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From: <ha...@us...> - 2006-11-23 14:59:39
|
Revision: 6302
http://svn.sourceforge.net/jmol/?rev=6302&view=rev
Author: hansonr
Date: 2006-11-23 06:59:38 -0800 (Thu, 23 Nov 2006)
Log Message:
-----------
load!
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/viewer/Eval.java
Modified: trunk/Jmol/src/org/jmol/viewer/Eval.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Eval.java 2006-11-23 07:48:15 UTC (rev 6301)
+++ trunk/Jmol/src/org/jmol/viewer/Eval.java 2006-11-23 14:59:38 UTC (rev 6302)
@@ -2550,13 +2550,16 @@
dataLabelString = new String[2];
dataLabelString[0] = dataLabel;
dataLabelString[1] = dataString;
- viewer.setData(dataType, dataLabelString);
- if (dataType.equalsIgnoreCase("model")) {
+ boolean isModel = dataType.equalsIgnoreCase("model");
+ if (!isSyntaxCheck || isScriptCheck && isModel)
+ viewer.setData(dataType, dataLabelString);
+ if (isModel) {
// only if first character is "|" do we consider "|" to be new line
char newLine = viewer.getInlineChar();
if (dataString.length() > 0 && dataString.charAt(0) != newLine)
newLine = '\0';
- viewer.loadInline(dataString, newLine);
+ if (!isSyntaxCheck || isScriptCheck)
+ viewer.loadInline(dataString, newLine);
return;
}
}
@@ -2637,7 +2640,8 @@
if (i == 0 || filename.length() == 0)
filename = viewer.getFullPathName();
loadScript.append(" " + StateManager.escape(filename) + ";");
- viewer.openFile(filename, params, loadScript.toString());
+ if (!isSyntaxCheck || isScriptCheck)
+ viewer.openFile(filename, params, loadScript.toString());
} else if (statement[i + 1].tok == Token.leftbrace
|| statement[i + 1].tok == Token.integer) {
filename = (String) statement[i++].value;
@@ -2696,7 +2700,8 @@
}
}
loadScript.append(";");
- viewer.openFile(filename, params, loadScript.toString());
+ if (!isSyntaxCheck || isScriptCheck)
+ viewer.openFile(filename, params, loadScript.toString());
} else {
String modelName = (String) statement[i].value;
i++;
@@ -2709,8 +2714,11 @@
i++;
}
loadScript.append(";");
- viewer.openFiles(modelName, filenames, loadScript.toString());
+ if (!isSyntaxCheck || isScriptCheck)
+ viewer.openFiles(modelName, filenames, loadScript.toString());
}
+ if (isSyntaxCheck && !isScriptCheck)
+ return;
String errMsg = viewer.getOpenFileError();
// int millis = (int)(System.currentTimeMillis() - timeBegin);
// Logger.debug("!!!!!!!!! took " + millis + " ms");
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From: <ha...@us...> - 2006-11-29 15:51:09
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Revision: 6355
http://svn.sourceforge.net/jmol/?rev=6355&view=rev
Author: hansonr
Date: 2006-11-29 07:51:07 -0800 (Wed, 29 Nov 2006)
Log Message:
-----------
bug fix "set bondMode or"
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/viewer/Eval.java
Modified: trunk/Jmol/src/org/jmol/viewer/Eval.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Eval.java 2006-11-29 15:08:41 UTC (rev 6354)
+++ trunk/Jmol/src/org/jmol/viewer/Eval.java 2006-11-29 15:51:07 UTC (rev 6355)
@@ -4516,7 +4516,7 @@
default:
invalidArgument();
}
- setBooleanProperty("bondSelelectionModeOr", bondmodeOr);
+ setBooleanProperty("bondModeOr", bondmodeOr);
}
void setSelectionHalo(int pt) throws ScriptException {
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From: <ha...@us...> - 2006-12-01 17:18:47
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Revision: 6361
http://svn.sourceforge.net/jmol/?rev=6361&view=rev
Author: hansonr
Date: 2006-12-01 09:17:56 -0800 (Fri, 01 Dec 2006)
Log Message:
-----------
cruel
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/viewer/Eval.java
Modified: trunk/Jmol/src/org/jmol/viewer/Eval.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Eval.java 2006-12-01 17:02:43 UTC (rev 6360)
+++ trunk/Jmol/src/org/jmol/viewer/Eval.java 2006-12-01 17:17:56 UTC (rev 6361)
@@ -5055,7 +5055,7 @@
}
if (type.equals("image")) {
if (fileName != null && fileName.indexOf(".") >= 0)
- type = filename.substring(fileName.lastIndexOf(".") + 1).toUpperCase();
+ type = fileName.substring(fileName.lastIndexOf(".") + 1).toUpperCase();
else
type = "JPG";
}
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From: <ha...@us...> - 2006-12-01 17:22:43
|
Revision: 6362
http://svn.sourceforge.net/jmol/?rev=6362&view=rev
Author: hansonr
Date: 2006-12-01 09:22:38 -0800 (Fri, 01 Dec 2006)
Log Message:
-----------
what was "PDF" doing in there?
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/viewer/Eval.java
Modified: trunk/Jmol/src/org/jmol/viewer/Eval.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Eval.java 2006-12-01 17:17:56 UTC (rev 6361)
+++ trunk/Jmol/src/org/jmol/viewer/Eval.java 2006-12-01 17:22:38 UTC (rev 6362)
@@ -5059,7 +5059,7 @@
else
type = "JPG";
}
- if (";JPEG;JPG64;JPG;PDF;PNG;SPT;HIS;".indexOf(";" + type + ";") < 0)
+ if (";JPEG;JPG64;JPG;PPM;PNG;SPT;HIS;".indexOf(";" + type + ";") < 0)
evalError(GT._("write what? {0} or {1} \"filename\"", new Object[] {
"STATE|HISTORY|IMAGE CLIPBOARD", "JPG|JPG64|PNG|PPM|SPT" }));
if (!isSyntaxCheck)
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From: <ha...@us...> - 2006-12-23 14:36:46
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Revision: 6539
http://svn.sourceforge.net/jmol/?rev=6539&view=rev
Author: hansonr
Date: 2006-12-23 06:36:44 -0800 (Sat, 23 Dec 2006)
Log Message:
-----------
11.1: better set debugScript
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/viewer/Eval.java
Modified: trunk/Jmol/src/org/jmol/viewer/Eval.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Eval.java 2006-12-22 15:49:11 UTC (rev 6538)
+++ trunk/Jmol/src/org/jmol/viewer/Eval.java 2006-12-23 14:36:44 UTC (rev 6539)
@@ -72,6 +72,7 @@
boolean tQuiet;
boolean logMessages = false;
+ boolean debugScript = false;
Eval(Viewer viewer) {
compiler = new Compiler(viewer);
@@ -473,7 +474,8 @@
long timeBegin = 0;
int ifLevel = 0;
ifs[0] = true;
- logMessages = (!isSyntaxCheck && Logger.isActiveLevel(Logger.LEVEL_DEBUG));
+ debugScript = (!isSyntaxCheck && viewer.getDebugScript());
+ logMessages = (debugScript && Logger.isActiveLevel(Logger.LEVEL_DEBUG));
if (logMessages) {
timeBegin = System.currentTimeMillis();
viewer.scriptStatus("Eval.instructionDispatchLoop():" + timeBegin);
@@ -498,9 +500,10 @@
delay((long) nSecDelay * 1000);
Logger.info(getCommand());
}
- if (logMessages || viewer.getDebugScript())
+ if (debugScript)
logDebugScript();
- Logger.debug(token.toString());
+ if (logMessages)
+ Logger.debug(token.toString());
if (ifLevel > 0 && !ifs[ifLevel] && token.tok != Token.endifcmd
&& token.tok != Token.ifcmd && token.tok != Token.elsecmd)
continue;
@@ -851,9 +854,11 @@
void logDebugScript() {
strbufLog.setLength(0);
- Logger.debug(statement[0].toString());
- for (int i = 1; i < statementLength; ++i)
- Logger.debug(statement[i].toString());
+ if (logMessages) {
+ Logger.debug(statement[0].toString());
+ for (int i = 1; i < statementLength; ++i)
+ Logger.debug(statement[i].toString());
+ }
strbufLog.append(statement[0].value.toString());
for (int i = 1; i < statementLength; ++i) {
strbufLog.append(' ');
@@ -918,6 +923,8 @@
strbufLog.append("\"" + token.value + "\"");
continue;
default:
+ if (!logMessages)
+ break;
strbufLog.append(token.toString());
continue;
}
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From: <ha...@us...> - 2007-01-05 03:49:03
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Revision: 6581
http://svn.sourceforge.net/jmol/?rev=6581&view=rev
Author: hansonr
Date: 2007-01-04 19:49:00 -0800 (Thu, 04 Jan 2007)
Log Message:
-----------
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/viewer/Eval.java
Modified: trunk/Jmol/src/org/jmol/viewer/Eval.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Eval.java 2007-01-04 21:49:39 UTC (rev 6580)
+++ trunk/Jmol/src/org/jmol/viewer/Eval.java 2007-01-05 03:49:00 UTC (rev 6581)
@@ -5150,7 +5150,7 @@
if (statementLength > 1) {
String saveName = optParameterAsString(2);
if (getToken(1).tok != Token.orientation)
- checkLength3();
+ checkLength23();
switch (getToken(1).tok) {
case Token.orientation:
float timeSeconds = (statementLength > 3 ? floatParameter(3) : 0);
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From: <ha...@us...> - 2007-02-10 11:34:24
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Revision: 6758
http://svn.sourceforge.net/jmol/?rev=6758&view=rev
Author: hansonr
Date: 2007-02-10 03:34:21 -0800 (Sat, 10 Feb 2007)
Log Message:
-----------
11.1.10 final tweak
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/viewer/Eval.java
Modified: trunk/Jmol/src/org/jmol/viewer/Eval.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Eval.java 2007-02-10 11:26:01 UTC (rev 6757)
+++ trunk/Jmol/src/org/jmol/viewer/Eval.java 2007-02-10 11:34:21 UTC (rev 6758)
@@ -3619,7 +3619,7 @@
isSpin);
return;
}
- if (nPoints < 2) {
+ if (nPoints < 2 && !isSyntaxCheck) {
// rotate MOLECULAR
// rotate MOLECULAR (atom1)
// rotate MOLECULAR x 10 (atom1)
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From: <ha...@us...> - 2007-02-12 13:51:04
|
Revision: 6790
http://svn.sourceforge.net/jmol/?rev=6790&view=rev
Author: hansonr
Date: 2007-02-12 05:50:56 -0800 (Mon, 12 Feb 2007)
Log Message:
-----------
11.1.12 helpful message
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/viewer/Eval.java
Modified: trunk/Jmol/src/org/jmol/viewer/Eval.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Eval.java 2007-02-12 13:42:11 UTC (rev 6789)
+++ trunk/Jmol/src/org/jmol/viewer/Eval.java 2007-02-12 13:50:56 UTC (rev 6790)
@@ -841,6 +841,7 @@
break;
case Token.pause: //resume is done differently
pauseExecution();
+ viewer.scriptStatus("script execution paused -- type RESUME to continue.");
break;
default:
if ((token.tok & Token.unimplemented) != 0) {
@@ -3093,7 +3094,6 @@
String s = viewer.formatText(text);
Logger.warn(s);
if (!s.startsWith("_"))
-
viewer.scriptStatus(s);
}
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From: <ha...@us...> - 2007-02-12 16:54:31
|
Revision: 6793
http://svn.sourceforge.net/jmol/?rev=6793&view=rev
Author: hansonr
Date: 2007-02-12 08:54:29 -0800 (Mon, 12 Feb 2007)
Log Message:
-----------
11.1.12 better error handling during pause
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/viewer/Eval.java
Modified: trunk/Jmol/src/org/jmol/viewer/Eval.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Eval.java 2007-02-12 16:06:19 UTC (rev 6792)
+++ trunk/Jmol/src/org/jmol/viewer/Eval.java 2007-02-12 16:54:29 UTC (rev 6793)
@@ -491,11 +491,22 @@
String script = viewer.getInterruptScript();
if (script != "") {
resumePausedExecution();
- runScript(script);
+ error = false;
+ pc--; // in case there is an error, we point to the PAUSE command
+ try {
+ runScript(script);
+ } catch (Exception e) {
+ error = true;
+ errorMessage = e.toString();
+ }
+ pc++;
+ if (error)
+ viewer.scriptStatus(errorMessage);
pauseExecution();
}
}
} catch (Exception e) {
+
}
Logger.debug("script execution resumed");
}
@@ -526,6 +537,8 @@
if (lineEnd == 0)
lineEnd = Integer.MAX_VALUE;
for (; pc < aatoken.length && pc < pcEnd; pc++) {
+ if (!checkContinue())
+ break;
Token token = aatoken[pc][0];
statement = aatoken[pc];
if (linenumbers[pc] > lineEnd)
@@ -533,8 +546,6 @@
thisCommand = getCommand();
statementLength = statement.length;
iToken = 0;
- if (!checkContinue())
- break;
String script = viewer.getInterruptScript();
if (script != "")
runScript(script);
@@ -5121,6 +5132,8 @@
switch (statementLength) {
case 2:
setBooleanProperty(key, true);
+ if (!isSyntaxCheck)
+ showString(key + " = " + viewer.getParameterEscaped(key));
return;
case 3:
switch (statement[2].tok) {
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From: <ha...@us...> - 2007-02-17 23:33:36
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Revision: 6857
http://svn.sourceforge.net/jmol/?rev=6857&view=rev
Author: hansonr
Date: 2007-02-17 15:33:34 -0800 (Sat, 17 Feb 2007)
Log Message:
-----------
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/viewer/Eval.java
Modified: trunk/Jmol/src/org/jmol/viewer/Eval.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Eval.java 2007-02-17 23:25:43 UTC (rev 6856)
+++ trunk/Jmol/src/org/jmol/viewer/Eval.java 2007-02-17 23:33:34 UTC (rev 6857)
@@ -5013,7 +5013,7 @@
* ==============================================================
*/
-void set() throws ScriptException {
+ void set() throws ScriptException {
if (statementLength == 1) {
showString(viewer.getAllSettings());
return;
@@ -5198,22 +5198,23 @@
if (setParameter(key)) {
if (isSyntaxCheck)
return;
- } else {
- Object v = parameterExpression((getToken(2).tok == Token.opEQ ? 3 : 2), false);
+ } else {
+ Object v = parameterExpression((getToken(2).tok == Token.opEQ ? 3 : 2),
+ false);
if (isSyntaxCheck)
return;
if (v instanceof Boolean) {
- setBooleanProperty(key, ((Boolean)v).booleanValue());
+ setBooleanProperty(key, ((Boolean) v).booleanValue());
} else if (v instanceof Integer) {
- setIntProperty(key, ((Integer)v).intValue());
+ setIntProperty(key, ((Integer) v).intValue());
} else if (v instanceof Float) {
- setFloatProperty(key, ((Float)v).floatValue());
+ setFloatProperty(key, ((Float) v).floatValue());
} else if (v instanceof String) {
- setStringProperty(key, (String)v);
+ setStringProperty(key, (String) v);
} else if (v instanceof Point3f) {
- drawPoint(key, (Point3f)v, false);
- showString("draw " + key + " " + StateManager.escape((Point3f)v)
- + "; draw off");
+ drawPoint(key, (Point3f) v, false);
+ showString("draw " + key + " " + StateManager.escape((Point3f) v)
+ + " off;");
return;
}
}
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From: <ha...@us...> - 2007-02-21 02:39:55
|
Revision: 6886
http://svn.sourceforge.net/jmol/?rev=6886&view=rev
Author: hansonr
Date: 2007-02-20 18:39:54 -0800 (Tue, 20 Feb 2007)
Log Message:
-----------
better coding
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/viewer/Eval.java
Modified: trunk/Jmol/src/org/jmol/viewer/Eval.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Eval.java 2007-02-21 01:57:45 UTC (rev 6885)
+++ trunk/Jmol/src/org/jmol/viewer/Eval.java 2007-02-21 02:39:54 UTC (rev 6886)
@@ -7994,7 +7994,8 @@
}
/// Reverse Polish Notation Engine for IF, SET, and %{...} -- Bob Hanson 2/16/2007
- /// Just a simple RPN processor that can handle boolean, int, float, String, and Point3f
+ /// Just a simple RPN processor that can handle
+ /// boolean, int, float, String, Point3f, and BitSet
class Rpn {
@@ -8045,60 +8046,47 @@
}
boolean addOp(Token op) throws ScriptException {
+
+ // was an operand entered last?
+
switch (op.tok) {
case Token.opNot:
case Token.leftparen:
if (wasX)
return false;
break;
- case Token.rightparen:
- if (parenCount == 0 || !wasX)
- return false;
- if (oPt >= 0 && oStack[oPt].tok == Token.leftparen) {
- oPt--;
- return wasX = true;
- }
- break;
- case Token.rightsquare:
- if (squareCount == 0 || !wasX)
- return false;
- if (oPt >= 0 && oStack[oPt].tok == Token.leftsquare) {
- oPt--;
- doBitsetSelect();
- return wasX = true;
- }
- break;
default:
if (!wasX)
return false;
break;
}
+ //do we need to operate?
+
while (oPt >= 0 && op.tok != Token.leftparen
&& op.tok != Token.leftsquare && op.tok != Token.opNot
&& Token.prec(oStack[oPt]) >= Token.prec(op)) {
- if (op.tok == Token.rightparen) {
- if (parenCount == 0)
+
+ // ) and ] must wait until matching ( or [ is found
+
+ if (op.tok == Token.rightparen && oStack[oPt].tok == Token.leftparen
+ || op.tok == Token.rightsquare
+ && oStack[oPt].tok == Token.leftsquare) {
+ if (op.tok == Token.rightsquare && !doBitsetSelect())
return false;
- if (oStack[oPt].tok == Token.leftparen) {
- parenCount--;
- oPt--;
- break;
- }
- } else if (op.tok == Token.rightsquare) {
- if (oStack[oPt].tok == Token.leftsquare) {
- if (squareCount == 0)
- return false;
- squareCount--;
- oPt--;
- return doBitsetSelect();
- }
- }
+ break;
+ }
+
+ // if not, it's time to operate
+
if (!operate(op.tok))
return false;
-
+
}
+ // fix up counts and operand flag
+ // right ) and ] are not added to the stack
+
switch (op.tok) {
case Token.leftparen:
parenCount++;
@@ -8107,17 +8095,22 @@
squareCount++;
break;
case Token.rightparen:
+ wasX = true;
+ oPt--;
+ return (parenCount-- > 0);
case Token.rightsquare:
wasX = true;
- break;
+ oPt--;
+ return (squareCount-- > 0);
case Token.propselector:
wasX = (op.intValue != Token.distance && op.intValue != Token.label);
break;
default:
wasX = false;
}
- if (op.tok == Token.rightparen || op.tok == Token.rightsquare)
- return true;
+
+ //add the operator if possible
+
if (++oPt == maxLevel)
stackOverflow();
oStack[oPt] = op;
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From: <ha...@us...> - 2007-02-21 17:30:15
|
Revision: 6888
http://svn.sourceforge.net/jmol/?rev=6888&view=rev
Author: hansonr
Date: 2007-02-21 09:14:44 -0800 (Wed, 21 Feb 2007)
Log Message:
-----------
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/viewer/Eval.java
Modified: trunk/Jmol/src/org/jmol/viewer/Eval.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Eval.java 2007-02-21 17:14:14 UTC (rev 6887)
+++ trunk/Jmol/src/org/jmol/viewer/Eval.java 2007-02-21 17:14:44 UTC (rev 6888)
@@ -8119,7 +8119,7 @@
boolean addOp(Token op) throws ScriptException {
- dumpStacks();
+ //dumpStacks();
// Do we have the appropriate context for this operator?
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From: <ha...@us...> - 2007-02-21 21:44:15
|
Revision: 6900
http://svn.sourceforge.net/jmol/?rev=6900&view=rev
Author: hansonr
Date: 2007-02-21 13:44:12 -0800 (Wed, 21 Feb 2007)
Log Message:
-----------
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/viewer/Eval.java
Modified: trunk/Jmol/src/org/jmol/viewer/Eval.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Eval.java 2007-02-21 21:43:45 UTC (rev 6899)
+++ trunk/Jmol/src/org/jmol/viewer/Eval.java 2007-02-21 21:44:12 UTC (rev 6900)
@@ -4982,7 +4982,7 @@
}
BitSet bitSetForModelNumberSet(int[] frameList, int nFrames) {
-1 BitSet bs = new BitSet();
+ BitSet bs = new BitSet();
if (isSyntaxCheck)
return bs;
int modelCount = viewer.getModelCount();
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From: <ha...@us...> - 2007-02-23 19:51:20
|
Revision: 6920
http://svn.sourceforge.net/jmol/?rev=6920&view=rev
Author: hansonr
Date: 2007-02-23 11:51:15 -0800 (Fri, 23 Feb 2007)
Log Message:
-----------
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/viewer/Eval.java
Modified: trunk/Jmol/src/org/jmol/viewer/Eval.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Eval.java 2007-02-23 19:50:43 UTC (rev 6919)
+++ trunk/Jmol/src/org/jmol/viewer/Eval.java 2007-02-23 19:51:15 UTC (rev 6920)
@@ -3565,8 +3565,10 @@
void reset() throws ScriptException {
if (isSyntaxCheck)
return;
- if (statementLength == 1)
+ if (statementLength == 1) {
viewer.reset();
+ return;
+ }
String var = parameterAsString(1);
if (var.charAt(0) == '_')
invalidArgument();
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From: <ha...@us...> - 2007-02-25 23:01:10
|
Revision: 6933
http://svn.sourceforge.net/jmol/?rev=6933&view=rev
Author: hansonr
Date: 2007-02-25 15:01:09 -0800 (Sun, 25 Feb 2007)
Log Message:
-----------
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/viewer/Eval.java
Modified: trunk/Jmol/src/org/jmol/viewer/Eval.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Eval.java 2007-02-25 22:40:41 UTC (rev 6932)
+++ trunk/Jmol/src/org/jmol/viewer/Eval.java 2007-02-25 23:01:09 UTC (rev 6933)
@@ -8508,18 +8508,18 @@
}
boolean evaluateDistance(Token[] args) throws ScriptException {
- Token x2 = getX();
+ Token x1 = getX();
if (args.length != 1)
return false;
+ Token x2 = args[0];
Point3f pt = ptValue(x2);
Point4f plane = planeValue(x2);
- Token x1 = args[0];
if (x1.tok == Token.bitset)
return addX(getBitsetAverage(Token.bsSelect(x1), Token.distance, pt,
plane, (x1.intValue >= 0), null));
else if (x1.tok == Token.xyz)
- return addX(plane == null ? pt.distance((Point3f) x1.value)
- : Graphics3D.distanceToPlane(plane, (Point3f) x1.value));
+ return addX(plane == null ? pt.distance(ptValue(x1))
+ : Graphics3D.distanceToPlane(plane, ptValue(x1)));
return false;
}
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|
|
From: <ha...@us...> - 2007-02-26 03:17:46
|
Revision: 6935
http://svn.sourceforge.net/jmol/?rev=6935&view=rev
Author: hansonr
Date: 2007-02-25 19:17:44 -0800 (Sun, 25 Feb 2007)
Log Message:
-----------
11.1.15 operation order fix
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/viewer/Eval.java
Modified: trunk/Jmol/src/org/jmol/viewer/Eval.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Eval.java 2007-02-26 01:38:15 UTC (rev 6934)
+++ trunk/Jmol/src/org/jmol/viewer/Eval.java 2007-02-26 03:17:44 UTC (rev 6935)
@@ -5533,6 +5533,7 @@
Token getBitsetPropertySelector(int i) throws ScriptException {
int tok = getToken(++i).tok;
+ String s = parameterAsString(i).toLowerCase();
switch (tok) {
case Token.bonds:
case Token.atom:
@@ -5544,7 +5545,6 @@
case Token.list:
break;
case Token.identifier:
- String s = parameterAsString(i).toLowerCase();
if (s.equals("x"))
tok = Token.atomX;
else if (s.equals("y"))
@@ -5568,7 +5568,7 @@
if (!Compiler.tokAttr(tok, Token.atomproperty))
invalidArgument();
}
- return new Token(Token.propselector, tok);
+ return new Token(Token.propselector, tok, s);
}
Object getBitsetAverage(BitSet bs, int tok, Point3f ptRef, Point4f planeRef, boolean isAtoms,
@@ -8281,7 +8281,7 @@
Logger.info("\naddOp: " + op);
dumpStacks();
}
-
+ Token newOp = null;
boolean isLeftOp = false;
boolean isDotSelector = (op.tok == Token.propselector);
boolean isMathFunc = (Compiler.tokAttr(op.tok, Token.mathfunc) || isDotSelector
@@ -8292,10 +8292,8 @@
switch (op.tok) {
case Token.leftsquare: // two contexts: [x x].distance or {....}[n]
isLeftOp = !wasX;
- if (isLeftOp) {
- op = new Token(Token.leftsquare, 0);
- addX(op);
- }
+ if (isLeftOp)
+ op = newOp = new Token(Token.leftsquare, 0);
break;
case Token.hyphen:
if (wasX)
@@ -8310,7 +8308,7 @@
if (isMathFunc) {
if (!isDotSelector && wasX)
return false;
- addX(op);
+ newOp = op;
isLeftOp = true;
wasX = false;
}
@@ -8324,13 +8322,14 @@
//do we need to operate?
while (oPt >= 0
- && (!isLeftOp && op.tok != Token.leftsquare || op.tok == Token.leftsquare
+ && (!(isLeftOp || op.tok == Token.leftsquare) ||
+ (op.tok == Token.propselector || op.tok == Token.leftsquare)
&& oStack[oPt].tok == Token.propselector)
&& Token.prec(oStack[oPt]) >= Token.prec(op)) {
if (logMessages) {
dumpStacks();
- Logger.info("operating, oPt=" + oPt + " isLeftOp=" + isLeftOp
+ Logger.info("\noperating, oPt=" + oPt + " isLeftOp=" + isLeftOp
+ " oStack[oPt]=" + Token.nameOf(oStack[oPt].tok) + "/"
+ Token.prec(oStack[oPt]) + " op=" + Token.nameOf(op.tok) + "/"
+ Token.prec(op));
@@ -8358,6 +8357,11 @@
}
+ // now add a marker on the xStack if necessary
+
+ if (newOp != null)
+ addX(newOp);
+
// fix up counts and operand flag
// right ) and ] are not added to the stack
@@ -8523,21 +8527,40 @@
return false;
}
+ boolean evaluateMeasure(Token[] args, boolean isAngle) throws ScriptException {
+ int nPoints = args.length;
+ if (nPoints < (isAngle ? 3 : 2) || nPoints > (isAngle ? 4 : 2))
+ return false;
+ Point3f[] pts = new Point3f[nPoints];
+ for (int i = 0; i < nPoints; i++)
+ pts[i] = ptValue(args[i]);
+ switch (nPoints) {
+ case 2:
+ return addX(pts[0].distance(pts[1]));
+ case 3:
+ return addX(Measurement.computeAngle(pts[0], pts[1], pts[2], true));
+ case 4:
+ return addX(Measurement.computeTorsion(pts[0], pts[1], pts[2], pts[3], true));
+ }
+ return false;
+ }
+
boolean evaluateFind(Token[] args) throws ScriptException {
- Token x2 = getX();
+ Token x1 = getX();
if (args.length != 1)
return false;
- Token x1 = args[0];
+ Token x2 = args[0];
if (x1.tok == Token.string && x2.tok == Token.string)
return addX(Token.sValue(x1).indexOf(Token.sValue(x2)) + 1);
return false;
}
boolean evaluateLabel(Token[] args) throws ScriptException {
- Token x2 = getX();
+ System.out.println("eval label");
+ Token x1 = getX();
if (args.length != 1)
return false;
- Token x1 = args[0];
+ Token x2 = args[0];
if (x1.tok != Token.bitset || x2.tok != Token.string)
return false;
return addX(getBitsetIdent(Token.bsSelect(x1), Token.sValue(x2),
@@ -8548,6 +8571,7 @@
// within ( distance, expression)
// within ( group, etc., expression)
// within ( plane or hkl or coord atomcenter atomcenter atomcenter )
+ System.out.println("eval within");
if (args.length < 1)
return false;
Object withinSpec = args[0].value;
@@ -8666,38 +8690,22 @@
}
boolean evaluateSubstructure(Token[] args) throws ScriptException {
+ System.out.println("eval subs");
if (isSyntaxCheck)
return true;
if (args.length != 1)
return false;
String smiles = Token.sValue(args[0]);
PatternMatcher matcher = new PatternMatcher(viewer);
+ BitSet bs = new BitSet();
try {
- return addX(matcher.getSubstructureSet(smiles));
+ bs = matcher.getSubstructureSet(smiles);
} catch (InvalidSmilesException e) {
evalError(e.getMessage());
}
- return false;
+ return addX(bs);
}
- boolean evaluateMeasure(Token[] args, boolean isAngle) throws ScriptException {
- int nPoints = args.length;
- if (nPoints < (isAngle ? 3 : 2) || nPoints > (isAngle ? 4 : 2))
- return false;
- Point3f[] pts = new Point3f[nPoints];
- for (int i = 0; i < nPoints; i++)
- pts[i] = ptValue(args[i]);
- switch (nPoints) {
- case 2:
- return addX(pts[0].distance(pts[1]));
- case 3:
- return addX(Measurement.computeAngle(pts[0], pts[1], pts[2], true));
- case 4:
- return addX(Measurement.computeTorsion(pts[0], pts[1], pts[2], pts[3], true));
- }
- return false;
- }
-
boolean operate(int thisOp) throws ScriptException {
Token op = oStack[oPt--];
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|
|
From: <ha...@us...> - 2007-02-26 03:27:13
|
Revision: 6937
http://svn.sourceforge.net/jmol/?rev=6937&view=rev
Author: hansonr
Date: 2007-02-25 19:27:12 -0800 (Sun, 25 Feb 2007)
Log Message:
-----------
11.1.15 bug fix
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/viewer/Eval.java
Modified: trunk/Jmol/src/org/jmol/viewer/Eval.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Eval.java 2007-02-26 03:18:10 UTC (rev 6936)
+++ trunk/Jmol/src/org/jmol/viewer/Eval.java 2007-02-26 03:27:12 UTC (rev 6937)
@@ -8515,6 +8515,8 @@
Token x1 = getX();
if (args.length != 1)
return false;
+ if (isSyntaxCheck)
+ return addX(1f);
Token x2 = args[0];
Point3f pt = ptValue(x2);
Point4f plane = planeValue(x2);
@@ -8531,6 +8533,9 @@
int nPoints = args.length;
if (nPoints < (isAngle ? 3 : 2) || nPoints > (isAngle ? 4 : 2))
return false;
+ if (isSyntaxCheck)
+ return addX(1f);
+
Point3f[] pts = new Point3f[nPoints];
for (int i = 0; i < nPoints; i++)
pts[i] = ptValue(args[i]);
@@ -8549,6 +8554,8 @@
Token x1 = getX();
if (args.length != 1)
return false;
+ if (isSyntaxCheck)
+ return addX((int)1);
Token x2 = args[0];
if (x1.tok == Token.string && x2.tok == Token.string)
return addX(Token.sValue(x1).indexOf(Token.sValue(x2)) + 1);
@@ -8556,10 +8563,12 @@
}
boolean evaluateLabel(Token[] args) throws ScriptException {
- System.out.println("eval label");
+ //System.out.println("eval label");
Token x1 = getX();
if (args.length != 1)
return false;
+ if (isSyntaxCheck)
+ return addX("");
Token x2 = args[0];
if (x1.tok != Token.bitset || x2.tok != Token.string)
return false;
@@ -8571,11 +8580,12 @@
// within ( distance, expression)
// within ( group, etc., expression)
// within ( plane or hkl or coord atomcenter atomcenter atomcenter )
- System.out.println("eval within");
+ //System.out.println("eval within");
if (args.length < 1)
return false;
Object withinSpec = args[0].value;
String withinStr = "" + withinSpec;
+ BitSet bs = new BitSet();
float distance = 0;
boolean isSequence = false;
if (withinSpec instanceof String)
@@ -8589,7 +8599,8 @@
if (!isOneOf(withinStr,"plane;hkl;coord"))
return false;
}
- BitSet bs = new BitSet();
+ if (isSyntaxCheck)
+ return addX(bs);
Point3f pt = null;
Point4f plane = null;
int i = args.length - 1;
@@ -8679,6 +8690,8 @@
atoms1 = bsAll();
if (atoms2 != null) {
BitSet bsBonds = new BitSet();
+ if (isSyntaxCheck)
+ return addX(new Token(Token.bitset, Integer.MIN_VALUE, bsBonds));
viewer.makeConnections(fmin, fmax, order,
JmolConstants.CONNECT_IDENTIFY_ONLY, atoms1, atoms2, bsBonds);
return addX(new Token(Token.bitset, Integer.MIN_VALUE, bsBonds,
@@ -8690,14 +8703,14 @@
}
boolean evaluateSubstructure(Token[] args) throws ScriptException {
- System.out.println("eval subs");
- if (isSyntaxCheck)
- return true;
+ //System.out.println("eval subs");
if (args.length != 1)
return false;
+ BitSet bs = new BitSet();
+ if (isSyntaxCheck)
+ return addX(bs);
String smiles = Token.sValue(args[0]);
PatternMatcher matcher = new PatternMatcher(viewer);
- BitSet bs = new BitSet();
try {
bs = matcher.getSubstructureSet(smiles);
} catch (InvalidSmilesException e) {
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|
|
From: <ha...@us...> - 2007-02-27 18:56:31
|
Revision: 6972
http://svn.sourceforge.net/jmol/?rev=6972&view=rev
Author: hansonr
Date: 2007-02-27 10:56:24 -0800 (Tue, 27 Feb 2007)
Log Message:
-----------
11.1.15 int + float = float; int - float = float
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/viewer/Eval.java
Modified: trunk/Jmol/src/org/jmol/viewer/Eval.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Eval.java 2007-02-27 18:53:44 UTC (rev 6971)
+++ trunk/Jmol/src/org/jmol/viewer/Eval.java 2007-02-27 18:56:24 UTC (rev 6972)
@@ -8886,7 +8886,7 @@
return addX(Token.concatList(x1, x2, false, true));
return addX(Token.sValue(x1) + Token.sValue(x2));
}
- if (x1.tok == Token.integer)
+ if (x1.tok == Token.integer && x2.tok != Token.decimal)
return addX(x1.intValue + Token.iValue(x2));
if (x1.tok == Token.point3f) {
Point3f pt = new Point3f((Point3f) x1.value);
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|
|
From: <ni...@us...> - 2007-02-27 21:41:15
|
Revision: 6983
http://svn.sourceforge.net/jmol/?rev=6983&view=rev
Author: nicove
Date: 2007-02-27 13:41:02 -0800 (Tue, 27 Feb 2007)
Log Message:
-----------
Warnings
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/viewer/Eval.java
Modified: trunk/Jmol/src/org/jmol/viewer/Eval.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Eval.java 2007-02-27 21:30:47 UTC (rev 6982)
+++ trunk/Jmol/src/org/jmol/viewer/Eval.java 2007-02-27 21:41:02 UTC (rev 6983)
@@ -25,7 +25,6 @@
import org.jmol.g3d.Graphics3D;
import org.jmol.g3d.Font3D;
-import org.jmol.smiles.InvalidSmilesException;
import org.jmol.util.CommandHistory;
import org.jmol.util.Logger;
import org.jmol.util.TextFormat;
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|
|
From: <ha...@us...> - 2007-03-02 20:41:22
|
Revision: 7018
http://svn.sourceforge.net/jmol/?rev=7018&view=rev
Author: hansonr
Date: 2007-03-02 12:41:14 -0800 (Fri, 02 Mar 2007)
Log Message:
-----------
11.1.17 removes trailing \n in ident
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/viewer/Eval.java
Modified: trunk/Jmol/src/org/jmol/viewer/Eval.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Eval.java 2007-03-02 20:14:05 UTC (rev 7017)
+++ trunk/Jmol/src/org/jmol/viewer/Eval.java 2007-03-02 20:41:14 UTC (rev 7018)
@@ -5687,8 +5687,9 @@
str = frame.getBondAt(j).formatLabel(str, indices);
}
str = TextFormat.formatString(str, "#", ++n);
+ if (n > 1)
+ s.append("\n");
s.append(str);
- s.append("\n");
}
return s.toString();
}
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|
|
From: <ha...@us...> - 2007-03-05 05:41:56
|
Revision: 7028
http://svn.sourceforge.net/jmol/?rev=7028&view=rev
Author: hansonr
Date: 2007-03-04 21:41:46 -0800 (Sun, 04 Mar 2007)
Log Message:
-----------
11.1.17 fix for "x = frank" not working
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/viewer/Eval.java
Modified: trunk/Jmol/src/org/jmol/viewer/Eval.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Eval.java 2007-03-04 23:10:26 UTC (rev 7027)
+++ trunk/Jmol/src/org/jmol/viewer/Eval.java 2007-03-05 05:41:46 UTC (rev 7028)
@@ -5569,16 +5569,6 @@
rpn.addX(new Token(Token.point3f, centerParameter(i)));
i = iToken;
break;
- case Token.identifier:
- String name = parameterAsString(i);
- if (isSyntaxCheck) {
- v = name;
- } else {
- v = viewer.getParameter(name);
- if (v instanceof String)
- v = getStringObjectAsToken((String) v);
- }
- break;
case Token.leftbrace:
v = getPointOrPlane(i, false, true, true, false, 3, 4);
i = iToken;
@@ -5603,12 +5593,23 @@
i = iToken;
break;
default:
- if (!Compiler.tokAttr(theTok, Token.mathop)
- && !Compiler.tokAttr(theTok, Token.mathfunc))
- invalidArgument();
- if (!rpn.addOp(theToken)) {
- iToken--;
- invalidArgument();
+ if (Compiler.tokAttr(theTok, Token.mathop)
+ || Compiler.tokAttr(theTok, Token.mathfunc)) {
+ if (!rpn.addOp(theToken)) {
+ iToken--;
+ invalidArgument();
+ }
+ } else {
+ String name = parameterAsString(i);
+ if (isSyntaxCheck) {
+ v = name;
+ } else {
+ v = viewer.getParameter(name);
+ if (v instanceof String)
+ v = getStringObjectAsToken((String) v);
+ }
+ break;
+
}
}
if (v != null)
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|
|
From: <ha...@us...> - 2007-03-07 18:21:05
|
Revision: 7045
http://svn.sourceforge.net/jmol/?rev=7045&view=rev
Author: hansonr
Date: 2007-03-07 10:21:00 -0800 (Wed, 07 Mar 2007)
Log Message:
-----------
11.1.18 missing "break" causes x.bonds.length to be 50% off
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/viewer/Eval.java
Modified: trunk/Jmol/src/org/jmol/viewer/Eval.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Eval.java 2007-03-07 16:37:50 UTC (rev 7044)
+++ trunk/Jmol/src/org/jmol/viewer/Eval.java 2007-03-07 18:21:00 UTC (rev 7045)
@@ -6008,6 +6008,7 @@
fvMin = Math.min(fvMin, fv);
fvMax = Math.max(fvMax, fv);
fvAvg += fv;
+ break;
case Token.xyz:
pt.add(bond.atom1);
pt.add(bond.atom2);
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|
|
From: <ha...@us...> - 2007-03-31 18:54:13
|
Revision: 7290
http://svn.sourceforge.net/jmol/?rev=7290&view=rev
Author: hansonr
Date: 2007-03-31 11:54:11 -0700 (Sat, 31 Mar 2007)
Log Message:
-----------
11.1.28 bug fix for mo command in .c3xml files
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/viewer/Eval.java
Modified: trunk/Jmol/src/org/jmol/viewer/Eval.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Eval.java 2007-03-31 18:31:13 UTC (rev 7289)
+++ trunk/Jmol/src/org/jmol/viewer/Eval.java 2007-03-31 18:54:11 UTC (rev 7290)
@@ -7845,15 +7845,16 @@
if (moNumber != Integer.MAX_VALUE) {
if (tokAt(2) == Token.string)
title = parameterAsString(2);
- setMoData(JmolConstants.SHAPE_MO, moNumber, title);
+ setMoData(JmolConstants.SHAPE_MO, moNumber, modelIndex, title);
}
return true;
}
- void setMoData(int shape, int moNumber, String title) throws ScriptException {
+ void setMoData(int shape, int moNumber, int modelIndex, String title) throws ScriptException {
if (isSyntaxCheck)
return;
- int modelIndex = viewer.getDisplayModelIndex();
+ if (modelIndex == 0)
+ modelIndex = viewer.getDisplayModelIndex();
if (modelIndex < 0)
multipleModelsNotOK();
Hashtable moData = (Hashtable) viewer.getModelAuxiliaryInfo(modelIndex,
@@ -7862,10 +7863,10 @@
modelIndex, "jmolSurfaceInfo");
if (surfaceInfo != null
&& ((String) surfaceInfo.get("surfaceDataType")).equals("mo")) {
- viewer.loadShape(JmolConstants.SHAPE_ISOSURFACE);
- setShapeProperty(JmolConstants.SHAPE_ISOSURFACE, "init", null);
- setShapeProperty(JmolConstants.SHAPE_ISOSURFACE, "sign", Boolean.TRUE);
- setShapeProperty(JmolConstants.SHAPE_ISOSURFACE, "getSurface",
+ viewer.loadShape(shape);
+ setShapeProperty(shape, "init", new Integer(modelIndex));
+ setShapeProperty(shape, "sign", Boolean.TRUE);
+ setShapeProperty(shape, "getSurface",
surfaceInfo);
return;
@@ -8297,7 +8298,7 @@
if (++i == statementLength)
badArgumentCount();
int moNumber = intParameter(i);
- setMoData(iShape, moNumber, null);
+ setMoData(iShape, moNumber, modelIndex, null);
surfaceObjectSeen = true;
continue;
case Token.mep:
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|
|
From: <ha...@us...> - 2007-05-13 12:34:43
|
Revision: 7680
http://svn.sourceforge.net/jmol/?rev=7680&view=rev
Author: hansonr
Date: 2007-05-13 05:34:37 -0700 (Sun, 13 May 2007)
Log Message:
-----------
11.1.38 better handling of lcaoCartoon SELECT to make it more consistent with other isosurface commands
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/viewer/Eval.java
Modified: trunk/Jmol/src/org/jmol/viewer/Eval.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Eval.java 2007-05-13 12:27:42 UTC (rev 7679)
+++ trunk/Jmol/src/org/jmol/viewer/Eval.java 2007-05-13 12:34:37 UTC (rev 7680)
@@ -7934,8 +7934,14 @@
propertyName = (optParameterAsString(++i).equalsIgnoreCase("molecular") ? "molecular" : "create");
break;
case Token.select:
- propertyName = "selectType";
- propertyValue = parameterAsString(++i);
+ if (tokAt(i + 1) == Token.bitset || tokAt(i + 1) == Token.expressionBegin) {
+ propertyName = "select";
+ propertyValue = expression(i + 1);
+ i = iToken;
+ } else {
+ propertyName = "selectType";
+ propertyValue = parameterAsString(++i);
+ }
break;
case Token.identifier:
String str = parameterAsString(i);
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|
|
From: <ha...@us...> - 2007-05-14 02:52:17
|
Revision: 7689
http://svn.sourceforge.net/jmol/?rev=7689&view=rev
Author: hansonr
Date: 2007-05-13 19:52:15 -0700 (Sun, 13 May 2007)
Log Message:
-----------
11.1.39 bug fix in frame range 1.0 when file 1 has only one model.
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/viewer/Eval.java
Modified: trunk/Jmol/src/org/jmol/viewer/Eval.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Eval.java 2007-05-14 02:44:50 UTC (rev 7688)
+++ trunk/Jmol/src/org/jmol/viewer/Eval.java 2007-05-14 02:52:15 UTC (rev 7689)
@@ -5439,7 +5439,7 @@
nFrames = 2;
else if (!isHyphen && modelIndex2 != modelIndex)
isHyphen = true;
- isRange = (isRange || !isHyphen && modelIndex2 != modelIndex);
+ isRange = isRange || modelIndex == modelIndex2;//(isRange || !isHyphen && modelIndex2 != modelIndex);
}
}
}
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