[Jmol-commits] CVS: Jmol/src/org/openscience/jmol/viewer/managers ColorManager.java,1.47,1.48 ModelManager.java,1.78,1.79

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

Update of /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/managers
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv4560/src/org/openscience/jmol/viewer/managers

Modified Files:
	ColorManager.java ModelManager.java 
Log Message:
lots of cleanup


Index: ColorManager.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/managers/ColorManager.java,v
retrieving revision 1.47
retrieving revision 1.48
diff -u -r1.47 -r1.48
--- ColorManager.java	18 May 2004 21:11:14 -0000	1.47
+++ ColorManager.java	28 May 2004 14:44:19 -0000	1.48
@@ -278,7 +278,7 @@
       break;
     case JmolConstants.PALETTE_STRUCTURE:
       argb = JmolConstants.
-        argbsPdbStructure[atom.getSecondaryStructureType()];
+        argbsPdbStructure[atom.getProteinStructureType()];
       break;
     case JmolConstants.PALETTE_AMINO:
       {

Index: ModelManager.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/managers/ModelManager.java,v
retrieving revision 1.78
retrieving revision 1.79
diff -u -r1.78 -r1.79
--- ModelManager.java	27 May 2004 23:03:50 -0000	1.78
+++ ModelManager.java	28 May 2004 14:44:19 -0000	1.79
@@ -201,9 +201,11 @@
     this.minBondDistance = minBondDistance;
   }
 
+  /*
   public void deleteAtom(int atomIndex) {
     frame.deleteAtom(atomIndex);
   }
+  */
 
   public boolean frankClicked(int x, int y) {
     return (getShapeSize(JmolConstants.SHAPE_FRANK) != 0 &&
@@ -293,7 +295,7 @@
   ////////////////////////////////////////////////////////////////
 
   public String getAtomInfo(int i) {
-    return frame.atoms[i].getInfo();
+    return frame.getAtomAt(i).getInfo();
   }
 
 /*
@@ -309,66 +311,66 @@
 */
 
   public String getElementSymbol(int i) {
-    return frame.atoms[i].getElementSymbol();
+    return frame.getAtomAt(i).getElementSymbol();
   }
 
   public int getElementNumber(int i) {
-    return frame.atoms[i].getElementNumber();
+    return frame.getAtomAt(i).getElementNumber();
   }
 
   public String getAtomName(int i) {
-    return frame.atoms[i].getAtomName();
+    return frame.getAtomAt(i).getAtomName();
   }
 
   public int getAtomNumber(int i) {
-    return frame.atoms[i].getAtomNumber();
+    return frame.getAtomAt(i).getAtomNumber();
   }
 
   public float getAtomX(int i) {
-    return frame.atoms[i].getAtomX();
+    return frame.getAtomAt(i).getAtomX();
   }
 
   public float getAtomY(int i) {
-    return frame.atoms[i].getAtomY();
+    return frame.getAtomAt(i).getAtomY();
   }
 
   public float getAtomZ(int i) {
-    return frame.atoms[i].getAtomZ();
+    return frame.getAtomAt(i).getAtomZ();
   }
 
   public Point3f getAtomPoint3f(int i) {
-    return frame.atoms[i].getPoint3f();
+    return frame.getAtomAt(i).getPoint3f();
   }
 
   public float getAtomRadius(int i) {
-    return frame.atoms[i].getRadius();
+    return frame.getAtomAt(i).getRadius();
   }
 
   public short getAtomColix(int i) {
-    return frame.atoms[i].getColix();
+    return frame.getAtomAt(i).getColix();
   }
 
   public Point3f getBondPoint3f1(int i) {
-    return frame.bonds[i].atom1.getPoint3f();
+    return frame.getBondAt(i).atom1.getPoint3f();
   }
 
   public Point3f getBondPoint3f2(int i) {
-    return frame.bonds[i].atom2.getPoint3f();
+    return frame.getBondAt(i).atom2.getPoint3f();
   }
 
   public float getBondRadius(int i) {
-    return frame.bonds[i].getRadius();
+    return frame.getBondAt(i).getRadius();
   }
 
   public short getBondOrder(int i) {
-    return frame.bonds[i].getOrder();
+    return frame.getBondAt(i).getOrder();
   }
 
   public short getBondColix1(int i) {
-    return frame.bonds[i].getColix1();
+    return frame.getBondAt(i).getColix1();
   }
 
   public short getBondColix2(int i) {
-    return frame.bonds[i].getColix2();
+    return frame.getBondAt(i).getColix2();
   }
 }