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[Jmol-commits] CVS: Jmol/src/org/openscience/jmol ClientAtomAdapter.java,1.1,1.2 DeprecatedAtomAdapter.java,1.1,1.2 DisplayControl.java,1.119,1.120 Distributor.java,1.17,1.18 LabelManager.java,1.11,1.12
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From: Michael T H. <mic...@us...> - 2003-08-12 18:42:37
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Update of /cvsroot/jmol/Jmol/src/org/openscience/jmol
In directory sc8-pr-cvs1:/tmp/cvs-serv23184/src/org/openscience/jmol
Modified Files:
ClientAtomAdapter.java DeprecatedAtomAdapter.java
DisplayControl.java Distributor.java LabelManager.java
Log Message:
eliminated AtomColors and tweaked ClientAtomAdapter interface
Index: ClientAtomAdapter.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/ClientAtomAdapter.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- ClientAtomAdapter.java 12 Aug 2003 14:38:42 -0000 1.1
+++ ClientAtomAdapter.java 12 Aug 2003 18:18:09 -0000 1.2
@@ -35,10 +35,10 @@
public final static int COLORSCHEME_MAX = 2;
public int getAtomicNumber(Object clientAtom);
- public String getAtomicSymbol(Object clientAtom);
- public String getAtomTypeName(Object clientAtom);
- public double getVanderwaalsRadius(Object clientAtom);
+ public String getAtomicSymbol(int atomicNumber, Object clientAtom);
+ public String getAtomTypeName(int atomicNumber, Object clientAtom);
+ public double getVanderwaalsRadius(int atomicNumber, Object clientAtom);
public Point3d getPoint3d(Object clientAtom);
public ProteinProp getProteinProp(Object clientAtom);
- public Color getColor(Object clientAtom, int colorScheme);
+ public Color getColor(int atomicNumber, Object clientAtom, int colorScheme);
}
Index: DeprecatedAtomAdapter.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/DeprecatedAtomAdapter.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- DeprecatedAtomAdapter.java 12 Aug 2003 14:38:42 -0000 1.1
+++ DeprecatedAtomAdapter.java 12 Aug 2003 18:18:09 -0000 1.2
@@ -45,15 +45,15 @@
return ((Atom)clientAtom).getAtomicNumber();
}
- public String getAtomicSymbol(Object clientAtom) {
+ public String getAtomicSymbol(int atomicNumber, Object clientAtom) {
return ((Atom)clientAtom).getSymbol();
}
- public String getAtomTypeName(Object clientAtom) {
+ public String getAtomTypeName(int atomicNumber, Object clientAtom) {
return ((Atom)clientAtom).getAtomTypeName();
}
- public double getVanderwaalsRadius(Object clientAtom) {
+ public double getVanderwaalsRadius(int atomicNumber, Object clientAtom) {
return ((Atom)clientAtom).getVanderwaalsRadius();
}
@@ -65,7 +65,7 @@
return ((Atom)clientAtom).getProteinProp();
}
- public Color getColor(Object clientAtom, int colorScheme) {
+ public Color getColor(int atomicNumber, Object clientAtom, int colorScheme) {
if (colorScheme >= colorSchemes.length ||
colorSchemes[colorScheme] == null)
colorScheme = 0;
Index: DisplayControl.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/DisplayControl.java,v
retrieving revision 1.119
retrieving revision 1.120
diff -u -r1.119 -r1.120
--- DisplayControl.java 12 Aug 2003 14:52:20 -0000 1.119
+++ DisplayControl.java 12 Aug 2003 18:18:09 -0000 1.120
@@ -1567,19 +1567,24 @@
return labelManager.styleLabel;
}
- public String getLabelAtom(Object clientAtom) {
+ public String getLabelAtom(int atomicNumber, Object clientAtom,
+ int atomIndex) {
return labelManager.getLabelAtom(labelManager.styleLabel,
- (Atom)clientAtom);
+ atomicNumber, clientAtom, atomIndex);
}
- public String getLabelAtom(byte styleLabel, Object clientAtom) {
- return labelManager.getLabelAtom(styleLabel,
- (Atom)clientAtom);
+ public String getLabelAtom(byte styleLabel,
+ int atomicNumber, Object clientAtom,
+ int atomIndex) {
+ return labelManager.getLabelAtom(styleLabel, atomicNumber, clientAtom,
+ atomIndex);
}
- public String getLabelAtom(String strLabel, Object clientAtom) {
- return labelManager.getLabelAtom(strLabel,
- (Atom)clientAtom);
+ public String getLabelAtom(String strLabel,
+ int atomicNumber, Object clientAtom,
+ int atomIndex) {
+ return labelManager.getLabelAtom(strLabel, atomicNumber, clientAtom,
+ atomIndex);
}
public void setLabelFontSize(int points) {
@@ -1671,16 +1676,16 @@
return clientAtomAdapter.getAtomicNumber(clientAtom);
}
- public String getAtomicSymbol(Object clientAtom) {
- return clientAtomAdapter.getAtomicSymbol(clientAtom);
+ public String getAtomicSymbol(int atomicNumber, Object clientAtom) {
+ return clientAtomAdapter.getAtomicSymbol(atomicNumber, clientAtom);
}
- public String getAtomTypeName(Object clientAtom) {
- return clientAtomAdapter.getAtomTypeName(clientAtom);
+ public String getAtomTypeName(int atomicNumber, Object clientAtom) {
+ return clientAtomAdapter.getAtomTypeName(atomicNumber, clientAtom);
}
- public double getVanderwaalsRadius(Object clientAtom) {
- return clientAtomAdapter.getVanderwaalsRadius(clientAtom);
+ public double getVanderwaalsRadius(int atomicNumber, Object clientAtom) {
+ return clientAtomAdapter.getVanderwaalsRadius(atomicNumber, clientAtom);
}
public Point3d getPoint3d(Object clientAtom) {
@@ -1691,12 +1696,14 @@
return clientAtomAdapter.getProteinProp(clientAtom);
}
- public short getColixAtom(Object clientAtom) {
- return Colix.getColix(clientAtomAdapter.getColor(clientAtom,
- colorManager.modeAtomColorProfile));
+ public short getColixAtom(int atomicNumber, Object clientAtom) {
+ return Colix.getColix(clientAtomAdapter.getColor(
+ atomicNumber, clientAtom, colorManager.modeAtomColorProfile));
}
- public short getColixAtom(byte mode, Object clientAtom) {
- return Colix.getColix(clientAtomAdapter.getColor(clientAtom, mode));
+ public short getColixAtom(int atomicNumber, Object clientAtom, byte scheme) {
+ return Colix.getColix(clientAtomAdapter.getColor(atomicNumber,
+ clientAtom,
+ scheme));
}
}
Index: Distributor.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/Distributor.java,v
retrieving revision 1.17
retrieving revision 1.18
diff -u -r1.17 -r1.18
--- Distributor.java 12 Aug 2003 14:38:42 -0000 1.17
+++ Distributor.java 12 Aug 2003 18:18:09 -0000 1.18
@@ -90,7 +90,9 @@
while (iter.hasNext()) {
AtomShape atomShape = iter.next();
atomShape.setLabel(control.getLabelAtom(styleLabel,
- atomShape.clientAtom));
+ atomShape.atomicNumber,
+ atomShape.clientAtom,
+ atomShape.atomIndex));
}
}
@@ -98,7 +100,9 @@
while (iter.hasNext()) {
AtomShape atomShape = iter.next();
atomShape.setLabel(control.getLabelAtom(strLabel,
- atomShape.clientAtom));
+ atomShape.atomicNumber,
+ atomShape.clientAtom,
+ atomShape.atomIndex));
}
}
@@ -108,7 +112,8 @@
while (iter.hasNext()) {
AtomShape atomShape = iter.next();
if (colixDots == 0)
- colixT = control.getColixAtom(atomShape.clientAtom);
+ colixT = control.getColixAtom(atomShape.atomicNumber,
+ atomShape.clientAtom);
atomShape.setColixMarDots(colixT, marDots);
}
}
Index: LabelManager.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/LabelManager.java,v
retrieving revision 1.11
retrieving revision 1.12
diff -u -r1.11 -r1.12
--- LabelManager.java 21 Jul 2003 20:19:22 -0000 1.11
+++ LabelManager.java 12 Aug 2003 18:18:09 -0000 1.12
@@ -78,27 +78,30 @@
this.pointsLabelFontSize = points;
}
- public String getLabelAtom(byte styleLabel, Atom atom) {
+ public String getLabelAtom(byte styleLabel,
+ int atomicNumber, Object clientAtom,
+ int atomIndex) {
String label = null;
switch (styleLabel) {
case DisplayControl.SYMBOLS:
- label = atom.getSymbol();
+ label = control.getAtomicSymbol(atomicNumber, clientAtom);
break;
case DisplayControl.TYPES:
- label = atom.getAtomTypeName();
+ label = control.getAtomTypeName(atomicNumber, clientAtom);
break;
case DisplayControl.NUMBERS:
- // Note that this is incremented by one for display purposes
- label = "" + (atom.getAtomNumber() + 1);
+ label = "" + atomIndex;
break;
}
return label;
}
- public String getLabelAtom(String strFormat, Atom atom) {
+ public String getLabelAtom(String strFormat,
+ int atomicNumber, Object clientAtom,
+ int atomIndex) {
if (strFormat == null || strFormat.equals(""))
return null;
- ProteinProp pprop = atom.getProteinProp();
+ ProteinProp pprop = control.getProteinProp(clientAtom);
String strLabel = "";
String strExpansion = "";
int ich = 0;
@@ -117,11 +120,11 @@
ch = strFormat.charAt(ich++);
switch (ch) {
case 'i':
- strExpansion = "" + atom.getAtomNumber() + 1;
+ strExpansion = "" + atomIndex;
break;
case 'a': // FIXME -- mth -- a is not the same as e
case 'e':
- strExpansion = atom.getSymbol();
+ strExpansion = control.getAtomicSymbol(atomicNumber, clientAtom);
break;
case 'b': // these two are the same
case 't':
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