could be bad (memory things)

diff --git a/forester/java/src/org/forester/surfacing/AdjactantDirectedBinaryDomainCombination.java b/forester/java/src/org/forester/surfacing/AdjactantDirectedBinaryDomainCombination.java
index bb3a8a9..4675e17 100644 (file)
--- a/forester/java/src/org/forester/surfacing/AdjactantDirectedBinaryDomainCombination.java
+++ b/forester/java/src/org/forester/surfacing/AdjactantDirectedBinaryDomainCombination.java
@@ -33,8 +33,8 @@ public class AdjactantDirectedBinaryDomainCombination extends BasicBinaryDomainC
         if ( ( n_terminal == null ) || ( c_terminal == null ) ) {
             throw new IllegalArgumentException( "attempt to create binary domain combination using null" );
         }
-        _id_0 = n_terminal;
-        _id_1 = c_terminal;
+        _id_0 = n_terminal.getId();
+        _id_1 = c_terminal.getId();
     }
 
     public AdjactantDirectedBinaryDomainCombination( final String n_terminal, final String c_terminal ) {

diff --git a/forester/java/src/org/forester/surfacing/BasicBinaryDomainCombination.java b/forester/java/src/org/forester/surfacing/BasicBinaryDomainCombination.java
index 6861942..92f2d3c 100644 (file)
--- a/forester/java/src/org/forester/surfacing/BasicBinaryDomainCombination.java
+++ b/forester/java/src/org/forester/surfacing/BasicBinaryDomainCombination.java
@@ -30,30 +30,34 @@ import org.forester.util.ForesterUtil;
 
 public class BasicBinaryDomainCombination implements BinaryDomainCombination {
 
-    DomainId _id_0;
-    DomainId _id_1;
+    String _id_0;
+    String _id_1;
 
+    //DomainId _id_0;
+    //DomainId _id_1;
     BasicBinaryDomainCombination() {
         _id_0 = null;
         _id_1 = null;
     }
 
-    public BasicBinaryDomainCombination( final DomainId id_0, final DomainId id_1 ) {
+    public BasicBinaryDomainCombination( final String id_0, final String id_1 ) {
         if ( ( id_0 == null ) || ( id_1 == null ) ) {
             throw new IllegalArgumentException( "attempt to create binary domain combination using null" );
         }
-        if ( id_0.compareTo( id_1 ) < 0 ) {
-            _id_0 = id_0;
-            _id_1 = id_1;
+        final String my_id_0 = id_0.trim();
+        final String my_id_1 = id_1.trim();
+        if ( my_id_0.toLowerCase().compareTo( my_id_1.toLowerCase() ) < 0 ) {
+            _id_0 = my_id_0;
+            _id_1 = my_id_1;
         }
         else {
-            _id_0 = id_1;
-            _id_1 = id_0;
+            _id_0 = my_id_1;
+            _id_1 = my_id_0;
         }
     }
 
-    public BasicBinaryDomainCombination( final String id_0, final String id_1 ) {
-        this( new DomainId( id_0 ), new DomainId( id_1 ) );
+    public BasicBinaryDomainCombination( final DomainId id_0, final DomainId id_1 ) {
+        this( id_0.getId(), id_1.getId() );
     }
 
     @Override
@@ -94,17 +98,18 @@ public class BasicBinaryDomainCombination implements BinaryDomainCombination {
 
     @Override
     public DomainId getId0() {
-        return _id_0;
+        return new DomainId( _id_0 );
     }
 
     @Override
     public DomainId getId1() {
-        return _id_1;
+        return new DomainId( _id_1 );
     }
 
     @Override
     public int hashCode() {
-        return getId0().hashCode() + ( 19 * getId1().hashCode() );
+        // return getId0().hashCode() + ( 19 * getId1().hashCode() );
+        return ( _id_0 + _id_1 ).hashCode();
     }
 
     @Override
@@ -154,9 +159,9 @@ public class BasicBinaryDomainCombination implements BinaryDomainCombination {
     @Override
     public String toString() {
         final StringBuffer sb = new StringBuffer();
-        sb.append( getId0() );
+        sb.append( _id_0 );
         sb.append( BinaryDomainCombination.SEPARATOR );
-        sb.append( getId1() );
+        sb.append( _id_1 );
         return sb.toString();
     }
 

diff --git a/forester/java/src/org/forester/surfacing/DirectedBinaryDomainCombination.java b/forester/java/src/org/forester/surfacing/DirectedBinaryDomainCombination.java
index c47a278..8ec5a74 100644 (file)
--- a/forester/java/src/org/forester/surfacing/DirectedBinaryDomainCombination.java
+++ b/forester/java/src/org/forester/surfacing/DirectedBinaryDomainCombination.java
@@ -33,8 +33,8 @@ public class DirectedBinaryDomainCombination extends BasicBinaryDomainCombinatio
         if ( ( n_terminal == null ) || ( c_terminal == null ) ) {
             throw new IllegalArgumentException( "attempt to create binary domain combination using null" );
         }
-        _id_0 = n_terminal;
-        _id_1 = c_terminal;
+        _id_0 = n_terminal.getId();
+        _id_1 = c_terminal.getId();
     }
 
     public DirectedBinaryDomainCombination( final String n_terminal, final String c_terminal ) {

diff --git a/forester/java/src/org/forester/surfacing/SurfacingUtil.java b/forester/java/src/org/forester/surfacing/SurfacingUtil.java
index 3a9d10e..c6df0b2 100644 (file)
--- a/forester/java/src/org/forester/surfacing/SurfacingUtil.java
+++ b/forester/java/src/org/forester/surfacing/SurfacingUtil.java
@@ -2437,17 +2437,32 @@ public final class SurfacingUtil {
         try {
             writer.write( genome );
             writer.write( "\t" );
-            writer.write( stats.arithmeticMean() + "" );
-            writer.write( "\t" );
-            writer.write( stats.sampleStandardDeviation() + "" );
-            writer.write( "\t" );
-            writer.write( stats.median() + "" );
-            writer.write( "\t" );
-            writer.write( stats.getN() + "" );
-            writer.write( "\t" );
-            writer.write( stats.getMin() + "" );
-            writer.write( "\t" );
-            writer.write( stats.getMax() + "" );
+            if ( stats.getN() >= 1 ) {
+                writer.write( stats.arithmeticMean() + "" );
+                writer.write( "\t" );
+                if ( stats.getN() >= 2 ) {
+                    writer.write( stats.sampleStandardDeviation() + "" );
+                }
+                else {
+                    writer.write( "" );
+                }
+                writer.write( "\t" );
+                writer.write( stats.median() + "" );
+                writer.write( "\t" );
+                writer.write( stats.getN() + "" );
+                writer.write( "\t" );
+                writer.write( stats.getMin() + "" );
+                writer.write( "\t" );
+                writer.write( stats.getMax() + "" );
+            }
+            else {
+                writer.write( "\t" );
+                writer.write( "\t" );
+                writer.write( "\t" );
+                writer.write( "0" );
+                writer.write( "\t" );
+                writer.write( "\t" );
+            }
             writer.write( "\n" );
         }
         catch ( final IOException e ) {

diff --git a/forester/java/src/org/forester/surfacing/TestSurfacing.java b/forester/java/src/org/forester/surfacing/TestSurfacing.java
index 56bb6fa..8301b9b 100644 (file)
--- a/forester/java/src/org/forester/surfacing/TestSurfacing.java
+++ b/forester/java/src/org/forester/surfacing/TestSurfacing.java
@@ -1594,6 +1594,7 @@ public class TestSurfacing {
             final BasicBinaryDomainCombination s8 = new BasicBinaryDomainCombination( "b", "d" );
             final BinaryDomainCombination s9 = BasicBinaryDomainCombination.createInstance( " z-z=a-aa " );
             if ( !s9.toString().equals( "a-aa=z-z" ) ) {
+                System.out.println( s9.toString() );
                 return false;
             }
             if ( !s0.equals( s0 ) ) {