X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fapplication%2Frio.java;h=27c4ee0f4de5db6138374a5a52e4f47094c92d10;hb=7a194f3da2c3a659ecc67bff021d9f64c845e923;hp=4f90ca020aca7e85eca39b0eb48442fd21719f95;hpb=7a7a89b113566b2749f1e8e4fbb3064241145201;p=jalview.git

diff --git a/forester/java/src/org/forester/application/rio.java b/forester/java/src/org/forester/application/rio.java
index 4f90ca0..27c4ee0 100644
--- 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";
@@ -319,13 +320,13 @@ public class rio {
                     final NHXParser nhx = ( NHXParser ) p;
                     nhx.setReplaceUnderscores( false );
                     nhx.setIgnoreQuotes( true );
-                    nhx.setTaxonomyExtraction( TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+                    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.PFAM_STYLE_RELAXED );
+                    nex.setTaxonomyExtraction( TAXONOMY_EXTRACTION.AGGRESSIVE );
                 }
                 else {
                     throw new RuntimeException( "unknown parser type: " + p );
@@ -381,15 +382,15 @@ public class rio {
             final java.text.DecimalFormat df = new java.text.DecimalFormat( "0.#" );
             System.out.println( "Mean number of duplications  : " + df.format( stats.arithmeticMean() ) + " (sd: "
                     + df.format( stats.sampleStandardDeviation() ) + ") ("
-                    + df.format( 100.0 * stats.arithmeticMean() / rio.getIntNodesOfAnalyzedGeneTrees() ) + "%)" );
+                    + df.format( ( 100.0 * stats.arithmeticMean() ) / rio.getIntNodesOfAnalyzedGeneTrees() ) + "%)" );
             if ( stats.getN() > 3 ) {
                 System.out.println( "Median number of duplications: " + df.format( stats.median() ) + " ("
-                        + df.format( 100.0 * stats.median() / rio.getIntNodesOfAnalyzedGeneTrees() ) + "%)" );
+                        + df.format( ( 100.0 * stats.median() ) / rio.getIntNodesOfAnalyzedGeneTrees() ) + "%)" );
             }
             System.out.println( "Minimum duplications         : " + ( int ) stats.getMin() + " ("
-                    + df.format( 100.0 * stats.getMin() / rio.getIntNodesOfAnalyzedGeneTrees() ) + "%)" );
+                    + df.format( ( 100.0 * stats.getMin() ) / rio.getIntNodesOfAnalyzedGeneTrees() ) + "%)" );
             System.out.println( "Maximum duplications         : " + ( int ) stats.getMax() + " ("
-                    + df.format( 100.0 * stats.getMax() / rio.getIntNodesOfAnalyzedGeneTrees() ) + "%)" );
+                    + df.format( ( 100.0 * stats.getMax() ) / rio.getIntNodesOfAnalyzedGeneTrees() ) + "%)" );
             System.out.println( "Gene tree internal nodes     : " + rio.getIntNodesOfAnalyzedGeneTrees() );
             System.out.println( "Gene tree external nodes     : " + rio.getExtNodesOfAnalyzedGeneTrees() );
         }
@@ -489,8 +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 ) );