[Jmol-commits] CVS: Jmol/src/org/jmol/viewer Chain.java,1.7,1.8 Compiler.java,1.7,1.8 Eval.java,1.36,1.37 Frame.java,1.22,1.23 Mmset.java,1.8,1.9 Model.java,1.6,1.7

[Miguel <mig...@us...>]

Update of /cvsroot/jmol/Jmol/src/org/jmol/viewer
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv8650/src/org/jmol/viewer

Modified Files:
	Chain.java Compiler.java Eval.java Frame.java Mmset.java 
	Model.java 
Log Message:
fixed sequence code ranges to be completely independent of sequence code values


Index: Chain.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/jmol/viewer/Chain.java,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -r1.7 -r1.8
--- Chain.java	24 Jan 2005 19:42:52 -0000	1.7
+++ Chain.java	31 May 2005 14:05:30 -0000	1.8
@@ -88,6 +88,29 @@
     }
   }
 
+  void selectSeqcodeRange(int seqcodeA, int seqcodeB, BitSet bs) {
+    int indexA = getSeqcodeIndex(seqcodeA);
+    if (indexA < 0)
+      return;
+    int indexB = getSeqcodeIndex(seqcodeB);
+    if (indexB < 0)
+      return;
+    if (indexA > indexB) {
+      int t = indexA;
+      indexA = indexB;
+      indexB = t;
+    }
+    for (int i = indexA; i <= indexB; ++i)
+      groups[i].selectAtoms(bs);
+  }
+
+  int getSeqcodeIndex(int seqcode) {
+    int i;
+    for (i = groupCount; --i >= 0 && groups[i].seqcode != seqcode; )
+      {}
+    return i;
+  }
+
   int getSelectedGroupCount() {
     return selectedGroupCount;
   }

Index: Compiler.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/jmol/viewer/Compiler.java,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -r1.7 -r1.8
--- Compiler.java	20 Mar 2005 15:29:07 -0000	1.7
+++ Compiler.java	31 May 2005 14:05:31 -0000	1.8
@@ -1205,11 +1205,11 @@
       return false;
     if (tokPeek() == Token.hyphen) {
       tokenNext();
-      int seqcodeMin = seqcode;
+      int seqcodeA = seqcode;
       if (! clauseSequenceCode())
         return false;
       return generateResidueSpecCode(new Token(Token.spec_seqcode_range,
-                                               seqcodeMin,
+                                               seqcodeA,
                                                new Integer(seqcode)));
     }
     return generateResidueSpecCode(new Token(Token.spec_seqcode,

Index: Eval.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/jmol/viewer/Eval.java,v
retrieving revision 1.36
retrieving revision 1.37
diff -u -r1.36 -r1.37
--- Eval.java	27 May 2005 20:33:27 -0000	1.36
+++ Eval.java	31 May 2005 14:05:31 -0000	1.37
@@ -873,9 +873,9 @@
         stack[sp++] = getSpecSeqcode(instruction.intValue);
         break;
       case Token.spec_seqcode_range:
-        int min = instruction.intValue;
-        int last = ((Integer)instruction.value).intValue();
-        stack[sp++] = getSpecSeqcodeRange(min, last);
+        int seqcodeA = instruction.intValue;
+        int seqcodeB = ((Integer)instruction.value).intValue();
+        stack[sp++] = getSpecSeqcodeRange(seqcodeA, seqcodeB);
         break;
       case Token.spec_chain:
         stack[sp++] = getSpecChain((char)instruction.intValue);
@@ -1142,15 +1142,10 @@
     return bsResno;
   }
 
-  BitSet getSpecSeqcodeRange(int seqcodeMin, int seqcodeLast) {
+  BitSet getSpecSeqcodeRange(int seqcodeA, int seqcodeB) {
     Frame frame = viewer.getFrame();
     BitSet bsResidue = new BitSet();
-    for (int i = viewer.getAtomCount(); --i >= 0; ) {
-      Atom atom = frame.getAtomAt(i);
-      int atomSeqcode = atom.getSeqcode();
-      if (atomSeqcode >= seqcodeMin && atomSeqcode <= seqcodeLast)
-        bsResidue.set(i);
-    }
+    frame.selectSeqcodeRange(seqcodeA, seqcodeB, bsResidue);
     return bsResidue;
   }
 

Index: Frame.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/jmol/viewer/Frame.java,v
retrieving revision 1.22
retrieving revision 1.23
diff -u -r1.22 -r1.23
--- Frame.java	6 Mar 2005 02:32:10 -0000	1.22
+++ Frame.java	31 May 2005 14:05:31 -0000	1.23
@@ -1703,4 +1703,8 @@
     atoms[atomIndex].group.chain.selectAtoms(bsChain);
     return bsChain;
   }
+
+  void selectSeqcodeRange(int seqcodeA, int seqcodeB, BitSet bs) {
+    mmset.selectSeqcodeRange(seqcodeA, seqcodeB, bs);
+  }
 }

Index: Mmset.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/jmol/viewer/Mmset.java,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -r1.8 -r1.9
--- Mmset.java	24 Jan 2005 19:43:11 -0000	1.8
+++ Mmset.java	31 May 2005 14:05:31 -0000	1.9
@@ -211,6 +211,11 @@
       models[i].calcHydrogenBonds();
   }
 
+  void selectSeqcodeRange(int seqcodeA, int seqcodeB, BitSet bs) {
+    for (int i = modelCount; --i >= 0; )
+      models[i].selectSeqcodeRange(seqcodeA, seqcodeB, bs);
+  }
+
   static class Structure {
     String typeName;
     byte type;

Index: Model.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/jmol/viewer/Model.java,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- Model.java	24 Jan 2005 19:43:11 -0000	1.6
+++ Model.java	31 May 2005 14:05:31 -0000	1.7
@@ -86,6 +86,11 @@
       polymers[i].calcSelectedMonomersCount(bsSelected);
   }
 
+  void selectSeqcodeRange(int seqcodeA, int seqcodeB, BitSet bs) {
+    for (int i = chainCount; --i >= 0; )
+      chains[i].selectSeqcodeRange(seqcodeA, seqcodeB, bs);
+  }
+
   int getGroupCount() {
     int groupCount = 0;
     for (int i = chainCount; --i >= 0; )