[Jmol-commits] SF.net SVN: jmol:[15451] trunk/Jmol/src/org/jmol/modelset

[<ha...@us...>]

Revision: 15451
          http://jmol.svn.sourceforge.net/jmol/?rev=15451&view=rev
Author:   hansonr
Date:     2011-05-10 20:19:51 +0000 (Tue, 10 May 2011)

Log Message:
-----------
version=12.1.46_dev

# bug fix: select within(chain, atomno=xxx) will not select all desired atoms
#          if the chain is spread out over multiple regions of the file (1gzx)

Modified Paths:
--------------
    trunk/Jmol/src/org/jmol/modelset/AtomCollection.java
    trunk/Jmol/src/org/jmol/modelset/Chain.java

Modified: trunk/Jmol/src/org/jmol/modelset/AtomCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/AtomCollection.java	2011-05-10 20:18:59 UTC (rev 15450)
+++ trunk/Jmol/src/org/jmol/modelset/AtomCollection.java	2011-05-10 20:19:51 UTC (rev 15451)
@@ -2248,21 +2248,11 @@
       }
       break;
     case Token.chain:
-      for (i = i0; i >= 0; i = bsInfo.nextSetBit(i+1)) {
-        if (bs.get(i))
-          continue;
+      bsInfo = BitSetUtil.copy((BitSet) specInfo);
+      for (i = bsInfo.nextSetBit(0); i >= 0; i = bsInfo.nextSetBit(i + 1)) {
         Chain chain = atoms[i].getChain();
-        bs.set(i);
-        for (int j = i; --j >= 0;)
-          if (atoms[j].getChain() == chain)
-            bs.set(j);
-          else
-            break;
-        for (; ++i < atomCount;)
-          if (atoms[i].getChain() == chain)
-            bs.set(i);
-          else
-            break;
+        chain.setAtomBitSet(bs);
+        bsInfo.andNot(bs);
       }
       break;
     case Token.polymer:
@@ -2470,17 +2460,20 @@
     return (!isEmpty || returnEmpty ? bs : null);
   }
 
-  protected BitSet getChainBits(char chain) {
+  protected BitSet getChainBits(char chainId) {
     boolean caseSensitive = viewer.getChainCaseSensitive();
     if (!caseSensitive)
-      chain = Character.toUpperCase(chain);
+      chainId = Character.toUpperCase(chainId);
     BitSet bs = new BitSet();
-    for (int i = atomCount; --i >= 0;) {
-      char ch = atoms[i].getChainID();
-      if (!caseSensitive)
-        ch = Character.toUpperCase(ch);
-      if (chain == ch)
-        bs.set(i);
+    BitSet bsDone = new BitSet(atomCount);
+    for (int i = bsDone.nextClearBit(0); i < atomCount; i = bsDone.nextClearBit(i)) {
+      Chain chain = atoms[i].getChain();
+      if (chainId == (caseSensitive ? chain.chainID : Character.toUpperCase(chain.chainID))) {
+        chain.setAtomBitSet(bs);
+        bsDone.or(bs);
+      } else {
+        chain.setAtomBitSet(bsDone);
+      }
     }
     return bs;
   }

Modified: trunk/Jmol/src/org/jmol/modelset/Chain.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/Chain.java	2011-05-10 20:18:59 UTC (rev 15450)
+++ trunk/Jmol/src/org/jmol/modelset/Chain.java	2011-05-10 20:19:51 UTC (rev 15451)
@@ -37,53 +37,49 @@
   private boolean isDna, isRna;
   private BitSet bsSelectedGroups;
 
-  public Chain(ModelSet modelSet, Model model, char chainID) {
-    this.modelSet = modelSet;
-    this.model = model;
-    this.chainID = chainID;
-  }
-
-  public void setModelSet(ModelSet modelSet) {
-    this.modelSet = modelSet;
-  }
-  
   public char getChainID() {
     return chainID;
   }
   
-  public ModelSet getModelSet() {
-    return modelSet;
-  }
-  
   public boolean isDna() { return isDna; }
   public boolean isRna() { return isRna; }
 
   public void setIsDna(boolean TF) {isDna = TF;}
   public void setIsRna(boolean TF) {isRna = TF;}
 
-  public Group getGroup(int groupIndex) {
-    return groups[groupIndex];
+  public Atom getAtom(int index) {
+    return modelSet.atoms[index];
   }
   
-  public int getGroupCount() {
-    return groupCount;
+  Chain(ModelSet modelSet, Model model, char chainID) {
+    this.modelSet = modelSet;
+    this.model = model;
+    this.chainID = chainID;
   }
 
-  public int getAtomCount() {
-    return groups[groupCount - 1].lastAtomIndex + 1 - groups[0].firstAtomIndex;
+  void setModelSet(ModelSet modelSet) {
+    this.modelSet = modelSet;
   }
   
-  public Atom getAtom(int index) {
-    return modelSet.atoms[index];
+  ModelSet getModelSet() {
+    return modelSet;
   }
   
+  Group getGroup(int groupIndex) {
+    return groups[groupIndex];
+  }
+  
+  int getGroupCount() {
+    return groupCount;
+  }
+
   /**
    * prior to coloring by group, we need the chain count per chain
    * that is selected
    * 
    * @param bsSelected
    */
-  public void calcSelectedGroupsCount(BitSet bsSelected) {
+  void calcSelectedGroupsCount(BitSet bsSelected) {
     selectedGroupCount = 0;
     if (bsSelectedGroups == null)
       bsSelectedGroups = new BitSet();
@@ -98,7 +94,7 @@
     }
   }
 
-  public int selectSeqcodeRange(int index0, int seqcodeA, int seqcodeB,
+  int selectSeqcodeRange(int index0, int seqcodeA, int seqcodeB,
                                 BitSet bs) {
     int seqcode, indexA, indexB, minDiff;
     boolean isInexact = false;
@@ -152,11 +148,16 @@
     return selectedGroupCount;
   }
 
-  public void fixIndices(int atomsDeleted) {
+  void fixIndices(int atomsDeleted) {
     for (int i = 0; i < groupCount; i++) {
       groups[i].firstAtomIndex -= atomsDeleted;
       groups[i].leadAtomIndex -= atomsDeleted;
       groups[i].lastAtomIndex -= atomsDeleted;
     }
   }
+
+  void setAtomBitSet(BitSet bs) {
+    for (int i = 0; i < groupCount; i++)
+      bs.set(groups[i].firstAtomIndex, groups[i].lastAtomIndex + 1);
+  }
 }


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.