in progress

[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 6569c81..5b936d5 100644 (file)
--- a/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java
+++ b/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java
@@ -5,7 +5,7 @@
 // Copyright (C) 2008-2009 Christian M. Zmasek
 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
 // All rights reserved
-// 
+//
 // This library is free software; you can redistribute it and/or
 // modify it under the terms of the GNU Lesser General Public
 // License as published by the Free Software Foundation; either
@@ -15,7 +15,7 @@
 // but WITHOUT ANY WARRANTY; without even the implied warranty of
 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
 // Lesser General Public License for more details.
-// 
+//
 // You should have received a copy of the GNU Lesser General Public
 // License along with this library; if not, write to the Free Software
 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
@@ -41,6 +41,8 @@ import org.forester.phylogeny.data.Confidence;
 import org.forester.phylogeny.data.DomainArchitecture;
 import org.forester.phylogeny.data.Taxonomy;
 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
+import org.forester.util.BasicDescriptiveStatistics;
+import org.forester.util.DescriptiveStatistics;
 import org.forester.util.FailedConditionCheckException;
 import org.forester.util.ForesterUtil;
 
@@ -271,15 +273,28 @@ public class PhylogenyMethods {
         return max;
     }
 
-    public static int calculateMaximumNumberOfDescendantsPerNode( final Phylogeny phy ) {
-        int max = 0;
+    public static DescriptiveStatistics calculatNumberOfDescendantsPerNodeStatistics( final Phylogeny phy ) {
+        final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
         for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
-            final PhylogenyNode node = iter.next();
-            if ( node.getNumberOfDescendants() > max ) {
-                max = node.getNumberOfDescendants();
+            final PhylogenyNode n = iter.next();
+            if ( !n.isExternal() ) {
+                stats.addValue( n.getNumberOfDescendants() );
             }
         }
-        return max;
+        return stats;
+    }
+
+    public static DescriptiveStatistics calculatConfidenceStatistics( 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.getBranchData().isHasConfidences() ) {
+                    stats.addValue( n.getBranchData().getConfidence( 0 ).getValue() );
+                }
+            }
+        }
+        return stats;
     }
 
     /**
@@ -894,8 +909,10 @@ public class PhylogenyMethods {
                         blue += child_color.getBlue();
                     }
                 }
-                setBranchColorValue( node, new Color( ForesterUtil.roundToInt( red / n ), ForesterUtil
-                        .roundToInt( green / n ), ForesterUtil.roundToInt( blue / n ) ) );
+                setBranchColorValue( node,
+                                     new Color( ForesterUtil.roundToInt( red / n ),
+                                                ForesterUtil.roundToInt( green / n ),
+                                                ForesterUtil.roundToInt( blue / n ) ) );
             }
         }
     }
@@ -913,8 +930,8 @@ public class PhylogenyMethods {
             parent.removeChildNode( remove_me );
             for( final PhylogenyNode desc : descs ) {
                 parent.addAsChild( desc );
-                desc.setDistanceToParent( addPhylogenyDistances( remove_me.getDistanceToParent(), desc
-                        .getDistanceToParent() ) );
+                desc.setDistanceToParent( addPhylogenyDistances( remove_me.getDistanceToParent(),
+                                                                 desc.getDistanceToParent() ) );
             }
             remove_me.setParent( null );
             phylogeny.setIdHash( null );