From: cmzmasek Date: Mon, 12 Jun 2017 22:44:50 +0000 (-0700) Subject: in progress.. X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=7ae646b73c00d1458582858319ec62f05e40c71a;p=jalview.git in progress.. --- diff --git a/forester/java/src/org/forester/archaeopteryx/TreePanel.java b/forester/java/src/org/forester/archaeopteryx/TreePanel.java index 75ef09b..af3e9ee 100644 --- a/forester/java/src/org/forester/archaeopteryx/TreePanel.java +++ b/forester/java/src/org/forester/archaeopteryx/TreePanel.java @@ -78,6 +78,7 @@ import java.util.Collections; import java.util.HashMap; import java.util.HashSet; import java.util.Hashtable; +import java.util.Iterator; import java.util.List; import java.util.Map; import java.util.Set; @@ -533,20 +534,9 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee @Override final public void paintComponent( final Graphics g ) { - // Dimension currentSize = getSize(); - // if ( offscreenImage == null || !currentSize.equals( offscreenDimension ) ) { - // call the 'java.awt.Component.createImage(...)' method to get an - // image - // offscreenImage = createImage( currentSize.width, currentSize.height ); - // offscreenGraphics = offscreenImage.getGraphics(); - // offscreenDimension = currentSize; - // } - // super.paintComponent( g ); //why? - //final Graphics2D g2d = ( Graphics2D ) offscreenGraphics; final Graphics2D g2d = ( Graphics2D ) g; g2d.setRenderingHints( _rendering_hints ); paintPhylogeny( g2d, false, false, 0, 0, 0, 0 ); - //g.drawImage( offscreenImage, 0, 0, this ); } @Override @@ -1297,7 +1287,6 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee return _last_drag_point_y; } - final private double getMaxDistanceToRoot() { if ( _max_distance_to_root < 0 ) { recalculateMaxDistanceToRoot(); @@ -2394,19 +2383,28 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee final boolean to_graphics_file, final boolean to_pdf, final boolean is_in_found_nodes ) { + //// + //// TODO + //// Color c = null; + int res[] = null; + if ( _found_nodes_0 != null || _found_nodes_1 != null ) { + res = calcFoundNodesInSubtree( node ); + } if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) { c = Color.BLACK; } - else if ( is_in_found_nodes ) { - c = getColorForFoundNode( node ); - } - else if ( getControlPanel().isColorAccordingToSequence() ) { - c = getSequenceBasedColor( node ); - } - else if ( getControlPanel().isColorAccordingToTaxonomy() ) { - c = getTaxonomyBasedColor( node ); - } + //TODO + //FIXME + // else if ( is_in_found_nodes ) { + // c = getColorForFoundNode( node ); + // } + // else if ( getControlPanel().isColorAccordingToSequence() ) { + // c = getSequenceBasedColor( node ); + // } + // else if ( getControlPanel().isColorAccordingToTaxonomy() ) { + // c = getTaxonomyBasedColor( node ); + // } else if ( getOptions().isColorLabelsSameAsParentBranch() && getControlPanel().isUseVisualStyles() && ( PhylogenyMethods.getBranchColorValue( node ) != null ) ) { c = PhylogenyMethods.getBranchColorValue( node ); @@ -2856,7 +2854,8 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee && !ForesterUtil.isEmpty( last.getNodeData().getTaxonomy().getTaxonomyCode() ) ) { addLabelForCollapsed( first.getNodeData().getTaxonomy().getTaxonomyCode(), last.getNodeData().getTaxonomy().getTaxonomyCode(), - node.getAllExternalDescendants().size() ); + node.getAllExternalDescendants().size(), + node ); } else if ( getControlPanel().isShowTaxonomyScientificNames() && first.getNodeData().isHasTaxonomy() && last.getNodeData().isHasTaxonomy() @@ -2864,7 +2863,8 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee && !ForesterUtil.isEmpty( last.getNodeData().getTaxonomy().getScientificName() ) ) { addLabelForCollapsed( first.getNodeData().getTaxonomy().getScientificName(), last.getNodeData().getTaxonomy().getScientificName(), - node.getAllExternalDescendants().size() ); + node.getAllExternalDescendants().size(), + node ); } else if ( getControlPanel().isShowSeqNames() && first.getNodeData().isHasSequence() && last.getNodeData().isHasSequence() @@ -2872,13 +2872,15 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee && !ForesterUtil.isEmpty( last.getNodeData().getSequence().getName() ) ) { addLabelForCollapsed( first.getNodeData().getSequence().getName(), last.getNodeData().getSequence().getName(), - node.getAllExternalDescendants().size() ); + node.getAllExternalDescendants().size(), + node ); } else if ( getControlPanel().isShowNodeNames() && !ForesterUtil.isEmpty( first.getName() ) && !ForesterUtil.isEmpty( last.getName() ) ) { addLabelForCollapsed( first.getName(), last.getName(), - node.getAllExternalDescendants().size() ); + node.getAllExternalDescendants().size(), + node ); } } } @@ -2887,6 +2889,16 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee _sb.append( " [" ); _sb.append( node.getAllExternalDescendants().size() ); _sb.append( "]" ); + if ( _found_nodes_0 != null || _found_nodes_1 != null ) { + int[] res = calcFoundNodesInSubtree( node ); + if ( res[ 0 ] > 0 ) { + _sb.append( " [" ); + _sb.append( res[ 0 ] ); + _sb.append( "/" ); + _sb.append( res[ 1 ] ); + _sb.append( "]" ); + } + } } } else { @@ -3117,13 +3129,47 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } } - private final void addLabelForCollapsed( final String first, final String last, final int size ) { + private final void addLabelForCollapsed( final String first, + final String last, + final int size, + final PhylogenyNode node ) { _sb.append( first.length() < AptxConstants.MAX_LENGTH_FOR_COLLAPSED_NAME ? first : first.substring( 0, AptxConstants.MAX_LENGTH_FOR_COLLAPSED_NAME - 1 ) ); _sb.append( " ... " ); _sb.append( last.length() < AptxConstants.MAX_LENGTH_FOR_COLLAPSED_NAME ? last : last.substring( 0, AptxConstants.MAX_LENGTH_FOR_COLLAPSED_NAME - 1 ) ); _sb.append( " (" + size + ")" ); + if ( _found_nodes_0 != null || _found_nodes_1 != null ) { + ///// + ///// + int[] res = calcFoundNodesInSubtree( node ); + if ( res[ 0 ] > 0 ) { + _sb.append( " [" ); + _sb.append( res[ 0 ] ); + _sb.append( "/" ); + _sb.append( res[ 1 ] ); + _sb.append( "]" ); + } + } + } + + private final int[] calcFoundNodesInSubtree( final PhylogenyNode node ) { + final List all_descs = PhylogenyMethods.getAllDescendants( node ); + int res[] = new int[ 2 ]; + int found = 0; + int total = 0; + for( final PhylogenyNode desc : all_descs ) { + if ( desc.isHasNodeData() ) { + if ( ( _found_nodes_0 != null && _found_nodes_0.contains( desc.getId() ) ) + || ( _found_nodes_1 != null && _found_nodes_1.contains( desc.getId() ) ) ) { + ++found; + } + ++total; + } + } + res[ 0 ] = found; + res[ 1 ] = total; + return res; } private final boolean isAllowAttributedStrings() { @@ -3503,7 +3549,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee //if ( getControlPanel().isShowMolSequences() && ( node.getNodeData().isHasSequence() ) // && ( node.getNodeData().getSequence().isMolecularSequenceAligned() ) // && ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) ) { - // paintMolecularSequences( g, node, to_pdf ); + // paintMolecularSequences( g, node, to_pdf ); //} } diff --git a/forester/java/src/org/forester/phylogeny/Phylogeny.java b/forester/java/src/org/forester/phylogeny/Phylogeny.java index 379a933..0416f41 100644 --- a/forester/java/src/org/forester/phylogeny/Phylogeny.java +++ b/forester/java/src/org/forester/phylogeny/Phylogeny.java @@ -37,6 +37,8 @@ import java.util.List; import java.util.Map; import java.util.NoSuchElementException; import java.util.Vector; +import java.util.regex.Matcher; +import java.util.regex.Pattern; import org.forester.io.parsers.nhx.NHXParser; import org.forester.io.writers.PhylogenyWriter; @@ -56,6 +58,7 @@ import org.forester.phylogeny.iterators.PhylogenyNodeIterator; import org.forester.phylogeny.iterators.PostorderTreeIterator; import org.forester.phylogeny.iterators.PreorderTreeIterator; import org.forester.util.FailedConditionCheckException; +import org.forester.util.ForesterUtil; public class Phylogeny { @@ -448,6 +451,23 @@ public class Phylogeny { return nodes; } + public List getNodes( final Pattern p ) { + if ( isEmpty() ) { + return null; + } + final List nodes = new ArrayList<>(); + for( final PhylogenyNodeIterator iter = iteratorPreorder(); iter.hasNext(); ) { + final PhylogenyNode n = iter.next(); + if ( n.getName() != null ) { + final Matcher m = p.matcher( n.getName() ); + if ( m.find() ) { + nodes.add( n ); + } + } + } + return nodes; + } + public List getNodesViaSequenceName( final String seq_name ) { if ( isEmpty() ) { return null;