in progress...

[jalview.git] / forester / java / src / org / forester / application / annotator.java

diff --git a/forester/java/src/org/forester/application/annotator.java b/forester/java/src/org/forester/application/annotator.java
index bfd8f15..4374f53 100644 (file)
--- a/forester/java/src/org/forester/application/annotator.java
+++ b/forester/java/src/org/forester/application/annotator.java
@@ -94,8 +94,8 @@ public final class annotator {
                 }
                 catch ( final Exception e ) {
                     ForesterUtil
-                            .fatalError( PRG_NAME, "failed to read phylgenies from [" + infile + "] [" + e.getMessage()
-                                    + "]" );
+                    .fatalError( PRG_NAME, "failed to read phylgenies from [" + infile + "] [" + e.getMessage()
+                                 + "]" );
                 }
                 try {
                     obtainSeqInformation( phy );
@@ -103,15 +103,16 @@ public final class annotator {
                 catch ( final IOException e ) {
                     ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
                 }
-                try {
-                    inferTaxonomyFromDescendents( phy );
-                }
-                catch ( final IOException e ) {
-                    ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
-                }
-                catch ( final AncestralTaxonomyInferenceException e ) {
-                    ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
-                }
+                //                try {
+                //                    inferTaxonomyFromDescendents( phy );
+                //                }
+                //                catch ( final IOException e ) {
+                //                    ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
+                //                }
+                //                catch ( final AncestralTaxonomyInferenceException e ) {
+                //                    ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
+                //                }
+                //phy.setRerootable( false );
                 try {
                     final PhylogenyWriter w = new PhylogenyWriter();
                     w.toPhyloXML( phy, 0, outfile );
@@ -128,7 +129,7 @@ public final class annotator {
     }
 
     private static void inferTaxonomyFromDescendents( final Phylogeny phy ) throws IOException,
-            AncestralTaxonomyInferenceException {
+    AncestralTaxonomyInferenceException {
         AncestralTaxonomyInference.inferTaxonomyFromDescendents( phy );
     }