[Jmol-commits] CVS: Jmol/src/org/openscience/jmol/viewer/pdb PdbChain.java,1.6,1.7 PdbPolymer.java,1.4,1.5

[Michael T H. <mic...@us...>]

Update of /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/pdb
In directory sc8-pr-cvs1:/tmp/cvs-serv15928/src/org/openscience/jmol/viewer/pdb

Modified Files:
	PdbChain.java PdbPolymer.java 
Log Message:
removed dependancy upon sequential groupSequence


Index: PdbChain.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/pdb/PdbChain.java,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- PdbChain.java	10 Dec 2003 10:28:53 -0000	1.6
+++ PdbChain.java	12 Dec 2003 09:49:37 -0000	1.7
@@ -33,7 +33,6 @@
 
   public PdbModel model;
   public char chainID;
-  short firstGroupSequence;
   int groupCount;
   PdbGroup[] groups = new PdbGroup[16];
   PdbGroup[] mainchain;
@@ -55,23 +54,13 @@
   PdbGroup allocateGroup(short groupSequence, String group3) {
 
     PdbGroup group = new PdbGroup(this, groupSequence, group3);
-    
-    if (groupCount == 0)
-      firstGroupSequence = groupSequence;
-    int groupIndex = groupSequence - firstGroupSequence;
-    if (groupIndex < 0) {
-      System.out.println("residue out of sequence?");
-      return group;
-    }
-    if (groupIndex >= groups.length) {
-      PdbGroup[] t = new PdbGroup[groupIndex * 2];
+
+    if (groupCount == groups.length) {
+      PdbGroup[] t = new PdbGroup[groupCount * 2];
       System.arraycopy(groups, 0, t, 0, groupCount);
       groups = t;
     }
-    groups[groupIndex] = group;
-    if (groupIndex >= groupCount)
-      groupCount = groupIndex + 1;
-    return group;
+    return groups[groupCount++] = group;
   }
 
   public PdbGroup getResidue(int groupIndex) {
@@ -82,10 +71,6 @@
     return groupCount;
   }
 
-  public short getFirstResidueID() {
-    return firstGroupSequence;
-  }
-
   public Point3f getResidueAlphaCarbonPoint(int groupIndex) {
     return groups[groupIndex].getAlphaCarbonAtom().point3f;
   }
@@ -140,10 +125,6 @@
     if (polymer == null)
       polymer = new PdbPolymer(this);
     polymer.addSecondaryStructure(type, startResidueID, endResidueID);
-  }
-
-  public int getIndex(short groupID) {
-    return groupID - firstGroupSequence;
   }
 
   public void getAlphaCarbonMidPoint(int groupIndex, Point3f midPoint) {

Index: PdbPolymer.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/pdb/PdbPolymer.java,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- PdbPolymer.java	10 Dec 2003 12:22:59 -0000	1.4
+++ PdbPolymer.java	12 Dec 2003 09:49:37 -0000	1.5
@@ -43,7 +43,7 @@
     int firstNonMainchain = 0;
     for (int i = 0; i < chain.groupCount; ++i ) {
       PdbGroup group = chainGroups[i];
-      if (group == null || ! group.hasFullMainchain())
+      if (! group.hasFullMainchain())
         continue;
       ++count;
       if (firstNonMainchain == i)
@@ -58,7 +58,7 @@
       groups = new PdbGroup[count];
       for (int i = 0, j = 0; i < chain.groupCount; ++i) {
         PdbGroup group = chainGroups[i];
-        if (group == null || !group.hasFullMainchain())
+        if (! group.hasFullMainchain())
           continue;
         groups[j++] = group;
       }