Revision: 20367
http://sourceforge.net/p/jmol/code/20367
Author: hansonr
Date: 2015-03-07 17:51:32 +0000 (Sat, 07 Mar 2015)
Log Message:
-----------
Modified Paths:
--------------
branches/v14_2/Jmol/src/org/jmol/script/ScriptEval.java
branches/v14_2/Jmol/src/org/jmol/script/ScriptExpr.java
branches/v14_2/Jmol/src/org/jmol/script/ScriptMathProcessor.java
branches/v14_2/Jmol/src/org/jmol/scriptext/CmdExt.java
branches/v14_2/Jmol/src/org/jmol/scriptext/IsoExt.java
branches/v14_2/Jmol/src/org/jmol/scriptext/MathExt.java
branches/v14_2/Jmol/src/org/jmol/scriptext/SmilesExt.java
Modified: branches/v14_2/Jmol/src/org/jmol/script/ScriptEval.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/script/ScriptEval.java 2015-03-07
17:50:34 UTC (rev 20366)
+++ branches/v14_2/Jmol/src/org/jmol/script/ScriptEval.java 2015-03-07
17:51:32 UTC (rev 20367)
@@ -230,21 +230,6 @@
private static int iProcess;
- private JmolMathExtension mathExt;
- public JmolMathExtension getMathExt() {
- return (mathExt == null ? (mathExt = (JmolMathExtension)
getExt("Math")).init(this) : mathExt);
- }
-
- private JmolSmilesExtension smilesExt;
- public JmolSmilesExtension getSmilesExt() {
- return (smilesExt == null ? (smilesExt = (JmolSmilesExtension)
getExt("Smiles")).init(this) : smilesExt);
- }
-
- private JmolCmdExtension cmdIso;
- public JmolCmdExtension getIsoExt() {
- return (cmdIso == null ? (cmdIso = (JmolCmdExtension)
getExt("Iso")).init(this) : cmdIso);
- }
-
public ShapeManager sm;
public boolean isJS;
Modified: branches/v14_2/Jmol/src/org/jmol/script/ScriptExpr.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/script/ScriptExpr.java 2015-03-07
17:50:34 UTC (rev 20366)
+++ branches/v14_2/Jmol/src/org/jmol/script/ScriptExpr.java 2015-03-07
17:51:32 UTC (rev 20367)
@@ -23,6 +23,9 @@
import org.jmol.modelset.BondSet;
import org.jmol.modelset.Group;
import org.jmol.modelset.ModelSet;
+import org.jmol.scriptext.CmdExt;
+import org.jmol.scriptext.MathExt;
+import org.jmol.scriptext.SmilesExt;
import org.jmol.util.BSUtil;
import org.jmol.util.Elements;
import org.jmol.util.Escape;
@@ -49,11 +52,26 @@
public boolean debugHigh;
- private JmolCmdExtension cmdExt;
- public JmolCmdExtension getCmdExt() {
- return (cmdExt == null ? (cmdExt = (JmolCmdExtension)
getExt("Cmd")).init(this) : cmdExt);
+ private CmdExt cmdExt;
+ public CmdExt getCmdExt() {
+ return (cmdExt == null ? (cmdExt = (CmdExt) getExt("Cmd")).init(this) :
cmdExt);
}
+ private CmdExt isoExt;
+ public CmdExt getIsoExt() {
+ return (isoExt == null ? (isoExt = (CmdExt) getExt("Iso")).init(this) :
isoExt);
+ }
+
+ private MathExt mathExt;
+ public MathExt getMathExt() {
+ return (mathExt == null ? (mathExt = (MathExt) getExt("Math")).init(this)
: mathExt);
+ }
+
+ private SmilesExt smilesExt;
+ public SmilesExt getSmilesExt() {
+ return (smilesExt == null ? (smilesExt = (SmilesExt)
getExt("Smiles")).init(this) : smilesExt);
+ }
+
public Object getExt(String type) {
return Interface.getInterface("org.jmol.scriptext." + type + "Ext", vwr,
"script");
}
@@ -449,7 +467,7 @@
break;
//$FALL-THROUGH$
default:
- // turn x.y into x[y] prior to equal sign in special assignment
+ // turn x.y into x[y] prior to equal sign
rpn.addOp(T.tokenArrayOpen);
rpn.addXStr(optParameterAsString(++i));
rpn.addOp(T.tokenArrayClose);
Modified: branches/v14_2/Jmol/src/org/jmol/script/ScriptMathProcessor.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/script/ScriptMathProcessor.java
2015-03-07 17:50:34 UTC (rev 20366)
+++ branches/v14_2/Jmol/src/org/jmol/script/ScriptMathProcessor.java
2015-03-07 17:51:32 UTC (rev 20367)
@@ -841,7 +841,7 @@
// just exit; otherwise we add a new TRUE to xStack
if (!chk)
- return getMathExt().evaluate(this, op, args, tok);
+ return eval.getMathExt().evaluate(this, op, args, tok);
if (op.tok == T.propselector)
xPt--; // pop x in "x.func(...)"
return addXBool(true);
@@ -1660,7 +1660,7 @@
case T.stddev:
case T.sum:
case T.sum2:
- return addXObj(getMathExt().getMinMax(x2.getList(), op.intValue));
+ return addXObj(eval.getMathExt().getMinMax(x2.getList(), op.intValue));
case T.pop:
return addX(x2.pushPop(null, null));
case T.sort:
@@ -1755,10 +1755,6 @@
return false;
}
- private JmolMathExtension getMathExt() {
- return ((ScriptEval) eval).getMathExt();
- }
-
public SV evalOp(T token) throws ScriptException {
if (!addOp(token) || !operate())
return null;
Modified: branches/v14_2/Jmol/src/org/jmol/scriptext/CmdExt.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/scriptext/CmdExt.java 2015-03-07
17:50:34 UTC (rev 20366)
+++ branches/v14_2/Jmol/src/org/jmol/scriptext/CmdExt.java 2015-03-07
17:51:32 UTC (rev 20367)
@@ -45,7 +45,6 @@
import org.jmol.modelset.StateScript;
import org.jmol.modelset.Text;
import org.jmol.modelset.TickInfo;
-import org.jmol.script.JmolCmdExtension;
import org.jmol.script.SV;
import org.jmol.script.ScriptCompiler;
import org.jmol.script.ScriptContext;
@@ -90,7 +89,7 @@
import org.jmol.viewer.Viewer;
import org.jmol.viewer.Viewer.ACCESS;
-public class CmdExt implements JmolCmdExtension {
+public class CmdExt {
protected Viewer vwr;
protected ScriptEval e;
protected boolean chk;
@@ -103,14 +102,12 @@
// used by Reflection
}
- @Override
- public JmolCmdExtension init(Object se) {
+ public CmdExt init(Object se) {
e = (ScriptEval) se;
vwr = e.vwr;
return this;
}
- @Override
public String dispatch(int iTok, boolean b, T[] st) throws ScriptException {
chk = e.chk;
slen = e.slen;
@@ -3013,7 +3010,6 @@
* @param shapeManager
* @return true if successful; false if not
*/
- @Override
public boolean evalParallel(ScriptContext context,
ShapeManager shapeManager) {
ScriptEval se = new ScriptEval().setViewer(vwr);
@@ -4566,7 +4562,6 @@
return fmax;
}
- @Override
@SuppressWarnings("static-access")
public Object getBitsetIdent(BS bs, String label, Object tokenValue,
boolean useAtomMap, int index,
Modified: branches/v14_2/Jmol/src/org/jmol/scriptext/IsoExt.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/scriptext/IsoExt.java 2015-03-07
17:50:34 UTC (rev 20366)
+++ branches/v14_2/Jmol/src/org/jmol/scriptext/IsoExt.java 2015-03-07
17:51:32 UTC (rev 20367)
@@ -36,7 +36,6 @@
import org.jmol.java.BS;
import org.jmol.modelset.Atom;
import org.jmol.quantum.QS;
-import org.jmol.script.JmolCmdExtension;
import org.jmol.script.SV;
import org.jmol.script.ScriptError;
import org.jmol.script.ScriptEval;
@@ -73,8 +72,8 @@
public IsoExt() {}
- @Override
- public JmolCmdExtension init(Object eval) {
+ @Override
+ public IsoExt init(Object eval) {
e = (ScriptEval) eval;
vwr = e.vwr;
return this;
Modified: branches/v14_2/Jmol/src/org/jmol/scriptext/MathExt.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/scriptext/MathExt.java 2015-03-07
17:50:34 UTC (rev 20366)
+++ branches/v14_2/Jmol/src/org/jmol/scriptext/MathExt.java 2015-03-07
17:51:32 UTC (rev 20367)
@@ -41,7 +41,6 @@
import org.jmol.modelset.Atom;
import org.jmol.modelset.BondSet;
import org.jmol.modelset.ModelSet;
-import org.jmol.script.JmolMathExtension;
import org.jmol.script.SV;
import org.jmol.script.ScriptEval;
import org.jmol.script.ScriptException;
@@ -76,7 +75,7 @@
import org.jmol.viewer.JC;
import org.jmol.viewer.Viewer;
-public class MathExt implements JmolMathExtension {
+public class MathExt {
private Viewer vwr;
private ScriptEval e;
@@ -85,8 +84,7 @@
// used by Reflection
}
- @Override
- public JmolMathExtension init(Object se) {
+ public MathExt init(Object se) {
e = (ScriptEval) se;
vwr = e.vwr;
return this;
@@ -95,7 +93,6 @@
///////////// ScriptMathProcessor extensions ///////////
- @Override
public boolean evaluate(ScriptMathProcessor mp, T op, SV[] args, int tok)
throws ScriptException {
switch (tok) {
@@ -2064,7 +2061,7 @@
return false;
if (rand == null)
rand = new Random();
- float lower = 0, upper = 1, seed = Float.NaN;
+ float lower = 0, upper = 1;
switch (args.length) {
case 3:
rand.setSeed((int) SV.fValue(args[2]));
@@ -2705,7 +2702,6 @@
}
- @Override
@SuppressWarnings("unchecked")
public Object getMinMax(Object floatOrSVArray, int tok) {
float[] data = null;
@@ -2915,7 +2911,6 @@
return null;
}
- @Override
public BS setContactBitSets(BS bsA, BS bsB, boolean localOnly,
float distance, RadiusData rd,
boolean warnMultiModel) {
Modified: branches/v14_2/Jmol/src/org/jmol/scriptext/SmilesExt.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/scriptext/SmilesExt.java 2015-03-07
17:50:34 UTC (rev 20366)
+++ branches/v14_2/Jmol/src/org/jmol/scriptext/SmilesExt.java 2015-03-07
17:51:32 UTC (rev 20367)
@@ -29,7 +29,6 @@
import org.jmol.java.BS;
import org.jmol.modelset.Atom;
import org.jmol.modelset.BondSet;
-import org.jmol.script.JmolSmilesExtension;
import org.jmol.script.ScriptEval;
import org.jmol.script.ScriptException;
import org.jmol.util.BSUtil;
@@ -43,7 +42,7 @@
import javajs.util.M4;
import javajs.util.P3;
-public class SmilesExt implements JmolSmilesExtension {
+public class SmilesExt {
private ScriptEval e;
private SmilesMatcherInterface sm;
@@ -52,8 +51,7 @@
// used by Reflection
}
- @Override
- public JmolSmilesExtension init(Object se) {
+ public SmilesExt init(Object se) {
e = (ScriptEval) se;
sm = e.vwr.getSmilesMatcher();
return this;
@@ -81,7 +79,6 @@
* @return standard deviation
* @throws ScriptException
*/
- @Override
public float getSmilesCorrelation(BS bsA, BS bsB, String smiles,
Lst<P3> ptsA, Lst<P3> ptsB, M4 m4,
Lst<BS> vReturn, boolean isSmarts,
@@ -161,7 +158,6 @@
return 0;
}
- @Override
public Object getSmilesMatches(String pattern, String smiles, BS bsSelected,
BS bsMatch3D, boolean isSmarts,
boolean asOneBitset) throws ScriptException {
@@ -238,7 +234,6 @@
return list;
}
- @Override
public float[] getFlexFitList(BS bs1, BS bs2, String smiles1,
boolean isSmarts) throws ScriptException {
int[][] mapSet = AU.newInt2(2);
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