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[jalview.git] / forester / java / src / org / forester / clade_analysis / CladeAnalysisTest.java

diff --git a/forester/java/src/org/forester/clade_analysis/CladeAnalysisTest.java b/forester/java/src/org/forester/clade_analysis/CladeAnalysisTest.java
index a78e8fe..3d1f4b9 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 +590,125 @@ 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 );
+            res1.analyzeGreatestCommonPrefixes( 0.3 );
+            System.out.print( res1.toString());
+            System.out.println( "------------------------- ");
+            System.out.println();
+            
+            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( 0.3 );
+            System.out.print( res2.toString());
+            System.out.println( "------------------------- ");
+            System.out.println();
+           
+            final Result2 res3 = new Result2( "." );
+            res3.addGreatestCommonPrefix( "A.1.1.1", 0.1 );
+            res3.addGreatestCommonPrefix( "A.1.1.1.1", 0.6 );
+            res3.addGreatestCommonPrefix( "A.1", 0.1 );
+            res3.addGreatestCommonPrefix( "A.1.2", 0.1 );
+            res3.addGreatestCommonPrefix( "B.1", 0.1 );
+            res3.analyzeGreatestCommonPrefixes( 0.3 );
+            System.out.print( res3.toString());
+            System.out.println( "------------------------- ");
+            System.out.println();
+            
+            final Result2 res33 = new Result2( "." );
+            res33.addGreatestCommonPrefix( "A.1.1.1", 0.1 );
+            res33.addGreatestCommonPrefix( "A.1.1.1.1", 0.3 );
+            res33.addGreatestCommonPrefix( "A.1", 0.1 );
+            res33.addGreatestCommonPrefix( "A.1.2", 0.1 );
+            res33.addGreatestCommonPrefix( "B.1", 0.1 );
+            res33.addGreatestCommonPrefix( "B.1.1.1", 0.3 );
+            res33.analyzeGreatestCommonPrefixes( 0.3 );
+            System.out.print( res33.toString());
+            System.out.println( "------------------------- ");
+            System.out.println();
+            
+            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( 0.3 );
+            System.out.print( res4.toString());
+            System.out.println( "------------------------- ");
+            System.out.println();
+            
+            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( 0.3 );
+            System.out.print( res5.toString());
+            System.out.println( "------------------------- ");
+            System.out.println();
+           
+            final Result2 res6 = new Result2();
+            res6.addGreatestCommonPrefix( "A.1.1.1", 0.05 );
+            res6.addGreatestCommonPrefix( "A.1.1.1.1", 0.65 );
+            res6.addGreatestCommonPrefix( "A.1", 0.1 );
+            res6.addGreatestCommonPrefix( "A.1.2", 0.1 );
+            res6.addGreatestCommonPrefix( "B.1", 0.1 );
+            res6.analyzeGreatestCommonPrefixes( 0.3 );
+            System.out.print( res6.toString());
+            System.out.println( "------------------------- ");
+            System.out.println();
+           
+            final Result2 res7 = new Result2();
+            res7.addGreatestCommonPrefix( "A.1.1.1", 0.07 );
+            res7.addGreatestCommonPrefix( "A.1.1.1.1", 0.9 );
+            res7.addGreatestCommonPrefix( "A.1", 0.01 );
+            res7.addGreatestCommonPrefix( "A.1.2", 0.01 );
+            res7.addGreatestCommonPrefix( "B.1", 0.01 );
+            res7.analyzeGreatestCommonPrefixes( 0.3 );
+            System.out.print( res7.toString());
+            System.out.println( "------------------------- ");
+            System.out.println();
+            
+            final Result2 res8 = new Result2( "_/_" );
+            res8.addGreatestCommonPrefix( "AA_/_abc_/_def", 0.07 );
+            res8.addGreatestCommonPrefix( "AA_/_abc_/_sfc", 0.9 );
+            res8.addGreatestCommonPrefix( "AA_/_abc_/_xcd", 0.01 );
+            res8.addGreatestCommonPrefix( "AA_/_abc_/_memr", 0.01 );
+            res8.addGreatestCommonPrefix( "AA_/_abc_/_fkem_/_odem", 0.01 );
+            res8.analyzeGreatestCommonPrefixes( 0.3 );
+            System.out.print( res8.toString());
+            System.out.println( "------------------------- ");
+            System.out.println();
+           
+            final Result2 res9 = new Result2( "_/_" );
+            res9.addGreatestCommonPrefix( "AA_/_abc_/_def", 0.07 );
+            res9.addGreatestCommonPrefix( "AA_/_abc_/_sfc", 0.6 );
+            res9.addGreatestCommonPrefix( "AA_/_abc_/_xcd", 0.01 );
+            res9.addGreatestCommonPrefix( "AA_/_abc_/_memr", 0.01 );
+            res9.addGreatestCommonPrefix( "AA_/_abc_/_fkem_/_odem", 0.01 );
+            res9.addGreatestCommonPrefix( "BB_/_fke_/_dme_/_nx2", 0.3 );
+            res9.analyzeGreatestCommonPrefixes( 0.3 );
+            System.out.print( res9.toString());
+            System.out.println( "------------------------- ");
+            System.out.println();
+        }
+        catch ( final Exception e ) {
+            e.printStackTrace( System.out );
+            return false;
+        }
+        return true;
+    }
 }