in progress

diff --git a/forester/java/src/org/forester/io/parsers/HmmscanPerDomainTableParser.java b/forester/java/src/org/forester/io/parsers/HmmscanPerDomainTableParser.java
index 0bb224c..2aa4497 100644 (file)
--- a/forester/java/src/org/forester/io/parsers/HmmscanPerDomainTableParser.java
+++ b/forester/java/src/org/forester/io/parsers/HmmscanPerDomainTableParser.java
@@ -64,6 +64,7 @@ public final class HmmscanPerDomainTableParser {
     private static final ReturnType       RETURN_TYPE_DEFAULT         = ReturnType.UNORDERED_PROTEIN_DOMAIN_COLLECTION_PER_PROTEIN;
     private static final boolean          IGNORE_DUFS_DEFAULT         = false;
     private static final int              MAX_ALLOWED_OVERLAP_DEFAULT = -1;
+    private static final boolean          IGNORE_REPLACED_RRMS        = true;
     private final Set<DomainId>           _filter;
     private final FilterType              _filter_type;
     private final File                    _input_file;
@@ -447,6 +448,10 @@ public final class HmmscanPerDomainTableParser {
             else if ( isIgnoreDufs() && uc_id.startsWith( "DUF" ) ) {
                 ++_domains_ignored_due_to_duf;
             }
+            else if ( IGNORE_REPLACED_RRMS
+                    && ( uc_id.contains( "RRM_1" ) || uc_id.contains( "RRM_3" ) || uc_id.contains( "RRM_5" ) || uc_id
+                            .contains( "RRM_6" ) ) ) {
+            }
             else if ( isIgnoreVirusLikeIds()
                     && ( uc_id.contains( VIR ) || uc_id.contains( PHAGE ) || uc_id.contains( RETRO )
                             || uc_id.contains( TRANSPOS ) || uc_id.startsWith( RV ) || uc_id.startsWith( GAG )

diff --git a/forester/java/src/org/forester/surfacing/AdjactantDirectedBinaryDomainCombination.java b/forester/java/src/org/forester/surfacing/AdjactantDirectedBinaryDomainCombination.java
index 6e6da35..3da8ed4 100644 (file)
--- a/forester/java/src/org/forester/surfacing/AdjactantDirectedBinaryDomainCombination.java
+++ b/forester/java/src/org/forester/surfacing/AdjactantDirectedBinaryDomainCombination.java
@@ -36,8 +36,9 @@ 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.getId();
-        _id_1 = c_terminal.getId();
+        //   _id_0 = n_terminal.getId();
+        //  _id_1 = c_terminal.getId();
+        _data = n_terminal.getId() + BinaryDomainCombination.SEPARATOR + 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 6516903..67e5ffd 100644 (file)
--- a/forester/java/src/org/forester/surfacing/BasicBinaryDomainCombination.java
+++ b/forester/java/src/org/forester/surfacing/BasicBinaryDomainCombination.java
@@ -32,14 +32,16 @@ import org.forester.util.ForesterUtil;
 
 public class BasicBinaryDomainCombination implements BinaryDomainCombination {
 
-    String _id_0;
-    String _id_1;
+    String _data;
 
+    //String _id_0;
+    // String _id_1;
     //DomainId _id_0;
     //DomainId _id_1;
     BasicBinaryDomainCombination() {
-        _id_0 = null;
-        _id_1 = null;
+        //_id_0 = null;
+        // _id_1 = null;
+        _data = null;
     }
 
     public BasicBinaryDomainCombination( final String id_0, final String id_1 ) {
@@ -49,12 +51,14 @@ public class BasicBinaryDomainCombination implements BinaryDomainCombination {
         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;
+            //_id_0 = my_id_0;
+            //_id_1 = my_id_1;
+            _data = my_id_0 + BinaryDomainCombination.SEPARATOR + my_id_1;
         }
         else {
-            _id_0 = my_id_1;
-            _id_1 = my_id_0;
+            //_id_0 = my_id_1;
+            // _id_1 = my_id_0;
+            _data = my_id_1 + BinaryDomainCombination.SEPARATOR + my_id_0;
         }
     }
 
@@ -100,18 +104,20 @@ public class BasicBinaryDomainCombination implements BinaryDomainCombination {
 
     @Override
     public DomainId getId0() {
-        return new DomainId( _id_0 );
+        return new DomainId( _data.split( BinaryDomainCombination.SEPARATOR )[ 0 ] );
     }
 
     @Override
     public DomainId getId1() {
-        return new DomainId( _id_1 );
+        // return new DomainId( _id_1 );
+        return new DomainId( _data.split( BinaryDomainCombination.SEPARATOR )[ 1 ] );
     }
 
     @Override
     public int hashCode() {
         // return getId0().hashCode() + ( 19 * getId1().hashCode() );
-        return ( _id_0 + _id_1 ).hashCode();
+        // return ( _id_0 + _id_1 ).hashCode();
+        return _data.hashCode();
     }
 
     @Override
@@ -160,11 +166,12 @@ public class BasicBinaryDomainCombination implements BinaryDomainCombination {
 
     @Override
     public String toString() {
-        final StringBuffer sb = new StringBuffer();
-        sb.append( _id_0 );
-        sb.append( BinaryDomainCombination.SEPARATOR );
-        sb.append( _id_1 );
-        return sb.toString();
+        return _data;
+        //        final StringBuffer sb = new StringBuffer();
+        //        sb.append( _id_0 );
+        //        sb.append( BinaryDomainCombination.SEPARATOR );
+        //        sb.append( _id_1 );
+        //        return sb.toString();
     }
 
     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 237bb67..e57e137 100644 (file)
--- a/forester/java/src/org/forester/surfacing/DirectedBinaryDomainCombination.java
+++ b/forester/java/src/org/forester/surfacing/DirectedBinaryDomainCombination.java
@@ -36,8 +36,9 @@ 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.getId();
-        _id_1 = c_terminal.getId();
+        //_id_0 = n_terminal.getId();
+        //_id_1 = c_terminal.getId();
+        _data = n_terminal.getId() + BinaryDomainCombination.SEPARATOR + c_terminal.getId();
     }
 
     public DirectedBinaryDomainCombination( final String n_terminal, final String c_terminal ) {