[Jmol-commits] CVS: Jmol/src/org/openscience/jmol/viewer/datamodel Atom.java,1.22,1.23 AtomRenderer.java,1.20,1.21 BondRenderer.java,1.29,1.30 Frame.java,1.40,1.41

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

Update of /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/datamodel
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv22775/src/org/openscience/jmol/viewer/datamodel

Modified Files:
	Atom.java AtomRenderer.java BondRenderer.java Frame.java 
Log Message:
added Atom.VISIBILITY_FLAG - atoms that are not visible are now not selectable


Index: Atom.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/datamodel/Atom.java,v
retrieving revision 1.22
retrieving revision 1.23
diff -u -r1.22 -r1.23
--- Atom.java	28 Jan 2004 11:51:22 -0000	1.22
+++ Atom.java	5 Feb 2004 22:40:10 -0000	1.23
@@ -36,6 +36,8 @@
 
 public class Atom implements Bspt.Tuple {
 
+  public final static byte VISIBLE_FLAG = 1;
+
   public int atomIndex;
   public Object clientAtom;
   public PdbAtom pdbAtom;
@@ -44,7 +46,7 @@
   short x, y, z;
   short diameter;
   public byte atomicNumber;
-  public byte atomicCharge;
+  byte chargeAndFlags;
   short marAtom;
   short colixAtom;
   Bond[] bonds;
@@ -58,7 +60,7 @@
     this.atomIndex = atomIndex;
     this.clientAtom = clientAtom;
     this.atomicNumber = (byte) viewer.getAtomicNumber(clientAtom);
-    this.atomicCharge = (byte) viewer.getAtomicCharge(clientAtom);
+    this.chargeAndFlags = (byte)(viewer.getAtomicCharge(clientAtom) << 4);
     this.colixAtom = viewer.getColixAtom(this);
     setMarAtom(viewer.getMarAtom());
     this.point3f = new Point3f(viewer.getAtomX(clientAtom),
@@ -271,7 +273,7 @@
   }
 
   public int getAtomicCharge() {
-    return atomicCharge;
+    return chargeAndFlags >> 4;
   }
 
   public int getAtomno() {

Index: AtomRenderer.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/datamodel/AtomRenderer.java,v
retrieving revision 1.20
retrieving revision 1.21
diff -u -r1.20 -r1.21
--- AtomRenderer.java	31 Jan 2004 20:05:57 -0000	1.20
+++ AtomRenderer.java	5 Feb 2004 22:40:10 -0000	1.21
@@ -85,8 +85,11 @@
       return;
     boolean hasHalo = viewer.hasSelectionHalo(atom);
     int diameter = atom.diameter;
-    if (diameter == 0 && !hasHalo)
+    if (diameter == 0 && !hasHalo) {
+      atom.chargeAndFlags &= ~Atom.VISIBLE_FLAG;
       return;
+    }
+    atom.chargeAndFlags |= Atom.VISIBLE_FLAG;
     int effectiveDiameter = diameter;
     if (hasHalo) {
       int halowidth = diameter / 4;

Index: BondRenderer.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/datamodel/BondRenderer.java,v
retrieving revision 1.29
retrieving revision 1.30
diff -u -r1.29 -r1.30
--- BondRenderer.java	12 Jan 2004 15:51:42 -0000	1.29
+++ BondRenderer.java	5 Feb 2004 22:40:10 -0000	1.30
@@ -92,7 +92,9 @@
       return;
     int order = bond.order;
     Atom atomA = bond.atom1;
+    atomA.chargeAndFlags |= Atom.VISIBLE_FLAG;
     Atom atomB = bond.atom2;
+    atomB.chargeAndFlags |= Atom.VISIBLE_FLAG;
     if (bondsBackbone) {
       if (ssbondsBackbone && (order & JmolConstants.BOND_SULFUR_MASK) != 0) {
         // for ssbonds, always render the sidechain,

Index: Frame.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/datamodel/Frame.java,v
retrieving revision 1.40
retrieving revision 1.41
diff -u -r1.40 -r1.41
--- Frame.java	4 Feb 2004 23:38:19 -0000	1.40
+++ Frame.java	5 Feb 2004 22:40:10 -0000	1.41
@@ -458,6 +458,8 @@
     int r2Nearest = Integer.MAX_VALUE;
     for (int i = atomCount; --i >= 0; ) {
       Atom atom = atoms[i];
+      if ((atom.chargeAndFlags & Atom.VISIBLE_FLAG) == 0)
+        continue;
       int dx = atom.x - x;
       int dx2 = dx * dx;
       if (dx2 > r2Nearest)