X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fapplication%2Frio.java;h=1ee56283d6760826cde0fdc4d2fa986b5e9734c1;hb=612e51e63eb66025a04439fc380384a945a4a30f;hp=d3414a7e486ae1579d222fa0a8027db72e960d05;hpb=b819fa043cac2722618af63f0d4752ffa1a40890;p=jalview.git

diff --git a/forester/java/src/org/forester/application/rio.java b/forester/java/src/org/forester/application/rio.java
index d3414a7..1ee5628 100644
--- a/forester/java/src/org/forester/application/rio.java
+++ b/forester/java/src/org/forester/application/rio.java
@@ -88,7 +88,7 @@ public class rio {
         if ( cla.isOptionSet( HELP_OPTION_1 ) || cla.isOptionSet( HELP_OPTION_2 ) || ( args.length == 0 ) ) {
             printHelp();
         }
-        if ( ( args.length < 3 ) || ( args.length > 11 ) ) {
+        if ( ( args.length < 3 ) || ( args.length > 11 ) || ( cla.getNumberOfNames() < 3 ) ) {
             System.out.println();
             System.out.println( "error: incorrect number of arguments" );
             System.out.println();
@@ -287,6 +287,7 @@ public class rio {
         }
         if ( return_gene_tree != null ) {
             System.out.println( "Write best gene tree to   : " + return_gene_tree );
+            System.out.println( "Transfer taxonomic data   : " + transfer_taxonomy );
         }
         time = System.currentTimeMillis();
         final ALGORITHM algorithm;
@@ -318,13 +319,13 @@ public class rio {
                     final NHXParser nhx = ( NHXParser ) p;
                     nhx.setReplaceUnderscores( false );
                     nhx.setIgnoreQuotes( true );
-                    nhx.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGRESSIVE );
+                    nhx.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE );
                 }
                 else if ( p instanceof NexusPhylogeniesParser ) {
                     final NexusPhylogeniesParser nex = ( NexusPhylogeniesParser ) p;
                     nex.setReplaceUnderscores( false );
                     nex.setIgnoreQuotes( true );
-                    nex.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGRESSIVE );
+                    nex.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE );
                 }
                 else {
                     throw new RuntimeException( "unknown parser type: " + p );
@@ -369,9 +370,13 @@ public class rio {
                 writeTree( rio.getSpeciesTree(), return_species_tree, "Wrote (stripped) species tree to" );
             }
             if ( return_gene_tree != null ) {
+                String tt = "";
+                if ( transfer_taxonomy ) {
+                    tt = "(with transferred taxonomic data) ";
+                }
                 writeTree( rio.getMinDuplicationsGeneTree(),
                            return_gene_tree,
-                           "Wrote (one) minimal duplication gene tree to" );
+                           "Wrote (one) minimal duplication gene tree " + tt + "to" );
             }
             final java.text.DecimalFormat df = new java.text.DecimalFormat( "0.#" );
             System.out.println( "Mean number of duplications  : " + df.format( stats.arithmeticMean() ) + " (sd: "