JAL-2805 JAL-281 JAL-2847 set tree file made public as well (heh)

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

diff --git a/forester/java/src/org/forester/archaeopteryx/TreePanelUtil.java b/forester/java/src/org/forester/archaeopteryx/TreePanelUtil.java
index 9aeec3b..38f935b 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/TreePanelUtil.java
+++ b/forester/java/src/org/forester/archaeopteryx/TreePanelUtil.java
@@ -252,7 +252,7 @@ public class TreePanelUtil {
         }
     }
 
-    static void colorizeSubtree( final PhylogenyNode node, final BranchColor c ) {
+    public static void colorizeSubtree( final PhylogenyNode node, final BranchColor c ) {
         node.getBranchData().setBranchColor( c );
         final List<PhylogenyNode> descs = PhylogenyMethods.getAllDescendants( node );
         for( final PhylogenyNode desc : descs ) {
@@ -307,76 +307,76 @@ public class TreePanelUtil {
         }
     }
 
-    final static int collapseByTaxonomicRank( final Phylogeny tree, final String rank, final TreePanel tree_panel ) {
-        final Set<String> true_lineage_set = new HashSet<String>();
-        for( final PhylogenyNodeIterator iter = tree.iteratorPreorder(); iter.hasNext(); ) {
-            iter.next().setCollapse( false );
-        }
-        int collapsed = 0;
-        for( final PhylogenyNodeIterator it = tree.iteratorPostorder(); it.hasNext(); ) {
-            final PhylogenyNode n = it.next();
-            if ( !n.isExternal() && n.getNodeData().isHasTaxonomy() && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getRank() )
-                    && n.getNodeData().getTaxonomy().getRank().equalsIgnoreCase( rank ) /*&& !n.isRoot()*/ ) {
-                TreePanelUtil.collapseSubtree( n, true );
-                ++collapsed;
-                if ( !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) {
-                    true_lineage_set.add( n.getNodeData().getTaxonomy().getScientificName() );
-                }
-            }
-        }
-        for( final PhylogenyNodeIterator it = tree.iteratorPostorder(); it.hasNext(); ) {
-            final PhylogenyNode node = it.next();
-            if ( ( !node.isExternal() && !node.isCollapse() ) && node.getNodeData().isHasTaxonomy()
-                    && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getLineage() ) /* && !node.isRoot()*/ ) {
-                boolean success = false;
-                if ( !true_lineage_set.isEmpty() ) {
-                    for( final String lin : node.getNodeData().getTaxonomy().getLineage() ) {
-                        if ( true_lineage_set.contains( lin ) ) {
-                            TreePanelUtil.collapseSubtree( node, true );
-                            ++collapsed;
-                            success = true;
-                            break;
-                        }
-                    }
-                }
-                if ( !success ) {
-                    final Map<String, String> lineage_to_rank_map = MainPanel.getLineageToRankMap();
-                    for( final String lin : node.getNodeData().getTaxonomy().getLineage() ) {
-                        final Taxonomy temp_tax = new Taxonomy();
-                        temp_tax.setScientificName( lin );
-                        if ( lineage_to_rank_map.containsKey( lin )
-                                && !ForesterUtil.isEmpty( lineage_to_rank_map.get( lin ) )
-                                && lineage_to_rank_map.get( lin ).equalsIgnoreCase( rank ) ) {
-                             TreePanelUtil.collapseSubtree( node, true );
-                            ++collapsed;
-                            true_lineage_set.add( lin );
-                            break;
-                        }
-                        else {
-                            UniProtTaxonomy up = null;
-                            try {
-                                up = TaxonomyDataManager.obtainUniProtTaxonomy( temp_tax, null, null );
-                            }
-                            catch ( final Exception e ) {
-                                e.printStackTrace();
-                            }
-                            if ( ( up != null ) && !ForesterUtil.isEmpty( up.getRank() ) ) {
-                                lineage_to_rank_map.put( lin, up.getRank() );
-                                System.out.println( lin + "->" + up.getRank() );
-                                if ( up.getRank().equalsIgnoreCase( rank ) ) {
-                                    TreePanelUtil.collapseSubtree( node, true );
-                                    ++collapsed;
-                                    true_lineage_set.add( lin );
-                                    break;
-                                }
-                            }
-                        }
-                    }
-                }
-            }
-        }
-        return collapsed;
-    }
+//    final static int collapseByTaxonomicRank( final Phylogeny tree, final String rank, final TreePanel tree_panel ) {
+//        final Set<String> true_lineage_set = new HashSet<String>();
+//        for( final PhylogenyNodeIterator iter = tree.iteratorPreorder(); iter.hasNext(); ) {
+//            iter.next().setCollapse( false );
+//        }
+//        int collapsed = 0;
+//        for( final PhylogenyNodeIterator it = tree.iteratorPostorder(); it.hasNext(); ) {
+//            final PhylogenyNode n = it.next();
+//            if ( !n.isExternal() && n.getNodeData().isHasTaxonomy() && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getRank() )
+//                    && n.getNodeData().getTaxonomy().getRank().equalsIgnoreCase( rank ) /*&& !n.isRoot()*/ ) {
+//                TreePanelUtil.collapseSubtree( n, true );
+//                ++collapsed;
+//                if ( !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) {
+//                    true_lineage_set.add( n.getNodeData().getTaxonomy().getScientificName() );
+//                }
+//            }
+//        }
+//        for( final PhylogenyNodeIterator it = tree.iteratorPostorder(); it.hasNext(); ) {
+//            final PhylogenyNode node = it.next();
+//            if ( ( !node.isExternal() && !node.isCollapse() ) && node.getNodeData().isHasTaxonomy()
+//                    && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getLineage() ) /* && !node.isRoot()*/ ) {
+//                boolean success = false;
+//                if ( !true_lineage_set.isEmpty() ) {
+//                    for( final String lin : node.getNodeData().getTaxonomy().getLineage() ) {
+//                        if ( true_lineage_set.contains( lin ) ) {
+//                            TreePanelUtil.collapseSubtree( node, true );
+//                            ++collapsed;
+//                            success = true;
+//                            break;
+//                        }
+//                    }
+//                }
+//                if ( !success ) {
+//                    final Map<String, String> lineage_to_rank_map = MainPanel.getLineageToRankMap();
+//                    for( final String lin : node.getNodeData().getTaxonomy().getLineage() ) {
+//                        final Taxonomy temp_tax = new Taxonomy();
+//                        temp_tax.setScientificName( lin );
+//                        if ( lineage_to_rank_map.containsKey( lin )
+//                                && !ForesterUtil.isEmpty( lineage_to_rank_map.get( lin ) )
+//                                && lineage_to_rank_map.get( lin ).equalsIgnoreCase( rank ) ) {
+//                             TreePanelUtil.collapseSubtree( node, true );
+//                            ++collapsed;
+//                            true_lineage_set.add( lin );
+//                            break;
+//                        }
+//                        else {
+//                            UniProtTaxonomy up = null;
+//                            try {
+//                                up = TaxonomyDataManager.obtainUniProtTaxonomy( temp_tax, null, null );
+//                            }
+//                            catch ( final Exception e ) {
+//                                e.printStackTrace();
+//                            }
+//                            if ( ( up != null ) && !ForesterUtil.isEmpty( up.getRank() ) ) {
+//                                lineage_to_rank_map.put( lin, up.getRank() );
+//                                System.out.println( lin + "->" + up.getRank() );
+//                                if ( up.getRank().equalsIgnoreCase( rank ) ) {
+//                                    TreePanelUtil.collapseSubtree( node, true );
+//                                    ++collapsed;
+//                                    true_lineage_set.add( lin );
+//                                    break;
+//                                }
+//                            }
+//                        }
+//                    }
+//                }
+//            }
+//        }
+//        return collapsed;
+//    }
 
     final static int colorPhylogenyAccordingToRanks( final Phylogeny tree,
                                                      final String rank,