X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fsurfacing%2FSurfacingUtil.java;h=05a910121eb8af9ba7b5d88aaa426820ed296ce6;hb=d605114bdf420c6cb680b02bb10ea25f09db769c;hp=660cbfd0489fbdb81bfe50a3bc45d8a58c126db8;hpb=1a473590cdf1a3913674e374a6d169954c38a6f4;p=jalview.git

diff --git a/forester/java/src/org/forester/surfacing/SurfacingUtil.java b/forester/java/src/org/forester/surfacing/SurfacingUtil.java
index 660cbfd..05a9101 100644
--- a/forester/java/src/org/forester/surfacing/SurfacingUtil.java
+++ b/forester/java/src/org/forester/surfacing/SurfacingUtil.java
@@ -60,7 +60,6 @@ import org.forester.evoinference.matrix.character.CharacterStateMatrix;
 import org.forester.evoinference.matrix.character.CharacterStateMatrix.BinaryStates;
 import org.forester.evoinference.matrix.character.CharacterStateMatrix.Format;
 import org.forester.evoinference.matrix.character.CharacterStateMatrix.GainLossStates;
-import org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix;
 import org.forester.evoinference.matrix.distance.DistanceMatrix;
 import org.forester.go.GoId;
 import org.forester.go.GoNameSpace;
@@ -246,7 +245,7 @@ public final class SurfacingUtil {
                                                              final DistanceMatrix distance ) {
         checkForOutputFileWriteability( nj_tree_outfile );
         final NeighborJoining nj = NeighborJoining.createInstance();
-        final Phylogeny phylogeny = nj.execute( ( BasicSymmetricalDistanceMatrix ) distance );
+        final Phylogeny phylogeny = nj.execute( ( DistanceMatrix ) distance );
         phylogeny.setName( nj_tree_outfile.getName() );
         writePhylogenyToFile( phylogeny, nj_tree_outfile.toString() );
         return phylogeny;
@@ -1354,13 +1353,6 @@ public final class SurfacingUtil {
             if ( !intree.isRooted() ) {
                 ForesterUtil.fatalError( surfacing.PRG_NAME, "input tree [" + intree_file + "] is not rooted" );
             }
-            if ( intree.getNumberOfExternalNodes() < number_of_genomes ) {
-                ForesterUtil.fatalError( surfacing.PRG_NAME,
-                                         "number of external nodes [" + intree.getNumberOfExternalNodes()
-                                                 + "] of input tree [" + intree_file
-                                                 + "] is smaller than the number of genomes the be analyzed ["
-                                                 + number_of_genomes + "]" );
-            }
             final StringBuilder parent_names = new StringBuilder();
             final int nodes_lacking_name = getNumberOfNodesLackingName( intree, parent_names );
             if ( nodes_lacking_name > 0 ) {
@@ -1600,7 +1592,6 @@ public final class SurfacingUtil {
                 }
             }
         }
-        //
         final List<String> igns = PhylogenyMethods.deleteExternalNodesPositiveSelection( genomes, intree );
         if ( igns.size() > 0 ) {
             System.out.println( "Not using the following " + igns.size() + " nodes:" );
@@ -1609,16 +1600,29 @@ public final class SurfacingUtil {
             }
             System.out.println( "--" );
         }
+        //Test for node names:
+        final SortedSet<String> not_found = new TreeSet<String>();
+        final SortedSet<String> not_unique = new TreeSet<String>();
         for( final String[] input_file_propertie : input_file_properties ) {
-            try {
-                intree.getNode( input_file_propertie[ 1 ] );
+            final String name = input_file_propertie[ 1 ];
+            final List<PhylogenyNode> nodes = intree.getNodes( name );
+            if ( ( nodes == null ) || ( nodes.size() < 1 ) ) {
+                not_found.add( name );
             }
-            catch ( final IllegalArgumentException e ) {
-                ForesterUtil.fatalError( surfacing.PRG_NAME,
-                                         "node named [" + input_file_propertie[ 1 ]
-                                                 + "] not present/not unique in input tree" );
+            if ( nodes.size() > 1 ) {
+                not_unique.add( name );
             }
         }
+        if ( not_found.size() > 0 ) {
+            ForesterUtil.fatalError( surfacing.PRG_NAME,
+                                     "the following " + not_found.size()
+                                             + " node(s) are not present in the input tree: " + not_found );
+        }
+        if ( not_unique.size() > 0 ) {
+            ForesterUtil.fatalError( surfacing.PRG_NAME,
+                                     "the following " + not_unique.size()
+                                             + " node(s) are not unique in the input tree: " + not_unique );
+        }
     }
 
     public static void printOutPercentageOfMultidomainProteins( final SortedMap<Integer, Integer> all_genomes_domains_per_potein_histo,