[Jmol-commits] CVS: Jmol/src/org/openscience/jmol/viewer/datamodel FrameBuilder.java,1.45,1.46 GroupBuilder.java,1.7,NONE

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

Update of /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/datamodel
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv9733/src/org/openscience/jmol/viewer/datamodel

Modified Files:
	FrameBuilder.java 
Removed Files:
	GroupBuilder.java 
Log Message:
eliminated GroupBuilder as a separate class ... just part of FrameBuilder


Index: FrameBuilder.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/datamodel/FrameBuilder.java,v
retrieving revision 1.45
retrieving revision 1.46
diff -u -r1.45 -r1.46
--- FrameBuilder.java	14 Jun 2004 14:03:20 -0000	1.45
+++ FrameBuilder.java	14 Jun 2004 14:10:20 -0000	1.46
@@ -33,12 +33,10 @@
 

   final JmolViewer viewer;

   final ModelAdapter adapter;

-  final GroupBuilder groupBuilder;

 

   public FrameBuilder(JmolViewer viewer, ModelAdapter adapter) {

     this.viewer = viewer;

     this.adapter = adapter;

-    this.groupBuilder = new GroupBuilder(viewer, this);

   }

 

   protected void finalize() {

@@ -88,7 +86,7 @@
               iterAtom.getClientAtomReference());

     }

 

-    groupBuilder.finishBuildingGroup();

+    finishBuildingGroup();

     

     {

       ModelAdapter.BondIterator iterBond =

@@ -162,10 +160,11 @@
     this.bondCount = 0;

     bonds = new Bond[2 * atomCountEstimate];

     htAtomMap.clear();

-    groupBuilder.initializeBuild();

+    initializeGroupBuild();

   }

 

   void finalizeBuild() {

+    finalizeGroupBuild();

     currentModel = null;

     currentChain = null;

     atoms = null;

@@ -203,9 +202,9 @@
         groupInsertionCode != currentGroupInsertionCode) {

       currentGroupSequenceNumber = groupSequenceNumber;

       currentGroupInsertionCode = groupInsertionCode;

-      groupBuilder.finishBuildingGroup();

-      groupBuilder.startBuildingGroup(currentChain, group3,

-                                      groupSequenceNumber, groupInsertionCode);

+      finishBuildingGroup();

+      startBuildingGroup(currentChain, group3,

+                         groupSequenceNumber, groupInsertionCode);

     }

     Atom atom = new Atom(viewer,

                          currentModelIndex,

@@ -219,7 +218,7 @@
                          isHetero, atomSerial, chainID,

                          vectorX, vectorY, vectorZ);

 

-    groupBuilder.registerAtom(atom);

+    registerAtomWithGroup(atom);

 

     if (atomCount == atoms.length)

       atoms = (Atom[])Util.setLength(atoms, atomCount + ATOM_GROWTH_INCREMENT);

@@ -257,4 +256,102 @@
     if (bond != null)

       bonds[bondCount++] = bond;

   }

+

+  ////////////////////////////////////////////////////////////////

+  // special handling for groups

+  ////////////////////////////////////////////////////////////////

+

+  boolean hasPendingGroup;

+

+  void initializeGroupBuild() {

+    hasPendingGroup = false;

+  }

+

+  void finalizeGroupBuild() {

+    hasPendingGroup = false;

+    chain = null;

+  }

+

+  Chain chain;

+  String group3;

+  int seqcode;

+  int firstAtomIndex, lastAtomIndex;

+

+  int distinguishingBits;

+  final int[] specialAtomIndexes = new int[JmolConstants.ATOMID_MAX];

+

+  void startBuildingGroup(Chain chain, String group3,

+                          int groupSequenceNumber, char groupInsertionCode) {

+    if (hasPendingGroup)

+      throw new NullPointerException();

+    hasPendingGroup = true;

+    this.chain = chain;

+    this.group3 = group3;

+    this.seqcode = Group.getSeqcode(groupSequenceNumber, groupInsertionCode);

+    firstAtomIndex = -1;

+    distinguishingBits = 0;

+    for (int i = JmolConstants.ATOMID_MAX; --i >= 0; )

+      specialAtomIndexes[i] = Integer.MIN_VALUE;

+  }

+

+

+  void registerAtomWithGroup(Atom atom) {

+    if (! hasPendingGroup)

+      throw new NullPointerException();

+    int atomIndex = atom.atomIndex;

+    if (firstAtomIndex < 0)

+      firstAtomIndex = lastAtomIndex = atomIndex;

+    else if (++lastAtomIndex != atomIndex) {

+      System.out.println("unexpected atom index while building group\n" +

+                         " expected:" + lastAtomIndex +

+                         " received:" + atomIndex);

+      throw new NullPointerException();

+    }

+    int specialAtomID = atom.specialAtomID;

+    if (specialAtomID > 0) {

+      if (specialAtomID <  JmolConstants.ATOMID_DISTINGUISHING_ATOM_MAX)

+        distinguishingBits |= 1 << specialAtomID;

+      if (specialAtomIndexes[specialAtomID] < 0)

+        specialAtomIndexes[specialAtomID] = atomIndex;

+    }

+  }

+

+

+  void finishBuildingGroup() {

+    if (! hasPendingGroup)

+      return;

+    Group group = distinguishAndAllocateGroup();

+    propogateGroup(group, firstAtomIndex, lastAtomIndex);

+    chain.addGroup(group);

+    hasPendingGroup = false;

+    chain = null;

+  }

+  

+  Group distinguishAndAllocateGroup() {

+    Group group = null;

+    if ((distinguishingBits & JmolConstants.ATOMID_PROTEIN_MASK) ==

+        JmolConstants.ATOMID_PROTEIN_MASK) {

+      group = AminoMonomer.validateAndAllocate(chain, group3, seqcode,

+                                               firstAtomIndex, lastAtomIndex,

+                                               specialAtomIndexes);

+    } else if ((distinguishingBits & JmolConstants.ATOMID_ALPHA_ONLY_MASK) ==

+               JmolConstants.ATOMID_ALPHA_ONLY_MASK) {

+      group = AlphaMonomer.validateAndAllocate(chain, group3, seqcode,

+                                               firstAtomIndex, lastAtomIndex,

+                                               specialAtomIndexes);

+    } else if (((distinguishingBits & JmolConstants.ATOMID_NUCLEIC_MASK) ==

+                JmolConstants.ATOMID_NUCLEIC_MASK)) {

+      group = NucleicMonomer.validateAndAllocate(chain, group3, seqcode,

+                                                 firstAtomIndex, lastAtomIndex,

+                                                 specialAtomIndexes);

+    }

+    if (group == null)

+      group = new Group(chain, group3, seqcode, firstAtomIndex, lastAtomIndex);

+    return group;

+  }

+

+  void propogateGroup(Group group, int firstAtomIndex, int lastAtomIndex) {

+    for (int i = firstAtomIndex; i <= lastAtomIndex; ++i)

+      atoms[i].setGroup(group);

+  }

 }


--- GroupBuilder.java DELETED ---