inprogress

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

diff --git a/forester/java/src/org/forester/application/rio.java b/forester/java/src/org/forester/application/rio.java
index d3414a7..51a36bf 100644 (file)
--- a/forester/java/src/org/forester/application/rio.java
+++ b/forester/java/src/org/forester/application/rio.java
@@ -29,6 +29,7 @@ package org.forester.application;
 
 import java.io.File;
 import java.io.IOException;
+import java.math.RoundingMode;
 import java.util.ArrayList;
 import java.util.List;
 
@@ -56,7 +57,7 @@ public class rio {
 
     final static private String PRG_NAME                 = "rio";
     final static private String PRG_VERSION              = "4.000 beta 10";
-    final static private String PRG_DATE                 = "130325";
+    final static private String PRG_DATE                 = "140211";
     final static private String E_MAIL                   = "phyloxml@gmail.com";
     final static private String WWW                      = "https://sites.google.com/site/cmzmasek/home/software/forester";
     final static private String HELP_OPTION_1            = "help";
@@ -88,7 +89,7 @@ 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 +288,7 @@ 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 +320,13 @@ 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 +371,13 @@ 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: "
@@ -484,8 +490,9 @@ public class rio {
     private static void writeTable( final File table_outfile, final int gene_trees_analyzed, final IntMatrix m )
             throws IOException {
         final EasyWriter w = ForesterUtil.createEasyWriter( table_outfile );
-        final java.text.DecimalFormat df = new java.text.DecimalFormat( "0.###" );
+        final java.text.DecimalFormat df = new java.text.DecimalFormat( "0.####" );
         df.setDecimalSeparatorAlwaysShown( false );
+        df.setRoundingMode( RoundingMode.HALF_UP );
         for( int i = 0; i < m.size(); ++i ) {
             w.print( "\t" );
             w.print( m.getLabel( i ) );