowDefaultNodeShapes() ) && !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 ( draw_vertical ) {
if ( !to_graphics_file
&& !to_pdf
&& ( ( ( y2 < getVisibleRect().getMinY() - 20 ) && ( y1 < getVisibleRect().getMinY() - 20 ) ) || ( ( y2 > getVisibleRect()
drawLine( x1, y1, x1, y2, g );
}
}
- //}
}
// draw the horizontal line
if ( !to_graphics_file && !to_pdf
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;
drawRectFilled( x1a, y2 - ( w / 2 ), x2a - x1a, w, g );
}
}
- //}
if ( ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) ) {
if ( x1_r > x2a ) {
x1_r = x2a;
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 );
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 ) );
}
+ private 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 double starting_angle,
final int center_x,
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() );
}
ForesterUtil.roundToInt( node.getYcoord() - d ) );
_polygon.addPoint( ForesterUtil.roundToInt( node.getXcoord() + box_size ),
ForesterUtil.roundToInt( node.getYcoord() + d ) );
- if ( getOptions().getDefaultNodeFill() == NodeFill.SOLID ) {
+ if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.SOLID ) {
g.setColor( c );
g.fillPolygon( _polygon );
}
- else if ( getOptions().getDefaultNodeFill() == NodeFill.NONE ) {
+ else if ( getOptions().getDefaultNodeFill() == NodeVisualization.NodeFill.NONE ) {
g.setColor( getBackground() );
g.fillPolygon( _polygon );
g.setColor( c );
}
else {
outline_color = getGraphicsForNodeBoxWithColorForParentBranch( node );
+ if ( to_pdf && ( outline_color == getTreeColorSet().getBranchColor() ) ) {
+ outline_color = getTreeColorSet().getBranchColorForPdf();
+ }
}
- final int half_box_size = getOptions().getDefaultNodeShapeSize() / 2;
final int box_size = getOptions().getDefaultNodeShapeSize();
- if ( ( ( getOptions().isShowDefaultNodeShapes() ) /*&& !to_pdf && !to_graphics_file*/)
- || ( getControlPanel().isEvents() && node.isHasAssignedEvent() ) ) {
- if ( to_pdf || to_graphics_file ) {
- if ( node.isDuplication() || !getOptions().isPrintBlackAndWhite() ) {
+ 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,
- outline_color,
- getBackground(),
+ to_pdf ? Color.WHITE : outline_color,
+ to_pdf ? outline_color : getBackground(),
outline_color );
}
- }
- else {
- if ( getOptions().getDefaultNodeShape() == NodeShape.CIRCLE ) {
- if ( getOptions().getDefaultNodeFill() == NodeFill.GRADIENT ) {
- drawOvalGradient( x - half_box_size,
- y - half_box_size,
- box_size,
- box_size,
- g,
- outline_color,
- getBackground(),
- outline_color );
- }
- else if ( getOptions().getDefaultNodeFill() == NodeFill.NONE ) {
- drawOvalGradient( x - half_box_size,
- y - half_box_size,
- box_size,
- box_size,
- g,
- getBackground(),
- getBackground(),
- outline_color );
- }
- else if ( getOptions().getDefaultNodeFill() == NodeFill.SOLID ) {
- g.setColor( outline_color );
- drawOvalFilled( x - half_box_size, y - half_box_size, box_size, box_size, g );
+ 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().getDefaultNodeShape() == NodeShape.RECTANGLE ) {
- if ( getOptions().getDefaultNodeFill() == NodeFill.GRADIENT ) {
- drawRectGradient( x - half_box_size,
- y - half_box_size,
- box_size,
- box_size,
- g,
- outline_color,
- getBackground(),
- outline_color );
- }
- else if ( getOptions().getDefaultNodeFill() == NodeFill.NONE ) {
- drawRectGradient( x - half_box_size,
- y - half_box_size,
- box_size,
- box_size,
- g,
- getBackground(),
- getBackground(),
- outline_color );
- }
- else if ( getOptions().getDefaultNodeFill() == NodeFill.SOLID ) {
- g.setColor( outline_color );
- drawRectFilled( x - half_box_size, y - half_box_size, box_size, box_size, g );
+ 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 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 );
}
}
}
_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 ) );
}
}
+ 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( " " );
+ }
+ sb.append( properties.getProperty( ref ).asText() );
+ }
+ return sb;
+ }
+
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() ) {
git://source.jalview.org / jalview.git / blobdiff