in progress...

diff --git a/forester/java/src/org/forester/clade_analysis/AnalysisMulti.java b/forester/java/src/org/forester/clade_analysis/AnalysisMulti.java
index 219588c..d920d77 100644 (file)
--- a/forester/java/src/org/forester/clade_analysis/AnalysisMulti.java
+++ b/forester/java/src/org/forester/clade_analysis/AnalysisMulti.java
@@ -73,7 +73,7 @@ public final class AnalysisMulti {
         final ResultMulti res = new ResultMulti();
         for( int i = 0; i < qnodes.size(); ++i ) {
             final PhylogenyNode qnode = qnodes.get( i );
-            System.out.println( ">>" + qnode.getName() );
+            //System.out.println( ">>" + qnode.getName() );
             if ( qnode.isRoot() ) {
                 throw new IllegalArgumentException( "Query " + query + " is root." );
             }
@@ -119,7 +119,7 @@ public final class AnalysisMulti {
             }
             //final String greatest_common_prefix_up[] = analyzeSiblings( qnode_p, qnode_pp, separator, query, res );
             final String greatest_common_prefix_up = analyzeSiblings( qnode_p, qnode_pp, separator, query );
-            System.out.println( "greatest_common_prefix_up=" + greatest_common_prefix_up + " " + conf );
+            //System.out.println( "greatest_common_prefix_up=" + greatest_common_prefix_up + " " + conf );
             if ( !ForesterUtil.isEmpty( greatest_common_prefix_up ) ) {
                 res.addGreatestCommonPrefixUp( greatest_common_prefix_up, conf );
             }
@@ -127,7 +127,7 @@ public final class AnalysisMulti {
                 res.addGreatestCommonPrefixUp( UNKNOWN, conf );
             }
             final String greatest_common_prefix_down = analyzeSiblings( qnode, qnode_p, separator, query );
-            System.out.println( "greatest_common_prefix_down=" + greatest_common_prefix_down + " " + conf );
+           // System.out.println( "greatest_common_prefix_down=" + greatest_common_prefix_down + " " + conf );
             if ( !ForesterUtil.isEmpty( greatest_common_prefix_down ) ) {
                 res.addGreatestCommonPrefixDown( greatest_common_prefix_down, conf );
             }

diff --git a/forester/java/src/org/forester/clade_analysis/Prefix.java b/forester/java/src/org/forester/clade_analysis/Prefix.java
index 6362a3e..85fcbf7 100644 (file)
--- a/forester/java/src/org/forester/clade_analysis/Prefix.java
+++ b/forester/java/src/org/forester/clade_analysis/Prefix.java
@@ -2,51 +2,54 @@
 package org.forester.clade_analysis;
 
 import java.math.BigDecimal;
+import java.text.DecimalFormat;
 
 final class Prefix {
 
-    private final String _prefix;
-    private final BigDecimal _confidence;
-    private final String _separator;
-    private final String _first;
+    private final static DecimalFormat df = new DecimalFormat( "0.0#####" );
+    private final String               _prefix;
+    private final BigDecimal           _confidence;
+    private final String               _separator;
+    private final String               _first;
 
     Prefix( final String prefix, final String confidence, final String separator ) {
         _prefix = prefix;
-        _confidence = new BigDecimal( confidence);
-        _separator = separator ;
-        if ( _prefix.indexOf( _separator ) < 0) {
+        _confidence = new BigDecimal( confidence );
+        _separator = separator;
+        if ( _prefix.indexOf( _separator ) < 0 ) {
             _first = _prefix;
         }
         else {
-        _first = _prefix.substring( 0, _prefix.indexOf(_separator ) );
+            _first = _prefix.substring( 0, _prefix.indexOf( _separator ) );
         }
     }
-    
-    Prefix( final String prefix, final double confidence , final String separator) {
+
+    Prefix( final String prefix, final double confidence, final String separator ) {
         _prefix = prefix;
-        _confidence = new BigDecimal( confidence);
-        _separator = separator ;
-        if ( _prefix.indexOf( _separator ) < 0) {
+        _confidence = new BigDecimal( confidence );
+        _separator = separator;
+        if ( _prefix.indexOf( _separator ) < 0 ) {
             _first = _prefix;
         }
         else {
-            _first = _prefix.substring( 0, _prefix.indexOf(_separator ) );
-            }
+            _first = _prefix.substring( 0, _prefix.indexOf( _separator ) );
+        }
     }
 
     String getPrefix() {
         return _prefix;
     }
-    
+
     String getPrefixFirstElement() {
-       return _first;
+        return _first;
     }
+
     double getConfidence() {
         return _confidence.doubleValue();
     }
 
     @Override
     public String toString() {
-     return getPrefix() + ": " + getConfidence();
+        return getPrefix() + ": " + df.format( getConfidence() );
     }
 }

diff --git a/forester/java/src/org/forester/clade_analysis/ResultMulti.java b/forester/java/src/org/forester/clade_analysis/ResultMulti.java
index d3bfba3..f9822ec 100644 (file)
--- a/forester/java/src/org/forester/clade_analysis/ResultMulti.java
+++ b/forester/java/src/org/forester/clade_analysis/ResultMulti.java
@@ -117,13 +117,13 @@ public final class ResultMulti {
     @Override
     public final String toString() {
         final StringBuilder sb = new StringBuilder();
-        sb.append( "Cleaned:" );
-        sb.append( ForesterUtil.LINE_SEPARATOR );
-        for( final Prefix prefix : _all ) {
-            sb.append( prefix );
-            sb.append( ForesterUtil.LINE_SEPARATOR );
-        }
-        sb.append( ForesterUtil.LINE_SEPARATOR );
+      //  sb.append( "Cleaned:" );
+      //  sb.append( ForesterUtil.LINE_SEPARATOR );
+      //  for( final Prefix prefix : _all ) {
+       //     sb.append( prefix );
+       //     sb.append( ForesterUtil.LINE_SEPARATOR );
+       // }
+       // sb.append( ForesterUtil.LINE_SEPARATOR );
         sb.append( "Collapsed:" );
         sb.append( ForesterUtil.LINE_SEPARATOR );
         for( final Prefix prefix : _collapsed ) {
@@ -154,20 +154,20 @@ public final class ResultMulti {
         }
         if ( !ForesterUtil.isEmpty( _all_down ) ) {
             sb.append( ForesterUtil.LINE_SEPARATOR );
-            sb.append( "Cleaned Down:" );
-            sb.append( ForesterUtil.LINE_SEPARATOR );
-            for( final Prefix prefix : _all_down ) {
-                sb.append( prefix );
-                sb.append( ForesterUtil.LINE_SEPARATOR );
-            }
-            sb.append( ForesterUtil.LINE_SEPARATOR );
+        //    sb.append( "Cleaned Down:" );
+        //    sb.append( ForesterUtil.LINE_SEPARATOR );
+        //    for( final Prefix prefix : _all_down ) {
+        //        sb.append( prefix );
+        //        sb.append( ForesterUtil.LINE_SEPARATOR );
+         //   }
+           // sb.append( ForesterUtil.LINE_SEPARATOR );
             sb.append( "Collapsed Down:" );
             sb.append( ForesterUtil.LINE_SEPARATOR );
             for( final Prefix prefix : _collapsed_down ) {
                 sb.append( prefix );
                 sb.append( ForesterUtil.LINE_SEPARATOR );
             }
-            if ( _has_specifics_down ) {
+          /*  if ( _has_specifics_down ) {
                 sb.append( ForesterUtil.LINE_SEPARATOR );
                 sb.append( "Specifics Down:" );
                 sb.append( ForesterUtil.LINE_SEPARATOR );
@@ -188,24 +188,24 @@ public final class ResultMulti {
                         }
                     }
                 }
-            }
+            }*/
         }
         if ( !ForesterUtil.isEmpty( _all_up ) ) {
             sb.append( ForesterUtil.LINE_SEPARATOR );
-            sb.append( "Cleaned Up:" );
-            sb.append( ForesterUtil.LINE_SEPARATOR );
-            for( final Prefix prefix : _all_up ) {
-                sb.append( prefix );
-                sb.append( ForesterUtil.LINE_SEPARATOR );
-            }
-            sb.append( ForesterUtil.LINE_SEPARATOR );
+        //    sb.append( "Cleaned Up:" );
+        //    sb.append( ForesterUtil.LINE_SEPARATOR );
+        //    for( final Prefix prefix : _all_up ) {
+        //        sb.append( prefix );
+         //       sb.append( ForesterUtil.LINE_SEPARATOR );
+         //   }
+         //   sb.append( ForesterUtil.LINE_SEPARATOR );
             sb.append( "Collapsed Up:" );
             sb.append( ForesterUtil.LINE_SEPARATOR );
             for( final Prefix prefix : _collapsed_up ) {
                 sb.append( prefix );
                 sb.append( ForesterUtil.LINE_SEPARATOR );
             }
-            if ( _has_specifics ) {
+          /*  if ( _has_specifics ) {
                 sb.append( ForesterUtil.LINE_SEPARATOR );
                 sb.append( "Specifics Up:" );
                 sb.append( ForesterUtil.LINE_SEPARATOR );
@@ -226,7 +226,7 @@ public final class ResultMulti {
                         }
                     }
                 }
-            }
+            }*/
         }
         return sb.toString();
     }