From: cmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Tue, 26 Nov 2013 01:08:38 +0000 (+0000)
Subject: inprogress
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=92efbf3f36c205c03cdb7a542f0d2ab1ea7fdc2a;p=jalview.git

inprogress
---

diff --git a/forester/java/src/org/forester/surfacing/AdjactantDirectedBinaryDomainCombination.java b/forester/java/src/org/forester/surfacing/AdjactantDirectedBinaryDomainCombination.java
index 1bcbc60..619e8f6 100644
--- a/forester/java/src/org/forester/surfacing/AdjactantDirectedBinaryDomainCombination.java
+++ b/forester/java/src/org/forester/surfacing/AdjactantDirectedBinaryDomainCombination.java
@@ -35,8 +35,9 @@ public class AdjactantDirectedBinaryDomainCombination extends BasicBinaryDomainC
         if ( ( n_terminal == null ) || ( c_terminal == null ) ) {
             throw new IllegalArgumentException( "attempt to create binary domain combination using null" );
         }
-        _id0 = n_terminal;
-        _id1 = c_terminal;
+        // _id0 = n_terminal;
+        // _id1 = c_terminal;
+        _data = n_terminal + SEPARATOR + c_terminal;
     }
 
     public static AdjactantDirectedBinaryDomainCombination createInstance( final String ids ) {
diff --git a/forester/java/src/org/forester/surfacing/BasicBinaryDomainCombination.java b/forester/java/src/org/forester/surfacing/BasicBinaryDomainCombination.java
index 518c32e..350c2e9 100644
--- a/forester/java/src/org/forester/surfacing/BasicBinaryDomainCombination.java
+++ b/forester/java/src/org/forester/surfacing/BasicBinaryDomainCombination.java
@@ -31,27 +31,30 @@ import org.forester.util.ForesterUtil;
 
 public class BasicBinaryDomainCombination implements BinaryDomainCombination {
 
-    String _id0;
-    String _id1;
-    String _str;
+    // String _id0;
+    // String _id1;
+    String _data;
 
     public BasicBinaryDomainCombination( final String id0, final String id1 ) {
         if ( ( id0 == null ) || ( id1 == null ) ) {
             throw new IllegalArgumentException( "attempt to create binary domain combination using null" );
         }
         if ( id0.toLowerCase().compareTo( id1.toLowerCase() ) < 0 ) {
-            _id0 = id0;
-            _id1 = id1;
+            //  _id0 = id0;
+            //  _id1 = id1;
+            _data = id0 + SEPARATOR + id1;
         }
         else {
-            _id0 = id1;
-            _id1 = id0;
+            // _id0 = id1;
+            // _id1 = id0;
+            _data = id1 + SEPARATOR + id0;
         }
     }
 
     BasicBinaryDomainCombination() {
-        _id0 = null;
-        _id1 = null;
+        //_id0 = null;
+        // _id1 = null;
+        _data = null;
     }
 
     @Override
@@ -92,12 +95,14 @@ public class BasicBinaryDomainCombination implements BinaryDomainCombination {
 
     @Override
     public String getId0() {
-        return _id0;
+        return _data.substring( 0, _data.indexOf( SEPARATOR ) );
+        // return _id0;
     }
 
     @Override
     public String getId1() {
-        return _id1;
+        return _data.substring( _data.indexOf( SEPARATOR ) + 1 );
+        //return _id1;
     }
 
     @Override
@@ -155,7 +160,8 @@ public class BasicBinaryDomainCombination implements BinaryDomainCombination {
     }
 
     private String getAsStr() {
-        return _id0 + SEPARATOR + _id1;
+        // return _id0 + SEPARATOR + _id1;
+        return _data;
     }
 
     public static BinaryDomainCombination createInstance( final String ids ) {
diff --git a/forester/java/src/org/forester/surfacing/DirectedBinaryDomainCombination.java b/forester/java/src/org/forester/surfacing/DirectedBinaryDomainCombination.java
index 4716be8..dac4464 100644
--- a/forester/java/src/org/forester/surfacing/DirectedBinaryDomainCombination.java
+++ b/forester/java/src/org/forester/surfacing/DirectedBinaryDomainCombination.java
@@ -35,8 +35,9 @@ public class DirectedBinaryDomainCombination extends BasicBinaryDomainCombinatio
         if ( ( n_terminal == null ) || ( c_terminal == null ) ) {
             throw new IllegalArgumentException( "attempt to create binary domain combination using null" );
         }
-        _id0 = n_terminal;
-        _id1 = c_terminal;
+        //_id0 = n_terminal;
+        //_id1 = c_terminal;
+        _data = n_terminal + SEPARATOR + c_terminal;
     }
 
     public static BinaryDomainCombination createInstance( final String ids ) {
diff --git a/forester/java/src/org/forester/test/Test.java b/forester/java/src/org/forester/test/Test.java
index fc210a5..b1a9cd1 100644
--- a/forester/java/src/org/forester/test/Test.java
+++ b/forester/java/src/org/forester/test/Test.java
@@ -127,7 +127,7 @@ import org.forester.ws.wabi.TxSearch.TAX_RANK;
 @SuppressWarnings( "unused")
 public final class Test {
 
-    private final static boolean PERFORM_DB_TESTS          = true;
+    private final static boolean PERFORM_DB_TESTS          = false;
     private final static double  ZERO_DIFF                 = 1.0E-9;
     private final static String  PATH_TO_TEST_DATA         = System.getProperty( "user.dir" )
                                                                    + ForesterUtil.getFileSeparator() + "test_data"