inprogress

[jalview.git] / forester / java / src / org / forester / rio / RIO.java

diff --git a/forester/java/src/org/forester/rio/RIO.java b/forester/java/src/org/forester/rio/RIO.java
index 68256f4..cde7804 100644 (file)
--- a/forester/java/src/org/forester/rio/RIO.java
+++ b/forester/java/src/org/forester/rio/RIO.java
@@ -221,6 +221,12 @@ public final class RIO {
         while ( parser.hasNext() ) {
             final Phylogeny gt = parser.next();
             if ( no_range || ( ( i >= first ) && ( i <= last ) ) ) {
+                if ( gt.isEmpty() ) {
+                    throw new RIOException( "gene tree #" + i + " is empty" );
+                }
+                if ( gt.getNumberOfExternalNodes() == 1 ) {
+                    throw new RIOException( "gene tree #" + i + " has only one external node" );
+                }
                 if ( _verbose ) {
                     ForesterUtil.updateProgress( i, pf );
                 }
@@ -302,6 +308,12 @@ public final class RIO {
         int gene_tree_ext_nodes = 0;
         for( int i = 0; i < my_gene_trees.length; ++i ) {
             final Phylogeny gt = my_gene_trees[ i ];
+            if ( gt.isEmpty() ) {
+                throw new RIOException( "gene tree #" + i + " is empty" );
+            }
+            if ( gt.getNumberOfExternalNodes() == 1 ) {
+                throw new RIOException( "gene tree #" + i + " has only one external node" );
+            }
             if ( _verbose && ( my_gene_trees.length > 4 ) ) {
                 ForesterUtil.updateProgress( ( ( double ) i ) / my_gene_trees.length );
             }
@@ -814,13 +826,13 @@ public final class RIO {
             final NHXParser nhx = ( NHXParser ) p;
             nhx.setReplaceUnderscores( false );
             nhx.setIgnoreQuotes( true );
-            nhx.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.YES );
+            nhx.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGRESSIVE );
         }
         else if ( p instanceof NexusPhylogeniesParser ) {
             final NexusPhylogeniesParser nex = ( NexusPhylogeniesParser ) p;
             nex.setReplaceUnderscores( false );
             nex.setIgnoreQuotes( true );
-            nex.setTaxonomyExtraction( TAXONOMY_EXTRACTION.YES );
+            nex.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGRESSIVE );
         }
         return factory.create( gene_trees_file, p );
     }