phylotastic hackathon at NESCENT 120606

[jalview.git] / forester / java / src / org / forester / phylogeny / PhylogenyMethods.java

diff --git a/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java b/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java
index a042cee..dbf5d5f 100644 (file)
--- a/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java
+++ b/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java
@@ -593,13 +593,39 @@ public class PhylogenyMethods {
         return stats;
     }
 
-    public static DescriptiveStatistics calculatConfidenceStatistics( final Phylogeny phy ) {
+    public static DescriptiveStatistics calculatBranchLengthStatistics( final Phylogeny phy ) {
         final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
         for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
             final PhylogenyNode n = iter.next();
-            if ( !n.isExternal() ) {
+            if ( !n.isRoot() && ( n.getDistanceToParent() >= 0.0 ) ) {
+                stats.addValue( n.getDistanceToParent() );
+            }
+        }
+        return stats;
+    }
+
+    public static List<DescriptiveStatistics> calculatConfidenceStatistics( final Phylogeny phy ) {
+        final List<DescriptiveStatistics> stats = new ArrayList<DescriptiveStatistics>();
+        for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
+            final PhylogenyNode n = iter.next();
+            if ( !n.isExternal() && !n.isRoot() ) {
                 if ( n.getBranchData().isHasConfidences() ) {
-                    stats.addValue( n.getBranchData().getConfidence( 0 ).getValue() );
+                    for( int i = 0; i < n.getBranchData().getConfidences().size(); ++i ) {
+                        final Confidence c = n.getBranchData().getConfidences().get( i );
+                        if ( ( i > ( stats.size() - 1 ) ) || ( stats.get( i ) == null ) ) {
+                            stats.add( i, new BasicDescriptiveStatistics() );
+                        }
+                        if ( !ForesterUtil.isEmpty( c.getType() ) ) {
+                            if ( !ForesterUtil.isEmpty( stats.get( i ).getDescription() ) ) {
+                                if ( !stats.get( i ).getDescription().equalsIgnoreCase( c.getType() ) ) {
+                                    throw new IllegalArgumentException( "support values in node [" + n.toString()
+                                            + "] appear inconsistently ordered" );
+                                }
+                            }
+                            stats.get( i ).setDescription( c.getType() );
+                        }
+                        stats.get( i ).addValue( ( ( c != null ) && ( c.getValue() >= 0 ) ) ? c.getValue() : 0 );
+                    }
                 }
             }
         }
@@ -1560,6 +1586,49 @@ public class PhylogenyMethods {
         return nodes_to_delete.size();
     }
 
+    /**
+     * Arranges the order of childern for each node of this Phylogeny in such a
+     * way that either the branch with more children is on top (right) or on
+     * bottom (left), dependent on the value of boolean order.
+     * 
+     * @param order
+     *            decides in which direction to order
+     * @param pri 
+     */
+    public static void orderAppearance( final PhylogenyNode n,
+                                        final boolean order,
+                                        final boolean order_ext_alphabetically,
+                                        final DESCENDANT_SORT_PRIORITY pri ) {
+        if ( n.isExternal() ) {
+            return;
+        }
+        else {
+            PhylogenyNode temp = null;
+            if ( ( n.getNumberOfDescendants() == 2 )
+                    && ( n.getChildNode1().getNumberOfExternalNodes() != n.getChildNode2().getNumberOfExternalNodes() )
+                    && ( ( n.getChildNode1().getNumberOfExternalNodes() < n.getChildNode2().getNumberOfExternalNodes() ) == order ) ) {
+                temp = n.getChildNode1();
+                n.setChild1( n.getChildNode2() );
+                n.setChild2( temp );
+            }
+            else if ( order_ext_alphabetically ) {
+                boolean all_ext = true;
+                for( final PhylogenyNode i : n.getDescendants() ) {
+                    if ( !i.isExternal() ) {
+                        all_ext = false;
+                        break;
+                    }
+                }
+                if ( all_ext ) {
+                    PhylogenyMethods.sortNodeDescendents( n, pri );
+                }
+            }
+            for( int i = 0; i < n.getNumberOfDescendants(); ++i ) {
+                orderAppearance( n.getChildNode( i ), order, order_ext_alphabetically, pri );
+            }
+        }
+    }
+
     public static enum PhylogenyNodeField {
         CLADE_NAME,
         TAXONOMY_CODE,