in progress

[jalview.git] / forester / java / src / org / forester / archaeopteryx / TreePanel.java

diff --git a/forester/java/src/org/forester/archaeopteryx/TreePanel.java b/forester/java/src/org/forester/archaeopteryx/TreePanel.java
index 136bfd5..32de234 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/TreePanel.java
+++ b/forester/java/src/org/forester/archaeopteryx/TreePanel.java
@@ -267,7 +267,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         _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 );
@@ -575,6 +575,9 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                     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() );
@@ -764,6 +767,7 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
             return;
         }
         setWaitCursor();
+        Util.removeBranchColors( _phylogeny );
         Util.colorPhylogenyAccordingToConfidenceValues( _phylogeny, this );
         _control_panel.setColorBranches( true );
         if ( _control_panel.getColorBranchesCb() != null ) {
@@ -778,13 +782,44 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
             return;
         }
         setWaitCursor();
-        Util.colorPhylogenyAccordingToRanks( _phylogeny, rank, this );
-        _control_panel.setColorBranches( true );
-        if ( _control_panel.getColorBranchesCb() != null ) {
-            _control_panel.getColorBranchesCb().setSelected( true );
+        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 ) {
@@ -2967,6 +3002,12 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
                 _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 ) );
@@ -3116,6 +3157,22 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee
         }
     }
 
+    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() ) {