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 97eba29..ee17de9 100644 (file)
--- a/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java
+++ b/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java
@@ -42,7 +42,6 @@ import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 import java.util.regex.PatternSyntaxException;
 
-import org.forester.archaeopteryx.TreePanelUtil;
 import org.forester.io.parsers.FastaParser;
 import org.forester.io.parsers.PhylogenyParser;
 import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
@@ -66,7 +65,6 @@ import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
 import org.forester.phylogeny.iterators.PreorderTreeIterator;
 import org.forester.util.BasicDescriptiveStatistics;
 import org.forester.util.DescriptiveStatistics;
-import org.forester.util.FailedConditionCheckException;
 import org.forester.util.ForesterUtil;
 import org.forester.util.TaxonomyUtil;
 
@@ -1004,7 +1002,7 @@ public class PhylogenyMethods {
     private static enum NDF {
                              NodeName( "NN" ),
                              TaxonomyCode( "TC" ),
-                             TaxonomyCommonName( "CN" ),
+                             TaxonomyCommonName( "TN" ),
                              TaxonomyScientificName( "TS" ),
                              TaxonomyIdentifier( "TI" ),
                              TaxonomySynonym( "SY" ),
@@ -1698,6 +1696,9 @@ public class PhylogenyMethods {
                         n.getNodeData().getTaxonomy().setIdentifier( new Identifier( name ) );
                         break;
                     }
+                    case CLADE_NAME:
+                        n.setName( name );
+                        break;
                     default: {
                         throw new IllegalArgumentException( "don't know what to do with " + field );
                     }
@@ -2142,5 +2143,15 @@ public class PhylogenyMethods {
         }
         return n;
     }
+
+    public final static boolean isHasCollapsedNodes( final Phylogeny phy ) {
+        for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
+            final PhylogenyNode n = iter.next();
+            if ( !n.isExternal() && ( n.isCollapse() ) ) {
+                return true;
+            }
+        }
+        return false;
+    }
     
 }