X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FTreePanel.java;h=632131577a5c3ca3af78ca992ac053935cfd80d4;hb=3087ea10ac51cf1a8b2eb8d8abe010513ce9998f;hp=9bc89cc906f5f10d80e577e65447041cd643cc1b;hpb=814c97be10a4c55b0bb642668f9ef8e1f80d5a6c;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/TreePanel.java b/forester/java/src/org/forester/archaeopteryx/TreePanel.java index 9bc89cc..6321315 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; @@ -257,7 +258,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee 2.0f }, 0f ); private static final double TWO_PI = 2 * Math.PI; - private final static int WIGGLE = 2; + private final static int WIGGLE = 3; private static final String SHOW_ONLY_THIS_CONF_TYPE = null; //TODO remove me HashMap _nodeid_dist_to_leaf = new HashMap(); final private Arc2D _arc = new Arc2D.Double(); @@ -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 @@ -1297,17 +1287,6 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee return _last_drag_point_y; } - final private short getMaxBranchesToLeaf( final PhylogenyNode node ) { - if ( !_nodeid_dist_to_leaf.containsKey( node.getId() ) ) { - final short m = PhylogenyMethods.calculateMaxBranchesToLeaf( node ); - _nodeid_dist_to_leaf.put( node.getId(), m ); - return m; - } - else { - return _nodeid_dist_to_leaf.get( node.getId() ); - } - } - final private double getMaxDistanceToRoot() { if ( _max_distance_to_root < 0 ) { recalculateMaxDistanceToRoot(); @@ -1446,7 +1425,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee sortDescendants( node ); break; case GET_EXT_DESC_DATA: - showExtDescNodeData( node ); + showExtDescNodeData( node, '_' ); break; case UNCOLLAPSE_ALL: uncollapseAll( node ); @@ -2119,7 +2098,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee final boolean to_pdf, final boolean to_graphics_file ) { g.setFont( getTreeFontSet().getSmallFont() ); - if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) { + if ( to_pdf || ( to_graphics_file && getOptions().isPrintBlackAndWhite() ) ) { g.setColor( Color.BLACK ); } else { @@ -2404,19 +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 ); @@ -2543,7 +2531,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee else if ( getPhylogenyGraphicsType() == PHYLOGENY_GRAPHICS_TYPE.ROUNDED ) { x += ROUNDED_D; } - if ( ( to_pdf || to_graphics_file ) && getOptions().isPrintBlackAndWhite() ) { + if ( to_pdf || ( to_graphics_file && getOptions().isPrintBlackAndWhite() ) ) { g.setColor( Color.BLACK ); } else { @@ -2866,7 +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() @@ -2874,7 +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() @@ -2882,13 +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 ); } } } @@ -2897,6 +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 { @@ -3127,13 +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() { @@ -3455,7 +3491,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee if ( getOptions().isLineUpRendarableNodeData() ) { if ( getOptions().isRightLineUpDomains() ) { rds.render( ( float ) ( ( getMaxDistanceToRoot() * getXcorrectionFactor() ) - + _length_of_longest_text + + _length_of_longest_text + 50 //TODO why plus 50? + ( ( _longest_domain - rds.getTotalLength() ) * rds.getRenderingFactorWidth() ) ), node.getYcoord() - ( h / 2.0f ), g, @@ -3464,7 +3500,11 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } else { rds.render( ( float ) ( ( getMaxDistanceToRoot() * getXcorrectionFactor() ) - + _length_of_longest_text ), node.getYcoord() - ( h / 2.0f ), g, this, to_pdf ); + + _length_of_longest_text + 50 ), + node.getYcoord() - ( h / 2.0f ), + g, + this, + to_pdf ); } } else { @@ -3513,7 +3553,7 @@ 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 ); //} } @@ -4037,7 +4077,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee _urt_factor_ov = urt_factor_ov; } - private void showExtDescNodeData( final PhylogenyNode node ) { + private void showExtDescNodeData( final PhylogenyNode node, final char separator ) { final List data = new ArrayList(); final List nodes = node.getAllExternalDescendants(); if ( ( getFoundNodes0() != null ) || ( getFoundNodes1() != null ) ) { @@ -4077,44 +4117,50 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee if ( n.getNodeData().isHasSequence() && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getMolecularSequence() ) ) { final StringBuilder ann = new StringBuilder(); - if ( !ForesterUtil.isEmpty( n.getName() ) ) { + if ( getControlPanel().isShowNodeNames() && !ForesterUtil.isEmpty( n.getName() ) ) { ann.append( n.getName() ); - ann.append( "|" ); + ann.append( separator ); + } + if ( n.getNodeData().isHasTaxonomy() ) { + if ( getControlPanel().isShowTaxonomyCode() + && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) { + ann.append( n.getNodeData().getTaxonomy().getTaxonomyCode() ); + ann.append( separator ); + } + if ( getControlPanel().isShowTaxonomyScientificNames() + && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) { + ann.append( n.getNodeData().getTaxonomy().getScientificName() ); + ann.append( separator ); + } + if ( getControlPanel().isShowTaxonomyCommonNames() + && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getCommonName() ) ) { + ann.append( n.getNodeData().getTaxonomy().getCommonName() ); + ann.append( separator ); + } } - if ( !ForesterUtil.isEmpty( n.getNodeData().getSequence().getSymbol() ) ) { - ann.append( "SYM=" ); + if ( getControlPanel().isShowSeqSymbols() + && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getSymbol() ) ) { ann.append( n.getNodeData().getSequence().getSymbol() ); - ann.append( "|" ); + ann.append( separator ); } - if ( !ForesterUtil.isEmpty( n.getNodeData().getSequence().getName() ) ) { - ann.append( "NAME=" ); + if ( getControlPanel().isShowSeqNames() + && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getName() ) ) { ann.append( n.getNodeData().getSequence().getName() ); - ann.append( "|" ); + ann.append( separator ); } - if ( !ForesterUtil.isEmpty( n.getNodeData().getSequence().getGeneName() ) ) { - ann.append( "GN=" ); + if ( getControlPanel().isShowGeneNames() + && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getGeneName() ) ) { ann.append( n.getNodeData().getSequence().getGeneName() ); - ann.append( "|" ); + ann.append( separator ); } - if ( n.getNodeData().getSequence().getAccession() != null ) { - ann.append( "ACC=" ); + if ( getControlPanel().isShowSequenceAcc() + && n.getNodeData().getSequence().getAccession() != null ) { 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( "|" ); - } + ann.append( separator ); } - String ann_str; - if ( ann.charAt( ann.length() - 1 ) == '|' ) { + + final String ann_str; + if ( ann.length() > 0 && ann.charAt( ann.length() - 1 ) == separator ) { ann_str = ann.substring( 0, ann.length() - 1 ); } else { @@ -4979,7 +5025,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee * @param y * @return pointer to the node at x,y, null if not found */ - final PhylogenyNode findNode( final int x, final int y ) { + public final PhylogenyNode findNode( final int x, final int y ) { if ( ( _phylogeny == null ) || _phylogeny.isEmpty() ) { return null; } @@ -5017,15 +5063,15 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee return _domain_structure_e_value_thr_exp; } - final Set getFoundNodes0() { + public final Set getFoundNodes0() { return _found_nodes_0; } - final Set getFoundNodes1() { + public final Set getFoundNodes1() { return _found_nodes_1; } - List getFoundNodesAsListOfPhylogenyNodes() { + public List getFoundNodesAsListOfPhylogenyNodes() { final List additional_nodes = new ArrayList(); if ( getFoundNodes0() != null ) { for( final Long id : getFoundNodes0() ) { @@ -5943,11 +5989,11 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee _current_external_nodes_data_buffer = sb; } - final void setFoundNodes0( final Set found_nodes ) { + public final void setFoundNodes0( final Set found_nodes ) { _found_nodes_0 = found_nodes; } - final void setFoundNodes1( final Set found_nodes ) { + public final void setFoundNodes1( final Set found_nodes ) { _found_nodes_1 = found_nodes; }