in progress...

diff --git a/forester/java/src/org/forester/application/cladinator.java b/forester/java/src/org/forester/application/cladinator.java
index 0aef757..ddc1aef 100644 (file)
--- a/forester/java/src/org/forester/application/cladinator.java
+++ b/forester/java/src/org/forester/application/cladinator.java
@@ -121,24 +121,24 @@ public final class cladinator {
             System.out.println( "Query                        : " + query );
             System.out.print( "Greatest Common Prefix       : " + res.getGreatestCommonPrefix() );
             if ( !ForesterUtil.isEmpty( res.getGreatestCommonPrefix() )
-                    && !ForesterUtil.isEmpty( res.getGreatestCommonCladeConfidence() ) ) {
-                System.out.println( "\t(" + res.getGreatestCommonCladeConfidence() + ")" );
+                    && !ForesterUtil.isEmpty( res.getGreatestCommonCladeSubtreeConfidence() ) ) {
+                System.out.println( "\t(" + res.getGreatestCommonCladeSubtreeConfidence() + ")" );
             }
             else {
                 System.out.println();
             }
             System.out.print( "Greatest Common Prefix Up    : " + res.getGreatestCommonPrefixUp() );
             if ( !ForesterUtil.isEmpty( res.getGreatestCommonPrefixUp() )
-                    && !ForesterUtil.isEmpty( res.getGreatestCommonCladeUpConfidence() ) ) {
-                System.out.println( "\t(" + res.getGreatestCommonCladeUpConfidence() + ")" );
+                    && !ForesterUtil.isEmpty( res.getGreatestCommonCladeUpSubtreeConfidence() ) ) {
+                System.out.println( "\t(" + res.getGreatestCommonCladeUpSubtreeConfidence() + ")" );
             }
             else {
                 System.out.println();
             }
             System.out.print( "Greatest Common Prefix Down  : " + res.getGreatestCommonPrefixDown() );
             if ( !ForesterUtil.isEmpty( res.getGreatestCommonPrefixDown() )
-                    && !ForesterUtil.isEmpty( res.getGreatestCommonCladeDownConfidence() ) ) {
-                System.out.println( "\t(" + res.getGreatestCommonCladeDownConfidence() + ")" );
+                    && !ForesterUtil.isEmpty( res.getGreatestCommonCladeDownSubtreeConfidence() ) ) {
+                System.out.println( "\t(" + res.getGreatestCommonCladeDownSubtreeConfidence() + ")" );
             }
             else {
                 System.out.println();

diff --git a/forester/java/src/org/forester/clade_analysis/Analysis.java b/forester/java/src/org/forester/clade_analysis/Analysis.java
index 99b9439..4803f54 100644 (file)
--- a/forester/java/src/org/forester/clade_analysis/Analysis.java
+++ b/forester/java/src/org/forester/clade_analysis/Analysis.java
@@ -90,18 +90,18 @@ public final class Analysis {
        
         final String conf = obtainConfidence( qnode_pp );
         if ( conf != null ) {
-            res.setGreatestCommonCladeConfidence(conf);
+            res.setGreatestCommonCladeSubtreeConfidence(conf);
         }
         
         final String greatest_common_prefix_up[] = analyzeSiblings( qnode_p, qnode_pp, separator );
         res.setGreatestCommonPrefixUp( greatest_common_prefix_up[ 0 ] );
         if ( greatest_common_prefix_up[ 1 ] != null ) {
-            res.setGreatestCommonCladeUpConfidence( greatest_common_prefix_up[ 1 ] );
+            res.setGreatestCommonCladeUpSubtreeConfidence( greatest_common_prefix_up[ 1 ] );
         }
         final String greatest_common_prefix_down[] = analyzeSiblings( qnode, qnode_p, separator );
         res.setGreatestCommonPrefixDown( greatest_common_prefix_down[ 0 ] );
         if ( greatest_common_prefix_down[ 1 ] != null ) {
-            res.setGreatestCommonCladeDownConfidence( greatest_common_prefix_down[ 1 ] );
+            res.setGreatestCommonCladeDownSubtreeConfidence( greatest_common_prefix_down[ 1 ] );
         }
         return res;
     }

diff --git a/forester/java/src/org/forester/clade_analysis/CladeAnalysisTest.java b/forester/java/src/org/forester/clade_analysis/CladeAnalysisTest.java
index a78e8fe..d91e36e 100644 (file)
--- a/forester/java/src/org/forester/clade_analysis/CladeAnalysisTest.java
+++ b/forester/java/src/org/forester/clade_analysis/CladeAnalysisTest.java
@@ -2,6 +2,7 @@
 package org.forester.clade_analysis;
 
 import java.io.File;
+import java.util.List;
 
 import org.forester.io.parsers.PhylogenyParser;
 import org.forester.io.parsers.util.ParserUtils;
@@ -25,6 +26,10 @@ public class CladeAnalysisTest {
             System.out.println( "Clade analysis 2 failed" );
             failed = true;
         }
+        if ( !testCladeAnalysis3() ) {
+            System.out.println( "Clade analysis 3 failed" );
+            failed = true;
+        }
         if ( !failed ) {
             System.out.println( "OK" );
         }
@@ -37,6 +42,9 @@ public class CladeAnalysisTest {
         if ( !testCladeAnalysis2() ) {
             return false;
         }
+        if ( !testCladeAnalysis3() ) {
+            return false;
+        }
         return true;
     }
 
@@ -582,4 +590,60 @@ public class CladeAnalysisTest {
         }
         return true;
     }
+    
+    private static boolean testCladeAnalysis3() {
+        try {
+          final Result2 res1 = new Result2();
+          res1.addGreatestCommonPrefix( "A.1.1", 0.3 );
+          res1.addGreatestCommonPrefix( "A.1.2", 0.3 );
+          res1.addGreatestCommonPrefix( "A.1.3", 0.3 );
+          res1.addGreatestCommonPrefix( "B.1", 0.1 );
+          
+          List<String> x = ForesterUtil.spliIntoPrefixes( "A.1.2.3.4", "." );
+         // System.out.println( x );
+          x =ForesterUtil.spliIntoPrefixes( "A", "." );
+         // System.out.println( x );
+          
+          
+          res1.analyzeGreatestCommonPrefixes( "." );
+          
+          final Result2 res2 = new Result2();
+          res2.addGreatestCommonPrefix( "A.1.1.1", 0.1 );
+          res2.addGreatestCommonPrefix( "A.1", 0.7 );
+          res2.addGreatestCommonPrefix( "A.1.2", 0.1 );
+          res2.addGreatestCommonPrefix( "B.1", 0.1 );
+          res2.analyzeGreatestCommonPrefixes( "." );
+          
+          final Result2 res3 = new Result2();
+          res3.addGreatestCommonPrefix( "A.1.1.1", 0.7 );
+          res3.addGreatestCommonPrefix( "A.1", 0.1 );
+          res3.addGreatestCommonPrefix( "A.1.2", 0.1 );
+          res3.addGreatestCommonPrefix( "B.1", 0.1 );
+          res3.analyzeGreatestCommonPrefixes( "." );
+          
+          
+          final Result2 res4 = new Result2();
+          res4.addGreatestCommonPrefix( "A.1.1.1.1", 0.35);
+          res4.addGreatestCommonPrefix( "A.1.1.1.2", 0.35 );
+          res4.addGreatestCommonPrefix( "A.1", 0.1 );
+          res4.addGreatestCommonPrefix( "A.1.2", 0.1 );
+          res4.addGreatestCommonPrefix( "B.1", 0.1 );
+          res4.analyzeGreatestCommonPrefixes( "." );
+          
+          final Result2 res5 = new Result2();
+          res5.addGreatestCommonPrefix( "A.1.1.1.1", 0.2);
+          res5.addGreatestCommonPrefix( "C.2.3", 0.2 );
+          res5.addGreatestCommonPrefix( "A.1.5", 0.1 );
+          res5.addGreatestCommonPrefix( "A.3.1.4", 0.2 );
+          res5.addGreatestCommonPrefix( "B.1.1", 0.2 );
+          res5.addGreatestCommonPrefix( "B.1.2", 0.09 );
+          res5.addGreatestCommonPrefix( "D.1.1.1.1", 0.01 );
+          res5.analyzeGreatestCommonPrefixes( "." );
+        }
+        catch ( final Exception e ) {
+            e.printStackTrace( System.out );
+            return false;
+        }
+        return true;
+    }
 }

diff --git a/forester/java/src/org/forester/clade_analysis/Result.java b/forester/java/src/org/forester/clade_analysis/Result.java
index e7686e1..e11fcd5 100644 (file)
--- a/forester/java/src/org/forester/clade_analysis/Result.java
+++ b/forester/java/src/org/forester/clade_analysis/Result.java
@@ -36,9 +36,9 @@ public final class Result {
     private final List<String> _warnings                              = new ArrayList<>();
     private int                _lec_ext_nodes                         = 0;
     private int                _p_ext_nodes                           = 0;
-    private String             _greatest_common_clade_confidence      = "";
-    private String             _greatest_common_clade_confidence_up   = "";
-    private String             _greatest_common_clade_confidence_down = "";
+    private String             _greatest_common_clade_subtree_confidence      = "";
+    private String             _greatest_common_clade_subtree_confidence_up   = "";
+    private String             _greatest_common_clade_subtree_confidence_down = "";
 
     void addWarning( final String warning ) {
         _warnings.add( warning );
@@ -56,16 +56,16 @@ public final class Result {
         _greatest_common_prefix_down = greatest_common_prefix_down;
     }
 
-    void setGreatestCommonCladeConfidence( final String greatest_common_clade_confidence ) {
-        _greatest_common_clade_confidence = greatest_common_clade_confidence;
+    void setGreatestCommonCladeSubtreeConfidence( final String greatest_common_clade_confidence ) {
+        _greatest_common_clade_subtree_confidence = greatest_common_clade_confidence;
     }
 
-    void setGreatestCommonCladeUpConfidence( final String greatest_common_clade_confidence_up ) {
-        _greatest_common_clade_confidence_up = greatest_common_clade_confidence_up;
+    void setGreatestCommonCladeUpSubtreeConfidence( final String greatest_common_clade_confidence_up ) {
+        _greatest_common_clade_subtree_confidence_up = greatest_common_clade_confidence_up;
     }
 
-    void setGreatestCommonCladeDownConfidence( final String greatest_common_clade_confidence_down ) {
-        _greatest_common_clade_confidence_down = greatest_common_clade_confidence_down;
+    void setGreatestCommonCladeDownSubtreeConfidence( final String greatest_common_clade_confidence_down ) {
+        _greatest_common_clade_subtree_confidence_down = greatest_common_clade_confidence_down;
     }
 
     public String getGreatestCommonPrefix() {
@@ -80,16 +80,16 @@ public final class Result {
         return _greatest_common_prefix_down;
     }
 
-    public String getGreatestCommonCladeConfidence() {
-        return _greatest_common_clade_confidence;
+    public String getGreatestCommonCladeSubtreeConfidence() {
+        return _greatest_common_clade_subtree_confidence;
     }
 
-    public String getGreatestCommonCladeUpConfidence() {
-        return _greatest_common_clade_confidence_up;
+    public String getGreatestCommonCladeUpSubtreeConfidence() {
+        return _greatest_common_clade_subtree_confidence_up;
     }
 
-    public String getGreatestCommonCladeDownConfidence() {
-        return _greatest_common_clade_confidence_down;
+    public String getGreatestCommonCladeDownSubtreeConfidence() {
+        return _greatest_common_clade_subtree_confidence_down;
     }
 
     public List<String> getWarnings() {

diff --git a/forester/java/src/org/forester/util/ForesterUtil.java b/forester/java/src/org/forester/util/ForesterUtil.java
index 971032d..d3d61d9 100644 (file)
--- a/forester/java/src/org/forester/util/ForesterUtil.java
+++ b/forester/java/src/org/forester/util/ForesterUtil.java
@@ -1659,4 +1659,21 @@ public final class ForesterUtil {
 
     private ForesterUtil() {
     }
+
+    public static List<String> spliIntoPrefixes(final String prefix, final String separator ) {
+        final String[] a = prefix.split( Pattern.quote( separator ) );
+        final List<String> l= new ArrayList<String>();
+        for( int i = 0; i < a.length; ++i ) {
+            final StringBuilder sb = new StringBuilder();
+            for( int j = 0; j <= i; ++j ) {
+                sb.append( a[ j ] );
+                if ( j < i ) {
+                    sb.append( separator );
+                }
+            }
+            //System.out.println( sb.toString() );
+            l.add( sb.toString());
+        }
+        return l;
+    }
 }