[Jmol-commits] CVS: Jmol/src/org/openscience/jmol/viewer/pdb PdbChain.java,1.14,1.15 PdbFile.java,1.13,1.14 PdbGroup.java,1.19,1.20 PdbAtom.java,1.18,NONE

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

Update of /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/pdb
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv26994/src/org/openscience/jmol/viewer/pdb

Modified Files:
	PdbChain.java PdbFile.java PdbGroup.java 
Removed Files:
	PdbAtom.java 
Log Message:
eliminated PdbAtom


Index: PdbChain.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/pdb/PdbChain.java,v
retrieving revision 1.14
retrieving revision 1.15
diff -u -r1.14 -r1.15
--- PdbChain.java	12 Mar 2004 23:43:39 -0000	1.14
+++ PdbChain.java	25 Mar 2004 22:46:57 -0000	1.15
@@ -34,7 +34,7 @@
 final public class PdbChain {
 
   public PdbModel pdbmodel;
-  char chainID;
+  public char chainID;
   int groupCount;
   PdbGroup[] groups = new PdbGroup[16];
 
@@ -55,9 +55,9 @@
     polymer = new PdbPolymer(this);
   }
   
-  PdbGroup allocateGroup(int sequence, String group3) {
-
-    PdbGroup group = new PdbGroup(this, sequence, group3);
+  PdbGroup allocateGroup(int sequenceNumber, char insertionCode,
+                         String group3) {
+    PdbGroup group = new PdbGroup(this, sequenceNumber, insertionCode, group3);
 
     if (groupCount == groups.length) {
       PdbGroup[] t = new PdbGroup[groupCount * 2];

Index: PdbFile.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/pdb/PdbFile.java,v
retrieving revision 1.13
retrieving revision 1.14
diff -u -r1.13 -r1.14
--- PdbFile.java	25 Mar 2004 11:13:01 -0000	1.13
+++ PdbFile.java	25 Mar 2004 22:46:57 -0000	1.14
@@ -126,18 +126,21 @@
   }
 
   int modelNumberCurrent = Integer.MIN_VALUE;
-  char chainIDCurrent = '\uFFFF';
-  int seqcodeCurrent;
+  char chainIDCurrent;
+  int sequenceNumberCurrent;
+  char insertionCodeCurrent;
   PdbGroup groupCurrent;
 
   void setCurrentResidue(int modelNumber, char chainID,
-                         int seqcode, String group3) {
+                         int sequenceNumber, char insertionCode,
+                         String group3) {
     modelNumberCurrent = modelNumber;
     chainIDCurrent = chainID;
-    seqcodeCurrent = seqcode;
+    sequenceNumberCurrent = sequenceNumber;
+    insertionCodeCurrent = insertionCode;
     PdbModel model = getOrAllocateModel(modelNumber);
     PdbChain chain = model.getOrAllocateChain(chainID);
-    groupCurrent = chain.allocateGroup(seqcode, group3);
+    groupCurrent = chain.allocateGroup(sequenceNumber, insertionCode, group3);
   }
 
   /*
@@ -162,20 +165,19 @@
   }
   */
 
-  public PdbAtom allocatePdbAtom(Atom atom) {
-    int modelNumber = atom.getModelNumber();
-    char chainID = atom.getChainID();
-    int sequenceNum = atom.getSequenceNumber();
-    char insertionCode = atom.getInsertionCode();
-    int seqcode = PdbGroup.getSeqcode(sequenceNum, insertionCode);
-    if (modelNumber != modelNumberCurrent ||
+  public PdbGroup registerAtom(Atom atom, int modelNumber, char chainID,
+                               int sequenceNumber, char insertionCode,
+                               String group3) {
+    if (sequenceNumber != sequenceNumberCurrent ||
+        insertionCode != insertionCodeCurrent ||
         chainID != chainIDCurrent ||
-        seqcode != seqcodeCurrent)
+        modelNumber != modelNumberCurrent)
       setCurrentResidue(modelNumber, chainID,
-                        seqcode, atom.getGroup3());
-    return groupCurrent.allocatePdbAtom(atom);
+                        sequenceNumber, insertionCode, group3);
+    groupCurrent.registerAtom(atom);
+    return groupCurrent;
   }
-
+  
   public int getModelCount() {
     return modelCount;
   }

Index: PdbGroup.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/pdb/PdbGroup.java,v
retrieving revision 1.19
retrieving revision 1.20
diff -u -r1.19 -r1.20
--- PdbGroup.java	25 Mar 2004 11:13:01 -0000	1.19
+++ PdbGroup.java	25 Mar 2004 22:46:57 -0000	1.20
@@ -40,9 +40,10 @@
   public PdbStructure structure;
   public int[] mainchainIndices;
 
-  public PdbGroup(PdbChain chain, int seqcode, String group3) {
+  public PdbGroup(PdbChain chain,
+                  int sequenceNumber, char insertionCode, String group3) {
     this.chain = chain;
-    this.seqcode = seqcode;
+    this.seqcode = getSeqcode(sequenceNumber, insertionCode);
     this.groupID = getGroupID(group3);
   }
 
@@ -173,13 +174,11 @@
   }
   */
 
-  PdbAtom allocatePdbAtom(Atom atom) {
-    PdbAtom pdbAtom = new PdbAtom(this, atom);
-    if (pdbAtom.atomID < JmolConstants.ATOMID_MAINCHAIN_MAX) {
-      if (! registerMainchainAtomIndex(pdbAtom.atomID, atom.atomIndex))
-        pdbAtom.atomID += JmolConstants.ATOMID_MAINCHAIN_IMPOSTERS;
+  void registerAtom(Atom atom) {
+    if (atom.atomID < JmolConstants.ATOMID_MAINCHAIN_MAX) {
+      if (! registerMainchainAtomIndex(atom.atomID, atom.atomIndex))
+        atom.atomID += JmolConstants.ATOMID_MAINCHAIN_IMPOSTERS;
     }
-    return pdbAtom;
   }
 
   boolean registerMainchainAtomIndex(short atomid, int atomIndex) {

--- PdbAtom.java DELETED ---