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From: <ha...@us...> - 2008-06-09 22:59:24
|
Revision: 9473
http://jmol.svn.sourceforge.net/jmol/?rev=9473&view=rev
Author: hansonr
Date: 2008-06-09 15:59:22 -0700 (Mon, 09 Jun 2008)
Log Message:
-----------
version=11.5.40_dev # bug fix: missing echocallback, scriptcallback, measurecallback "set"able variables
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/viewer/Eval.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/StateManager.java
trunk/Jmol/src/org/jmol/viewer/Token.java
Modified: trunk/Jmol/src/org/jmol/viewer/Eval.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Eval.java 2008-06-08 09:31:25 UTC (rev 9472)
+++ trunk/Jmol/src/org/jmol/viewer/Eval.java 2008-06-09 22:59:22 UTC (rev 9473)
@@ -8236,7 +8236,7 @@
private void setPicking() throws ScriptException {
if (statementLength == 2) {
- setStringProperty("picking", "ident");
+ setStringProperty("picking", "identify");
return;
}
if (statementLength > 4 || tokAt(2) == Token.string) {
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-06-08 09:31:25 UTC (rev 9472)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-06-09 22:59:22 UTC (rev 9473)
@@ -3,6 +3,8 @@
version=11.5.40_dev
+# bug fix: missing echocallback, scriptcallback, measurecallback "set"able variables
+# bug fix: "set picking identify" should be equivalent to "set picking ident"
# bug fix: popup menu had stereo reversed
# new feature: signed applet shows frank "Jmol-S" which is NOT removable.
Modified: trunk/Jmol/src/org/jmol/viewer/StateManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/StateManager.java 2008-06-08 09:31:25 UTC (rev 9472)
+++ trunk/Jmol/src/org/jmol/viewer/StateManager.java 2008-06-09 22:59:22 UTC (rev 9473)
@@ -742,9 +742,11 @@
+ ";picking;pickingstyle;propertycolorschemeoverload;radius;rgbblue;rgbgreen;rgbred"
+ ";scaleangstromsperinch;selectionhalos;showscript;showselections;solvent;strandcount"
+ ";spinx;spiny;spinz;spinfps"
- + ";animframecallback;loadstructcallback;messagecallback;minimizationcallback;hovercallback"
- + ";resizecallback;pickcallback;synccallback" + ";undo;";
+ + ";animframecallback;echocallback;evalcallback;loadstructcallback"
+ + ";measurecallback;messagecallback;minimizationcallback;hovercallback"
+ + ";resizecallback;pickcallback;scriptcallback;synccallback;undo;";
+
boolean isJmolVariable(String key) {
return key.charAt(0) == '_'
|| htParameterValues.containsKey(key = key.toLowerCase())
Modified: trunk/Jmol/src/org/jmol/viewer/Token.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Token.java 2008-06-08 09:31:25 UTC (rev 9472)
+++ trunk/Jmol/src/org/jmol/viewer/Token.java 2008-06-09 22:59:22 UTC (rev 9473)
@@ -1263,7 +1263,8 @@
"hidden", new Token(hidden),
"hydrogen", new Token(hydrogen),
"hydrogens", null,
- "ident", new Token(ident),
+ "identify", new Token(ident),
+ "ident", null,
"info", new Token(info),
"insertion", new Token(insertion),
"insertions", null,
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|
|
From: <ha...@us...> - 2008-06-13 14:35:25
|
Revision: 9481
http://jmol.svn.sourceforge.net/jmol/?rev=9481&view=rev
Author: hansonr
Date: 2008-06-13 07:34:50 -0700 (Fri, 13 Jun 2008)
Log Message:
-----------
version=11.5.40_dev selectX
# new feature: new command:
#
# selectx {atomExpression} booleanEvaluation
#
# same as select() function, but simpler to implement
#
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/viewer/Compiler.java
trunk/Jmol/src/org/jmol/viewer/Eval.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/Token.java
Modified: trunk/Jmol/src/org/jmol/viewer/Compiler.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Compiler.java 2008-06-13 12:08:23 UTC (rev 9480)
+++ trunk/Jmol/src/org/jmol/viewer/Compiler.java 2008-06-13 14:34:50 UTC (rev 9481)
@@ -1411,6 +1411,7 @@
boolean isImplicitExpression;
boolean isSetOrDefine;
+ boolean isSelectX;
Token tokenCommand;
int tokCommand;
@@ -1431,6 +1432,7 @@
tokCommand = tokenCommand.tok;
isImplicitExpression = tokAttr(tokCommand, Token.implicitExpression);
isSetOrDefine = (tokCommand == Token.set || tokCommand == Token.define);
+ isSelectX = (tokCommand == Token.selectx);
isCommaAsOrAllowed = tokAttr(tokCommand, Token.expressionCommand);
int size = ltoken.size();
if (size == 1 && !tokAttr(tokCommand, Token.flowCommand)
@@ -1525,7 +1527,7 @@
if (!isImplicitExpression
&& !(isEmbeddedExpression && lastToken == Token.tokenCoordinateEnd))
addTokenToPostfix(Token.tokenExpressionEnd);
- if (moreTokens() && !isEmbeddedExpression)
+ if (!isSelectX && moreTokens() && !isEmbeddedExpression)
return error(ERROR_endOfExpressionExpected);
}
atokenInfix = new Token[ltokenPostfix.size()];
Modified: trunk/Jmol/src/org/jmol/viewer/Eval.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Eval.java 2008-06-13 12:08:23 UTC (rev 9480)
+++ trunk/Jmol/src/org/jmol/viewer/Eval.java 2008-06-13 14:34:50 UTC (rev 9481)
@@ -987,6 +987,9 @@
case Token.select:
select();
break;
+ case Token.selectx:
+ selectX();
+ break;
case Token.translate:
translate();
break;
@@ -5343,6 +5346,21 @@
}
}
+ private void selectX() throws ScriptException {
+ // NOTE this is called by restrict()
+ if (statementLength == 1) {
+ viewer.select(null, tQuiet || scriptLevel > scriptReportingLevel);
+ return;
+ }
+ Object v = tokenSetting(0).value;
+ if (!(v instanceof BitSet))
+ error(ERROR_invalidArgument);
+ checkStatementLength(++iToken);
+ if (isSyntaxCheck)
+ return;
+ viewer.select((BitSet)v, tQuiet || scriptLevel > scriptReportingLevel);
+ }
+
private void subset() throws ScriptException {
BitSet bs = (statementLength == 1 ? null : expression(-1));
if (isSyntaxCheck)
@@ -6925,7 +6943,7 @@
}
private int intSetting(int pt) throws ScriptException {
- Vector v = (Vector) parameterExpression(pt, 0, "XXX", true);
+ Vector v = (Vector) parameterExpression(pt, -1, "XXX", true);
if (v == null || v.size() == 0)
error(ERROR_invalidArgument);
return Token.iValue((Token) v.elementAt(0));
@@ -6939,7 +6957,7 @@
}
private float floatSetting(int pt) throws ScriptException {
- Vector v = (Vector) parameterExpression(pt, 0, "XXX", true);
+ Vector v = (Vector) parameterExpression(pt, -1, "XXX", true);
if (v == null || v.size() == 0)
error(ERROR_invalidArgument);
return Token.fValue((Token) v.elementAt(0));
@@ -6948,14 +6966,14 @@
private String stringSetting(int pt, boolean isJmolSet) throws ScriptException {
if (isJmolSet && statementLength == pt + 1)
return parameterAsString(pt);
- Vector v = (Vector) parameterExpression(pt, 0, "XXX", true);
+ Vector v = (Vector) parameterExpression(pt, -1, "XXX", true);
if (v == null || v.size() == 0)
error(ERROR_invalidArgument);
return Token.sValue((Token) v.elementAt(0));
}
private Token tokenSetting(int pt) throws ScriptException {
- Vector v = (Vector) parameterExpression(pt, 0, "XXX", true);
+ Vector v = (Vector) parameterExpression(pt, -1, "XXX", true);
if (v == null || v.size() == 0)
error(ERROR_invalidArgument);
return (Token) v.elementAt(0);
@@ -7157,6 +7175,9 @@
Hashtable localVars)
throws ScriptException {
Object v;
+ boolean isOneExpressionOnly = (pt < 0);
+ if (isOneExpressionOnly)
+ pt = -pt;
boolean isSetCmd = (key != null && key.length() > 0);
Rpn rpn = new Rpn(64, isSetCmd && tokAt(pt) == Token.leftsquare, asVector);
if (ptMax < pt)
@@ -7164,20 +7185,28 @@
out: for (int i = pt; i < ptMax; i++) {
v = null;
switch (getToken(i).tok) {
+ case Token.selectx:
+ if (i != 0)
+ error(ERROR_invalidArgument);
+ // fall through
case Token.select:
- if (getToken(++i).tok != Token.leftparen
- || getToken(++i).tok != Token.identifier)
- error(ERROR_invalidArgument);
- String dummy = parameterAsString(i);
- if (getToken(++i).tok != Token.semicolon)
- error(ERROR_invalidArgument);
- v = tokenSetting(++i).value;
+ String dummy = "x";
+ boolean isSelectX = (theTok == Token.selectx);
+ if (!isSelectX) {
+ if (getToken(++i).tok != Token.leftparen
+ || getToken(++i).tok != Token.identifier)
+ error(ERROR_invalidArgument);
+ dummy = parameterAsString(i);
+ if (getToken(++i).tok != Token.semicolon)
+ error(ERROR_invalidArgument);
+ }
+ v = tokenSetting(-(++i)).value;
if (!(v instanceof BitSet))
error(ERROR_invalidArgument);
BitSet bsAtoms = (BitSet) v;
- if (getToken(i = iToken).tok != Token.semicolon)
+ i = iToken;
+ if (!isSelectX && getToken(i++).tok != Token.semicolon)
error(ERROR_invalidArgument);
- ++i; //skip semicolon
BitSet bsSelect = new BitSet();
BitSet bsX = new BitSet();
Token.Token2 t = null;
@@ -7193,9 +7222,15 @@
if (((Boolean) parameterExpression(i, -1, null, false, j, localVars))
.booleanValue())
bsSelect.set(j);
- if (tokAt(iToken) != Token.rightparen)
+ if (!isSelectX && tokAt(iToken) != Token.rightparen)
error(ERROR_invalidArgument);
}
+ if (isSelectX) {
+ Vector resx = new Vector();
+ if (v instanceof BitSet)
+ resx.addElement(new Token(Token.bitset, v));
+ return resx;
+ }
i = iToken;
v = bsSelect;
break;
@@ -7227,6 +7262,13 @@
case Token.expressionBegin:
v = expression(statement, i, 0, true, true, true, true);
i = iToken;
+ if (isOneExpressionOnly) {
+ iToken++; // skip end expression
+ Vector res = new Vector();
+ if (v instanceof BitSet)
+ res.addElement(new Token(Token.bitset, v));
+ return res;
+ }
break;
case Token.expressionEnd:
i++;
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-06-13 12:08:23 UTC (rev 9480)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-06-13 14:34:50 UTC (rev 9481)
@@ -3,6 +3,12 @@
version=11.5.40_dev
+# new feature: new command:
+#
+# selectx {atomExpression} booleanEvaluation
+#
+# same as select() function, but simpler to implement
+#
# new feature: full math on individual atom properties using
# a new function:
#
Modified: trunk/Jmol/src/org/jmol/viewer/Token.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Token.java 2008-06-13 12:08:23 UTC (rev 9480)
+++ trunk/Jmol/src/org/jmol/viewer/Token.java 2008-06-13 14:34:50 UTC (rev 9481)
@@ -181,7 +181,7 @@
final static int rotate = command | 27 | numberOrExpression;
final static int save = command | 28;
// final static int script = command | 29; with mathfunc
- // final static int select = command | 30 | expressionCommand; with mathfunc
+ final static int selectx = command | 30 | implicitExpression;
final static int set = command | 31 | implicitExpression | colorparam;
final static int show = command | 32;
final static int slab = command | 33 | numberOrExpression;
@@ -498,6 +498,7 @@
final static int point = 1 | 3 << 3 | mathfunc;
final static int select = 2 | 3 << 3 | mathfunc | expressionCommand;
+
// xxx(a,b,c,d)
final static int angle = 1 | 4 << 3 | mathfunc;
@@ -1102,6 +1103,7 @@
"script", new Token(script, varArgCount),
"source", null,
"select", new Token(select, varArgCount),
+ "selectX", new Token(selectx, varArgCount),
"selectionHalos", new Token(selectionHalo, onDefault1),
"selectionHalo", null,
"set", new Token(set, varArgCount),
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|
|
From: <ha...@us...> - 2008-06-15 07:29:28
|
Revision: 9490
http://jmol.svn.sourceforge.net/jmol/?rev=9490&view=rev
Author: hansonr
Date: 2008-06-15 00:29:27 -0700 (Sun, 15 Jun 2008)
Log Message:
-----------
11.5.41 VERSION bug fixes
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/viewer/Eval.java
trunk/Jmol/src/org/jmol/viewer/JmolConstants.java
Modified: trunk/Jmol/src/org/jmol/viewer/Eval.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Eval.java 2008-06-15 06:54:58 UTC (rev 9489)
+++ trunk/Jmol/src/org/jmol/viewer/Eval.java 2008-06-15 07:29:27 UTC (rev 9490)
@@ -8998,7 +8998,7 @@
value = viewer.getColorSchemeList(name, true);
} else if (str.equalsIgnoreCase("menu")) {
if (!isSyntaxCheck)
- value = viewer.getMenu();
+ value = viewer.getMenu("");
} else if (str.equalsIgnoreCase("strandCount")) {
msg = "set strandCountForStrands " + viewer.getStrandCount(JmolConstants.SHAPE_STRANDS)
+ "; set strandCountForMeshRibbon " + viewer.getStrandCount(JmolConstants.SHAPE_MESHRIBBON);
Modified: trunk/Jmol/src/org/jmol/viewer/JmolConstants.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/JmolConstants.java 2008-06-15 06:54:58 UTC (rev 9489)
+++ trunk/Jmol/src/org/jmol/viewer/JmolConstants.java 2008-06-15 07:29:27 UTC (rev 9490)
@@ -2190,8 +2190,9 @@
"C7", // 49 - base methyl carbon, unique to DT
"H1", // 50 - NOT backbone
- "H3", // 51 - NOT backbone
- null, null, null, //52
+ "H2", // 51 - NOT backbone -- see 1jve
+ "H3", // 52 - NOT backbone
+ null, null, //53
null, null, null, null, null, //55
null, null, null, null, //60 - 63
@@ -2243,7 +2244,6 @@
"HA2",
"HA3",
"HA2",
- "H2",
"H5'",
"H5''",
"H2'",
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|
|
From: <ha...@us...> - 2008-06-15 21:17:11
|
Revision: 9491
http://jmol.svn.sourceforge.net/jmol/?rev=9491&view=rev
Author: hansonr
Date: 2008-06-15 14:17:09 -0700 (Sun, 15 Jun 2008)
Log Message:
-----------
11.5.41 VERSION
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/viewer/Compiler.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/viewer/Compiler.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Compiler.java 2008-06-15 07:29:27 UTC (rev 9490)
+++ trunk/Jmol/src/org/jmol/viewer/Compiler.java 2008-06-15 21:17:09 UTC (rev 9491)
@@ -293,7 +293,7 @@
break;
String scrap = script.substring(pt, pt1);
if ((pt2 = scrap.indexOf(JmolConstants.EMBEDDED_SCRIPT_TAG)) >= 0)
- return scrap.substring(pt2 + 30);
+ return cleanScriptComments(scrap.substring(pt2 + 30));
script = script.substring(0, pt) + script.substring(pt1 + 3);
}
while ((pt = script.indexOf("/*")) >= 0) {
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-06-15 07:29:27 UTC (rev 9490)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-06-15 21:17:09 UTC (rev 9491)
@@ -1,8 +1,9 @@
# Developers: to add a description of changes you have made,
# add it on line starting with # below the "version=..." line
-version=11.5.41_dev
+version=11.5.41
+# bug fix: Jmol Embedded scripts containing script comments /* */
# new feature: getproperty menu current
# bug fix: 11.5.40 cannot read most state scripts.
# -----------------------------------------------------------------------------
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From: <ha...@us...> - 2008-06-23 01:03:10
|
Revision: 9513
http://jmol.svn.sourceforge.net/jmol/?rev=9513&view=rev
Author: hansonr
Date: 2008-06-22 18:03:03 -0700 (Sun, 22 Jun 2008)
Log Message:
-----------
11.5.42 VERSION (b)
# bug fix: color of NaN float values changed from "center of color scheme" to GRAY
# bug fix: connect "_1" was inadvertently dropped in 11.5.26.
# bug fix: state script fails to save data for atoms created using the quaternion command
# bug fix: axes/boundbox/unitcell dotted not working since 11.5.6
# bug fix: spin thread not stopped for applet destroy()
# bug fix: quaternion derivative for i/i+1 assigned to i+1 instead of i; now assigned to i
# bug fix: quaternion calculation using published algorithms was giving inverted quaternions
#
# new feature: set PICKLABEL "xxx" -- allows customized pick reports
#
# for example: set pickLabel "%n x = %x, y = %y, z = %z"
#
# new feature: "quaternion derivative" --> "quaternion difference", which is more
# appropriate, we think, with "absolute" and "relative" qualifiers:
#
# quaternion absolute difference # in the molecular frame
# quaternion relative difference # in the (local) frame of first quaternion:
#
# dq_absolute = q2 * q1_inverse
# dq_relative = q1_inverse * q2
#
# absolute involves un-doing q1's rotation (making it the reference frame), then applying q2.
# relative involves applying q2 (maintaining the original reference frame), then undoing q1.
#
# new feature: quaternion [w|x|y|z|a|r] [difference][2] [draw]
# new feature: draw quaternion [w|x|y|z|a|r] [difference][2]
# new feature: write quaternion [w|x|y|z|a|r] [difference][2] [draw]
# and with that: write("quaternion" [,"w"|"x"|"y"|"z"|"a"|"r"][,"difference"|"difference2"][,"draw"])
#
# new feature: set quaternionFrame "N" -- for solid state NMR PISEMA 15N chemical shift frame
# using alpha = 0 and beta = 17 degrees.
#
# new feature: select whatever; quaternion draw
# draws x,y,z and n vectors for a quaternion center
#
# new feature: straightness, defined as:
#
# straightness = 2*|n(dq1).dot(n(dq2))| - 1
#
# where q1 and q2 are quaternions defined generally as:
#
# q = frame{ vA, (vC x vA), vC }
#
# using quaternionFrame "p", which I define as
#
# protein:
#
# vA = C--CA
# vB = C--N[i+1]
#
# purine:
#
# vA = N9--C4
# vB = N9--C8
#
# pyrimidine:
#
# vA = N1--C2
# vB = N1--C6
#
# Differences dq1 and dq2 are absolute quaternion differences
# on the two sides of a residue:
#
# dq1 === q[i] * q[i-1]_inverse
# dq2 === q[i+1] * q[i]_inverse
#
# and n(dq) = the normal vector associated with this quaternion.
# Range is from -1 to 1
#
# applications (note that CALCULATE must be invoked first):
#
# calculate straightness # must be invoked first;
# color straightness;
# select straightness < 0.70; # rounds to nearest hundredth
# selectX {*} x.straightness < 0.995 # does not round
#
# new feature: "%T" label format for straightness
#
# -----------------------------------------------------------------------------
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/viewer/Eval.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/viewer/Eval.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Eval.java 2008-06-23 00:06:48 UTC (rev 9512)
+++ trunk/Jmol/src/org/jmol/viewer/Eval.java 2008-06-23 01:03:03 UTC (rev 9513)
@@ -4463,7 +4463,8 @@
private void dataFrame(int datatype) throws ScriptException {
String type = "";
boolean isQuaternion = false;
- boolean isDraw = false;
+ boolean isDraw = (tokAt(0) == Token.draw);
+ int pt0 = (isDraw ? 1 : 0);
boolean isDerivative = false;
boolean isSecondDerivative = false;
switch (datatype) {
@@ -4483,7 +4484,7 @@
isSecondDerivative = (isDerivative && type.indexOf("2") > 0);
if (isDerivative)
pt--;
- type = ((pt == 0 ? "" : optParameterAsString(pt))+"w").substring(0, 1);
+ type = ((pt <= pt0 ? "" : optParameterAsString(pt))+"w").substring(0, 1);
if (type == "a" || type == "r")
isDerivative = true;
if (!Parser.isOneOf(type, "w;x;y;z;r;a")) // a absolute; r relative
@@ -9514,6 +9515,10 @@
viewer.loadShape(JmolConstants.SHAPE_DRAW);
if (tokAt(1) == Token.list && listIsosurface(JmolConstants.SHAPE_DRAW))
return;
+ if (tokAt(1) == Token.quaternion) {
+ dataFrame(JmolConstants.JMOL_DATA_QUATERNION);
+ return;
+ }
boolean havePoints = false;
boolean isInitialized = false;
boolean isSavedState = false;
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-06-23 00:06:48 UTC (rev 9512)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-06-23 01:03:03 UTC (rev 9513)
@@ -28,6 +28,7 @@
# relative involves applying q2 (maintaining the original reference frame), then undoing q1.
#
# new feature: quaternion [w|x|y|z|a|r] [difference][2] [draw]
+# new feature: draw quaternion [w|x|y|z|a|r] [difference][2]
# new feature: write quaternion [w|x|y|z|a|r] [difference][2] [draw]
# and with that: write("quaternion" [,"w"|"x"|"y"|"z"|"a"|"r"][,"difference"|"difference2"][,"draw"])
#
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|
|
From: <ha...@us...> - 2008-06-30 15:01:18
|
Revision: 9536
http://jmol.svn.sourceforge.net/jmol/?rev=9536&view=rev
Author: hansonr
Date: 2008-06-30 08:00:22 -0700 (Mon, 30 Jun 2008)
Log Message:
-----------
version=11.5.43
# new feature/feature change:
#
# selectX is no longer necessary. Simply use
#
# select {atomExpression} (property expression)
#
# with no "x." An implied variable "_x" can be used explicitly:
#
# select {*} (straightness < 0.995) # does not round
# select {*.ca} (atomY < atomX)
# select {*.ca} (phi < select(y; {*.ca}; y.resno = _x.resno + 1).phi))
#
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/viewer/Compiler.java
trunk/Jmol/src/org/jmol/viewer/Eval.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/Token.java
Modified: trunk/Jmol/src/org/jmol/viewer/Compiler.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Compiler.java 2008-06-30 05:09:59 UTC (rev 9535)
+++ trunk/Jmol/src/org/jmol/viewer/Compiler.java 2008-06-30 15:00:22 UTC (rev 9536)
@@ -1414,7 +1414,6 @@
boolean isImplicitExpression;
boolean isSetOrDefine;
- boolean isSelectX;
Token tokenCommand;
int tokCommand;
@@ -1435,7 +1434,6 @@
tokCommand = tokenCommand.tok;
isImplicitExpression = tokAttr(tokCommand, Token.implicitExpression);
isSetOrDefine = (tokCommand == Token.set || tokCommand == Token.define);
- isSelectX = (tokCommand == Token.selectx);
isCommaAsOrAllowed = tokAttr(tokCommand, Token.expressionCommand);
int size = ltoken.size();
if (size == 1 && !tokAttr(tokCommand, Token.flowCommand)
@@ -1456,9 +1454,6 @@
//compile expressions
-// isEmbeddedExpression = (tokAttr(tokCommand, Token.embeddedExpression));
-// boolean checkExpression = (tokAttrOr(tokCommand, Token.expressionCommand,
- // Token.embeddedExpression));
isEmbeddedExpression = tokCommand != Token.function && (!tokAttrOr(tokCommand, Token.expressionCommand, Token.specialstring));
boolean checkExpression = isEmbeddedExpression || (tokAttr(tokCommand, Token.expressionCommand));
@@ -1508,6 +1503,7 @@
int firstToken = (isSetOrDefine && !isSetBrace ? 2 : 1);
ltokenPostfix = new Vector();
itokenInfix = 0;
+ Token tokenBegin = null;
for (int i = 0; i < firstToken && addNextToken(); i++) {
}
while (moreTokens()) {
@@ -1523,15 +1519,27 @@
continue;
}
if (!isImplicitExpression)
- addTokenToPostfix(Token.tokenExpressionBegin);
+ addTokenToPostfix(tokenBegin = new Token(Token.expressionBegin, "implicitExpressionBegin"));
if (!clauseOr(isCommaAsOrAllowed || !isImplicitExpression
&& tokPeek(Token.leftparen)))
return false;
if (!isImplicitExpression
- && !(isEmbeddedExpression && lastToken == Token.tokenCoordinateEnd))
+ && !(isEmbeddedExpression && lastToken == Token.tokenCoordinateEnd)) {
addTokenToPostfix(Token.tokenExpressionEnd);
- if (!isSelectX && moreTokens() && !isEmbeddedExpression)
- return error(ERROR_endOfExpressionExpected);
+ tokenBegin.intValue = ltokenPostfix.size();
+ }
+ if (moreTokens()) {
+ if (tokCommand != Token.select && !isEmbeddedExpression)
+ return error(ERROR_endOfExpressionExpected);
+ if (tokCommand == Token.select) {
+ // advanced select, with two expressions, the first
+ // being an atom expression; the second being a property selector expression
+ tokCommand = Token.nada;
+ isEmbeddedExpression = true;
+ isImplicitExpression = true;
+ isCommaAsOrAllowed = false;
+ }
+ }
}
atokenInfix = new Token[ltokenPostfix.size()];
ltokenPostfix.copyInto(atokenInfix);
Modified: trunk/Jmol/src/org/jmol/viewer/Eval.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Eval.java 2008-06-30 05:09:59 UTC (rev 9535)
+++ trunk/Jmol/src/org/jmol/viewer/Eval.java 2008-06-30 15:00:22 UTC (rev 9536)
@@ -989,9 +989,6 @@
case Token.select:
select();
break;
- case Token.selectx:
- selectX();
- break;
case Token.translate:
translate();
break;
@@ -5376,7 +5373,16 @@
}
error(ERROR_invalidArgument);
}
- BitSet bs = expression(1);
+ BitSet bs = null;
+ if (getToken(1).intValue != statementLength) {
+ Object v = tokenSetting(0).value;
+ if (!(v instanceof BitSet))
+ error(ERROR_invalidArgument);
+ checkStatementLength(++iToken);
+ bs = (BitSet) v;
+ } else {
+ bs = expression(1);
+ }
if (isSyntaxCheck)
return;
if (isBondSet) {
@@ -5386,20 +5392,6 @@
}
}
- private void selectX() throws ScriptException {
- if (statementLength == 1) {
- viewer.select(null, tQuiet || scriptLevel > scriptReportingLevel);
- return;
- }
- Object v = tokenSetting(0).value;
- if (!(v instanceof BitSet))
- error(ERROR_invalidArgument);
- checkStatementLength(++iToken);
- if (isSyntaxCheck)
- return;
- viewer.select((BitSet)v, tQuiet || scriptLevel > scriptReportingLevel);
- }
-
private void subset() throws ScriptException {
BitSet bs = (statementLength == 1 ? null : expression(-1));
if (isSyntaxCheck)
@@ -7034,7 +7026,9 @@
}
int tokProperty = Token.nada;
if (tokAt(pt) == Token.dot) {
- Token token = getBitsetPropertySelector(pt++, true);
+ Token token = getBitsetPropertySelector(++pt, true);
+ if (token == null)
+ error(ERROR_invalidArgument);
if (tokAt(++pt) != Token.opEQ)
error(ERROR_invalidArgument);
pt++;
@@ -7212,15 +7206,17 @@
private Object parameterExpression(int pt, int ptMax, String key,
boolean asVector) throws ScriptException {
- return parameterExpression(pt, ptMax, key, asVector, -1, null);
+ return parameterExpression(pt, ptMax, key, asVector, -1, null, null);
}
private Object parameterExpression(int pt, int ptMax, String key,
boolean asVector, int ptAtom,
- Hashtable localVars)
+ Hashtable localVars, String localVar)
throws ScriptException {
Object v;
+ boolean isSelectX = (pt == 0);
boolean isOneExpressionOnly = (pt < 0);
+ boolean isImplicitAtomProperty = (localVar != null);
if (isOneExpressionOnly)
pt = -pt;
int nParen = 0;
@@ -7230,14 +7226,18 @@
ptMax = statementLength;
out: for (int i = pt; i < ptMax; i++) {
v = null;
- switch (getToken(i).tok) {
- case Token.selectx:
- if (i != 0)
- error(ERROR_invalidArgument);
- // fall through
+ int tok = getToken(i).tok;
+ if (isImplicitAtomProperty && tokAt(i + 1) != Token.dot) {
+ if (Compiler.tokAttr(tok, Token.atomproperty)) {
+ rpn.addX((Token) localVars.get(localVar));
+ if (!rpn.addOp(new Token(Token.propselector, tok, parameterAsString(i).toLowerCase())))
+ error(ERROR_invalidArgument);
+ continue;
+ }
+ }
+ switch (tok) {
case Token.select:
- String dummy = "x";
- boolean isSelectX = (theTok == Token.selectx);
+ String dummy = "_x";
if (!isSelectX) {
if (getToken(++i).tok != Token.leftparen
|| getToken(++i).tok != Token.identifier)
@@ -7265,8 +7265,8 @@
bsX.clear();
bsX.set(j);
t.intValue2 = j;
- if (((Boolean) parameterExpression(i, -1, null, false, j, localVars))
- .booleanValue())
+ if (((Boolean) parameterExpression(i, -1, null, false, j,
+ localVars, isSelectX ? dummy : null)).booleanValue())
bsSelect.set(j);
if (!isSelectX && tokAt(iToken) != Token.rightparen)
error(ERROR_invalidArgument);
@@ -7317,7 +7317,9 @@
error(ERROR_invalidArgument);
break;
case Token.dot:
- Token token = getBitsetPropertySelector(i, false);
+ Token token = getBitsetPropertySelector(i + 1, false);
+ if (token == null)
+ error(ERROR_invalidArgument);
//check for added min/max modifier
if (tokAt(iToken + 1) == Token.dot) {
if (tokAt(iToken + 2) == Token.all) {
@@ -7565,16 +7567,17 @@
private Token getBitsetPropertySelector(int i, boolean mustBeSettable)
throws ScriptException {
- int tok = getToken(++i).tok;
- String s = parameterAsString(i).toLowerCase();
+ int tok = getToken(i).tok;
+ String s = null;
switch (tok) {
default:
if (Compiler.tokAttrOr(tok, Token.atomproperty, Token.mathproperty))
break;
- error(ERROR_invalidArgument);
+ return null;
case Token.property:
break;
case Token.identifier:
+ s = parameterAsString(i).toLowerCase();
if (s.equals("x"))
tok = Token.atomX;
else if (s.equals("y"))
@@ -7584,11 +7587,13 @@
else if (s.equals("w"))
tok = Token.qw;
else
- error(ERROR_invalidArgument);
+ return null;
break;
}
if (mustBeSettable && !Compiler.tokAttr(tok, Token.settable))
- error(ERROR_invalidArgument);
+ return null;
+ if (s == null)
+ s = parameterAsString(i).toLowerCase();
return new Token(Token.propselector, tok, s);
}
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-06-30 05:09:59 UTC (rev 9535)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-06-30 15:00:22 UTC (rev 9536)
@@ -3,6 +3,18 @@
version=11.5.43
+# new feature/feature change:
+#
+# selectX is no longer necessary. Simply use
+#
+# select {atomExpression} (property expression)
+#
+# with no "x." An implied variable "_x" can be used explicitly:
+#
+# select {*} (straightness < 0.995) # does not round
+# select {*.ca} (atomY < atomX)
+# select {*.ca} (phi < select(y; {*.ca}; y.resno = _x.resno + 1).phi))
+#
# new feature: quaterion % point4f --- "thetaDirected" --
# point4f is {x, y, z, w} (w ignored), where {x y z} is a
# preferred direction.
Modified: trunk/Jmol/src/org/jmol/viewer/Token.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Token.java 2008-06-30 05:09:59 UTC (rev 9535)
+++ trunk/Jmol/src/org/jmol/viewer/Token.java 2008-06-30 15:00:22 UTC (rev 9536)
@@ -181,7 +181,6 @@
final static int rotate = command | 27 | numberOrExpression;
final static int save = command | 28;
// final static int script = command | 29; with mathfunc
- final static int selectx = command | 30 | implicitExpression;
final static int set = command | 31 | implicitExpression | colorparam;
final static int show = command | 32;
final static int slab = command | 33 | numberOrExpression;
@@ -463,7 +462,7 @@
// ___.xxx(a)
- // a.distance(b) is in a different set -- x.distance(b,c) -- because it CAN take
+ // a.distance(b) is in a different set -- distance(b,c) -- because it CAN take
// two parameters and it CAN be a dot-function (but not both together)
final static int split = 0 | 1 << 3 | mathfunc | mathproperty;
@@ -1108,7 +1107,6 @@
"script", new Token(script, varArgCount),
"source", null,
"select", new Token(select, varArgCount),
- "selectX", new Token(selectx, varArgCount),
"selectionHalos", new Token(selectionHalo, onDefault1),
"selectionHalo", null,
"set", new Token(set, varArgCount),
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ha...@us...> - 2008-07-01 04:29:14
|
Revision: 9539
http://jmol.svn.sourceforge.net/jmol/?rev=9539&view=rev
Author: hansonr
Date: 2008-06-30 21:29:07 -0700 (Mon, 30 Jun 2008)
Log Message:
-----------
11.5.44 VERSION
# bug fix: select @x broken in 11.5.43
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/viewer/Compiler.java
trunk/Jmol/src/org/jmol/viewer/Eval.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/viewer/Compiler.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Compiler.java 2008-06-30 21:45:50 UTC (rev 9538)
+++ trunk/Jmol/src/org/jmol/viewer/Compiler.java 2008-07-01 04:29:07 UTC (rev 9539)
@@ -1526,7 +1526,6 @@
if (!isImplicitExpression
&& !(isEmbeddedExpression && lastToken == Token.tokenCoordinateEnd)) {
addTokenToPostfix(Token.tokenExpressionEnd);
- tokenBegin.intValue = ltokenPostfix.size();
}
if (moreTokens()) {
if (tokCommand != Token.select && !isEmbeddedExpression)
@@ -1534,6 +1533,7 @@
if (tokCommand == Token.select) {
// advanced select, with two expressions, the first
// being an atom expression; the second being a property selector expression
+ tokenBegin.intValue = 0;
tokCommand = Token.nada;
isEmbeddedExpression = true;
isImplicitExpression = true;
Modified: trunk/Jmol/src/org/jmol/viewer/Eval.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Eval.java 2008-06-30 21:45:50 UTC (rev 9538)
+++ trunk/Jmol/src/org/jmol/viewer/Eval.java 2008-07-01 04:29:07 UTC (rev 9539)
@@ -5374,7 +5374,7 @@
error(ERROR_invalidArgument);
}
BitSet bs = null;
- if (getToken(1).intValue != statementLength) {
+ if (getToken(1).intValue == 0) {
Object v = tokenSetting(0).value;
if (!(v instanceof BitSet))
error(ERROR_invalidArgument);
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-06-30 21:45:50 UTC (rev 9538)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-07-01 04:29:07 UTC (rev 9539)
@@ -1,8 +1,11 @@
# Developers: to add a description of changes you have made,
# add it on line starting with # below the "version=..." line
-version=11.5.44_dev
+version=11.5.44
+# bug fix: select @x broken in 11.5.43
+#
+
# -----------------------------------------------------------------------------
#version=11.5.43
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|
|
From: <ha...@us...> - 2008-07-01 12:21:29
|
Revision: 9540
http://jmol.svn.sourceforge.net/jmol/?rev=9540&view=rev
Author: hansonr
Date: 2008-07-01 05:20:45 -0700 (Tue, 01 Jul 2008)
Log Message:
-----------
version=11.5.44
# bug fix: select @x broken in 11.5.43
# bug fix: integer addition not remaining integer
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/viewer/Eval.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/viewer/Eval.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Eval.java 2008-07-01 04:29:07 UTC (rev 9539)
+++ trunk/Jmol/src/org/jmol/viewer/Eval.java 2008-07-01 12:20:45 UTC (rev 9540)
@@ -12451,6 +12451,7 @@
private boolean evaluateWithin(Token[] args) throws ScriptException {
if (args.length < 1)
return false;
+ int i = args.length;
Object withinSpec = args[0].value;
int tok = args[0].tok;
String withinStr = "" + withinSpec;
@@ -12458,9 +12459,16 @@
float distance = 0;
boolean isSequence = false;
boolean isBoundbox = false;
- int i = args.length;
boolean isWithinModelSet = false;
boolean isDistance = (tok == Token.decimal || tok == Token.integer);
+ if (withinStr.equals("branch")) {
+ if (i != 3 || !(args[1].value instanceof BitSet)
+ || !(args[2].value instanceof BitSet))
+ return false;
+ return addX(viewer.getConnectedBitSet(BitSetUtil
+ .firstSetBit((BitSet) args[2].value), BitSetUtil
+ .firstSetBit((BitSet) args[1].value)));
+ }
if (withinSpec instanceof String) {
isSequence = !Parser.isOneOf(withinStr,
"element;site;group;chain;structure;molecule;model;boundbox");
@@ -12499,8 +12507,9 @@
plane = (Point4f) args[i].value;
else if (args[i].value instanceof Point3f)
pt = (Point3f) args[i].value;
-
- if (i > 0 && plane == null && pt == null && !(args[i].value instanceof BitSet))
+
+ if (i > 0 && plane == null && pt == null
+ && !(args[i].value instanceof BitSet))
return false;
if (isSyntaxCheck)
return addX(bs);
@@ -12750,6 +12759,14 @@
case Token.plus:
if (x1.tok == Token.list || x2.tok == Token.list)
return addX(Token.concatList(x1, x2));
+ if (x1.tok == Token.integer) {
+ if (x2.tok == Token.string) {
+ if ((s = (Token.sValue(x2)).trim()).indexOf(".") < 0
+ && s.indexOf("+") <= 0 && s.lastIndexOf("-") <= 0)
+ return addX(x1.intValue + Token.iValue(x2));
+ } else if (x2.tok != Token.decimal)
+ return addX(x1.intValue + Token.iValue(x2));
+ }
switch (x1.tok) {
default:
return addX(Token.fValue(x1) + Token.fValue(x2));
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-07-01 04:29:07 UTC (rev 9539)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-07-01 12:20:45 UTC (rev 9540)
@@ -4,7 +4,7 @@
version=11.5.44
# bug fix: select @x broken in 11.5.43
-#
+# bug fix: integer addition not remaining integer
# -----------------------------------------------------------------------------
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|
|
From: <ha...@us...> - 2008-07-01 16:26:30
|
Revision: 9544
http://jmol.svn.sourceforge.net/jmol/?rev=9544&view=rev
Author: hansonr
Date: 2008-07-01 09:26:14 -0700 (Tue, 01 Jul 2008)
Log Message:
-----------
version=11.5.44 bug fixes
# bug fix: math calculation .xyz, .color averages broken in 11.5.42
# bug fix: select @x broken in 11.5.43
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/viewer/Eval.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/viewer/Eval.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Eval.java 2008-07-01 12:57:03 UTC (rev 9543)
+++ trunk/Jmol/src/org/jmol/viewer/Eval.java 2008-07-01 16:26:14 UTC (rev 9544)
@@ -7836,16 +7836,20 @@
break;
case Token.xyz:
pt.add(atom);
+ fv = 0;
break;
case Token.fracXyz:
pt.add(atom.getFractionalCoord());
+ fv = 0;
break;
case Token.vibXyz:
pt.add(viewer.getVibrationVector(i));
+ fv = 0;
break;
case Token.color:
pt.add(Graphics3D.colorPointFromInt(viewer.getColixArgb(atom
.getColix()), ptT));
+ fv = 0;
break;
default:
error(ERROR_unrecognizedAtomProperty, Token.nameOf(tok));
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-07-01 12:57:03 UTC (rev 9543)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-07-01 16:26:14 UTC (rev 9544)
@@ -3,6 +3,7 @@
version=11.5.44
+# bug fix: math calculation .xyz, .color averages broken in 11.5.42
# bug fix: select @x broken in 11.5.43
# bug fix: integer addition not remaining integer
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ha...@us...> - 2008-07-01 16:50:05
|
Revision: 9545
http://jmol.svn.sourceforge.net/jmol/?rev=9545&view=rev
Author: hansonr
Date: 2008-07-01 09:49:39 -0700 (Tue, 01 Jul 2008)
Log Message:
-----------
version=11.5.44 # bug fix: _applet variable not initializing properly
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/Viewer.java
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-07-01 16:26:14 UTC (rev 9544)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-07-01 16:49:39 UTC (rev 9545)
@@ -3,6 +3,7 @@
version=11.5.44
+# bug fix: _applet variable not initializing properly
# bug fix: math calculation .xyz, .color averages broken in 11.5.42
# bug fix: select @x broken in 11.5.43
# bug fix: integer addition not remaining integer
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2008-07-01 16:26:14 UTC (rev 9544)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2008-07-01 16:49:39 UTC (rev 9545)
@@ -268,6 +268,7 @@
this.syncId = (i < 0 ? "" : fullName
.substring(i + 1, fullName.length() - 1));
isApplet = (documentBase != null);
+
String str = appletProxyOrCommandOptions;
if (str == null)
str = "";
@@ -283,6 +284,7 @@
if (useCommandThread)
scriptManager.startCommandWatcher(true);
isSignedApplet = (isApplet && str.indexOf("-signed") >= 0);
+ setBooleanProperty("_applet", isApplet);
setBooleanProperty("_signedApplet", isSignedApplet);
setBooleanProperty("_useCommandThread", useCommandThread);
if (!isApplet) {
@@ -3161,7 +3163,6 @@
}
public void renderScreenImage(Graphics g, Dimension size, Rectangle clip) {
- //System.out.println("renderScreenImage");
if (isTainted || getSlabEnabled())
setModelVisibility();
isTainted = false;
@@ -3325,7 +3326,6 @@
// initiated WITHIN this applet (not sent to it)
// we append #NOSYNC; here so that the receiving applet does not attempt
// to pass it back to us or any other applet.
- //System.out.println(getHtmlName() + " evalstringquiet " + strScript);
if (allowSyncScript && syncingScripts && strScript.indexOf("#NOSYNC;") < 0 )
syncScript(strScript + " #NOSYNC;", null);
boolean isInterrupt = (strScript.length() > 0 && strScript.charAt(0) == '!');
@@ -6565,7 +6565,6 @@
boolean allButMe = (">".equals(applet));
boolean disableSend = ("~".equals(applet));
boolean justMe = disableSend || (".".equals(applet));
- //System.out.println(getHtmlName() + " syncscript " + script + " --- applet " + applet);
//null same as ">" -- "all others"
if (!justMe) {
statusManager.syncSend(script, (isAll || allButMe ? null : applet));
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ha...@us...> - 2008-07-06 15:14:32
|
Revision: 9565
http://jmol.svn.sourceforge.net/jmol/?rev=9565&view=rev
Author: hansonr
Date: 2008-07-06 08:14:19 -0700 (Sun, 06 Jul 2008)
Log Message:
-----------
version=11.5.45
# code: mouse manager refactoring
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/MouseManager.java
trunk/Jmol/src/org/jmol/viewer/PickingManager.java
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-07-06 14:06:10 UTC (rev 9564)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-07-06 15:14:19 UTC (rev 9565)
@@ -3,6 +3,8 @@
version=11.5.45
+# code: mouse manager refactoring
+
# bug fix: picking off structure did not clear picking for set picking spin
# bug fix: jmolScriptWait() improperly reporting to applet console
# bug fix: too many messages to applet console
Modified: trunk/Jmol/src/org/jmol/viewer/MouseManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/MouseManager.java 2008-07-06 14:06:10 UTC (rev 9564)
+++ trunk/Jmol/src/org/jmol/viewer/MouseManager.java 2008-07-06 15:14:19 UTC (rev 9565)
@@ -55,6 +55,8 @@
private static final boolean logMouseEvents = false;
+ abstract boolean handleOldJvm10Event(Event e);
+
MouseManager(Viewer viewer) {
this.viewer = viewer;
Component display = viewer.getAwtComponent();
@@ -323,17 +325,35 @@
Logger.debug("mouseClicked(" + x + "," + y + "," + modifiers
+ ",clickCount=" + clickCount + ",time=" + (time - previousClickTime)
+ ")");
- if (!viewer.haveModelSet())
- return;
+ if (viewer.haveModelSet())
+ checkPointOrAtomClicked(x, y, modifiers, clickCount);
+ }
+
+ private void checkPointOrAtomClicked(int x, int y, int modifiers, int clickCount) {
+ // points are always picked up first, then atoms
+ // so that atom picking can be superceded by draw picking
Point3f ptClicked = (drawMode ? null :
viewer.checkObjectClicked(x, y, modifiers));
- int nearestAtomIndex = (drawMode || ptClicked != null ? -1 : viewer.findNearestAtomIndex(x, y));
- if (nearestAtomIndex >= 0 && !viewer.isInSelectionSubset(nearestAtomIndex))
+ int nearestAtomIndex = (drawMode || ptClicked != null ? -1
+ : viewer.findNearestAtomIndex(x, y));
+ if (nearestAtomIndex >= 0
+ && (clickCount > 0 || !measurementMode)
+ && !viewer.isInSelectionSubset(nearestAtomIndex))
nearestAtomIndex = -1;
- if (clickCount == 1)
+ switch(clickCount) {
+ case 0:
+ // mouse move
+ setAttractiveMeasurementTarget(nearestAtomIndex, ptClicked);
+ return;
+ case 1:
+ // mouse single click
mouseSingleClick(x, y, modifiers, nearestAtomIndex, ptClicked);
- else if (clickCount == 2)
+ return;
+ case 2:
+ // mouse double click
mouseDoubleClick(x, y, modifiers, nearestAtomIndex, ptClicked);
+ return;
+ }
}
private void mouseSingleClick(int x, int y, int modifiers, int nearestAtomIndex,
@@ -355,14 +375,15 @@
- 50f, y * 100f / viewer.getScreenHeight() - 50f);
return;
}
- viewer.atomPicked(nearestAtomIndex, modifiers);
+ if (ptClicked == null)
+ viewer.atomPicked(nearestAtomIndex, modifiers);
if (measurementMode)
addToMeasurement(nearestAtomIndex, ptClicked, false);
break;
case ALT_LEFT:
case SHIFT_LEFT:
case ALT_SHIFT_LEFT:
- if (!drawMode && viewer.checkObjectClicked(x, y, modifiers) == null)
+ if (!drawMode && ptClicked == null)
viewer.atomPicked(nearestAtomIndex, modifiers);
break;
}
@@ -503,14 +524,8 @@
timeCurrent = mouseMovedTime = time;
mouseMovedX = xCurrent = x;
mouseMovedY = yCurrent = y;
- if (measurementMode || hoverActive) {
- Point3f ptClicked = viewer.checkObjectClicked(x, y, 0);
- int atomIndex = viewer.findNearestAtomIndex(x, y);
- if (!measurementMode && atomIndex >= 0
- && viewer.isInSelectionSubset(atomIndex))
- atomIndex = -1;
- setAttractiveMeasurementTarget(atomIndex, ptClicked);
- }
+ if (measurementMode || hoverActive)
+ checkPointOrAtomClicked(x, y, 0, 0);
}
final static float wheelClickFractionUp = 1.15f;
@@ -540,40 +555,40 @@
}
}
- abstract boolean handleOldJvm10Event(Event e);
-
- // note that these two may *not* be consistent
- // this term refers to the count of what has actually been selected
+/*
+ * Note that measurementCountPlusIndices[0] and measurementCount
+ * may not be the same. measurementCount refers to the count of what has
+ * actually been selected.
+ * measurementCountPlusIndices[0] may be one higher if there is
+ * an attractive measurement target (cursor is hovering near an atom)
+ *
+ * With the addition of draw point-measurements (set drawPicking TRUE),
+ * the attractive target may be -1
+ *
+ */
+
private int measurementCount = 0;
- // measurementCountPlusIndices[0] may be one higher if there is
- // an attractive measurement target
- // ie. the cursor is hovering near an atom
private int[] measurementCountPlusIndices = new int[5];
- // the attractive target may be -1
private void setAttractiveMeasurementTarget(int atomIndex, Point3f ptClicked) {
- if (ptClicked == null) {
- if (measurementCountPlusIndices[0] == measurementCount + 1
- && measurementCountPlusIndices[measurementCount + 1] == atomIndex) {
- viewer.refresh(0, "MouseManager:setAttractiveMeasurementTarget("
- + atomIndex + ")");
- return;
- }
- for (int i = measurementCount; i > 0; --i)
+ if (ptClicked == null)
+ for (int i = Math.max(measurementCountPlusIndices[0], measurementCount); i > 0; --i)
if (measurementCountPlusIndices[i] == atomIndex) {
viewer.refresh(0, "MouseManager:setAttractiveMeasurementTarget("
+ atomIndex + ")");
return;
}
- }
- int attractiveCount = measurementCount + 1;
- measurementCountPlusIndices[0] = attractiveCount;
- measurementCountPlusIndices[attractiveCount] = atomIndex;
+ setMeasurement(measurementCount + 1, atomIndex);
// note that if ptClicked is not valid, then measurementCountPlusIndices
// will be updated, and if it is valid, then it will still be updated
viewer.setPendingMeasurement(measurementCountPlusIndices, ptClicked);
}
+ private void setMeasurement(int i, int atomIndex) {
+ measurementCountPlusIndices[i] = atomIndex;
+ measurementCountPlusIndices[0] = i;
+ }
+
boolean haveMeasurementPoints;
private void addToMeasurement(int atomIndex, Point3f ptClicked,
@@ -594,15 +609,11 @@
if (measurementCount == 3 && !dblClick)
return;
haveMeasurementPoints |= (ptClicked != null);
- measurementCountPlusIndices[++measurementCount] = (ptClicked != null ? -1
- : atomIndex);
- measurementCountPlusIndices[0] = measurementCount;
- if (measurementCount == 4) {
+ setMeasurement(++measurementCount, ptClicked != null ? -1 : atomIndex);
+ if (measurementCount == 4)
toggleMeasurement();
- } else {
+ else
viewer.setPendingMeasurement(measurementCountPlusIndices, ptClicked);
- measurementCount = measurementCountPlusIndices[0];
- }
}
private void exitMeasurementMode() {
Modified: trunk/Jmol/src/org/jmol/viewer/PickingManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/PickingManager.java 2008-07-06 14:06:10 UTC (rev 9564)
+++ trunk/Jmol/src/org/jmol/viewer/PickingManager.java 2008-07-06 15:14:19 UTC (rev 9565)
@@ -103,7 +103,8 @@
//if (pickingMode == JmolConstants.PICKING_MEASURE
// || pickingStyleMeasure == JmolConstants.PICKINGSTYLE_MEASURE_ON)
queuedAtomCount = 0;
- return;
+ if (pickingMode != JmolConstants.PICKING_SPIN)
+ return;
}
String value;
@@ -206,10 +207,9 @@
queuedAtomCount = 0;
if (queuedAtomCount == 1 && queuedAtomIndexes[0] == atomIndex)
break;
- queueAtom(atomIndex);
+ if (atomIndex >= 0)
+ queueAtom(atomIndex);
if (queuedAtomCount < 2) {
- if (viewer.getSpinOn())
- viewer.script("spin off");
viewer.scriptStatus(queuedAtomCount == 1 ?
GT._("pick one more atom in order to spin the model around an axis") :
GT._("pick two atoms in order to spin the model around an axis"));
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|
|
From: <ha...@us...> - 2008-07-10 19:07:13
|
Revision: 9581
http://jmol.svn.sourceforge.net/jmol/?rev=9581&view=rev
Author: hansonr
Date: 2008-07-10 12:07:02 -0700 (Thu, 10 Jul 2008)
Log Message:
-----------
version=11.5.46_dev # bug fix: array size limited
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/viewer/Eval.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/viewer/Eval.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Eval.java 2008-07-10 18:17:08 UTC (rev 9580)
+++ trunk/Jmol/src/org/jmol/viewer/Eval.java 2008-07-10 19:07:02 UTC (rev 9581)
@@ -11575,57 +11575,57 @@
return false;
}
- boolean addX(boolean x) throws ScriptException {
- if (++xPt == maxLevel)
+ boolean addX(boolean x) {
+ if (++xPt >= maxLevel)
stackOverflow();
xStack[xPt] = (x ? Token.tokenOn : Token.tokenOff);
return true;
}
- boolean addX(int x) throws ScriptException {
- if (++xPt == maxLevel)
+ boolean addX(int x) {
+ if (++xPt >= maxLevel)
stackOverflow();
xStack[xPt] = Token.intToken(x);
return wasX = true;
}
- boolean addX(float x) throws ScriptException {
- if (++xPt == maxLevel)
+ boolean addX(float x) {
+ if (++xPt >= maxLevel)
stackOverflow();
xStack[xPt] = new Token(Token.decimal, new Float(x));
return wasX = true;
}
- boolean addX(String x) throws ScriptException {
- if (++xPt == maxLevel)
+ boolean addX(String x) {
+ if (++xPt >= maxLevel)
stackOverflow();
xStack[xPt] = new Token(Token.string, x);
return wasX = true;
}
- boolean addX(String[] x) throws ScriptException {
- if (++xPt == maxLevel)
+ boolean addX(String[] x) {
+ if (++xPt >= maxLevel)
stackOverflow();
xStack[xPt] = new Token(Token.list, x);
return wasX = true;
}
- boolean addX(Point3f x) throws ScriptException {
- if (++xPt == maxLevel)
+ boolean addX(Point3f x) {
+ if (++xPt >= maxLevel)
stackOverflow();
xStack[xPt] = new Token(Token.point3f, x);
return wasX = true;
}
- boolean addX(Point4f x) throws ScriptException {
- if (++xPt == maxLevel)
+ boolean addX(Point4f x) {
+ if (++xPt >= maxLevel)
stackOverflow();
xStack[xPt] = new Token(Token.point4f, x);
return wasX = true;
}
- boolean addX(BitSet x) throws ScriptException {
- if (++xPt == maxLevel)
+ boolean addX(BitSet x) {
+ if (++xPt >= maxLevel)
stackOverflow();
xStack[xPt] = new Token(Token.bitset, x);
return wasX = true;
@@ -11794,7 +11794,7 @@
//add the operator if possible
- if (++oPt == maxLevel)
+ if (++oPt >= maxLevel)
stackOverflow();
oStack[oPt] = op;
return true;
@@ -12294,7 +12294,7 @@
return addX(sList3);
}
- private boolean evaluateArray(Token[] args) throws ScriptException {
+ private boolean evaluateArray(Token[] args) {
if (isSyntaxCheck)
return addX("");
int len = args.length;
@@ -12307,7 +12307,7 @@
return addX(array);
}
- private boolean evaluateMath(Token[] args, int tok) throws ScriptException {
+ private boolean evaluateMath(Token[] args, int tok) {
if (tok == Token.quaternion || tok == Token.axisangle) {
// quaternion(vector, theta)
// quaternion(q0, q1, q2, q3)
@@ -12371,7 +12371,7 @@
return false;
}
- private boolean evaluateRandom(Token[] args) throws ScriptException {
+ private boolean evaluateRandom(Token[] args) {
if (args.length > 2)
return false;
if (isSyntaxCheck)
@@ -12382,7 +12382,7 @@
return addX((float)(Math.random() * range) + lower);
}
- private boolean evaluateCross(Token[] args) throws ScriptException {
+ private boolean evaluateCross(Token[] args) {
if (args.length != 2)
return false;
Token x1 = args[0];
@@ -12397,7 +12397,7 @@
return addX(new Point3f(a));
}
- private boolean evaluateLoad(Token[] args) throws ScriptException {
+ private boolean evaluateLoad(Token[] args) {
if (args.length != 1)
return false;
if (isSyntaxCheck)
@@ -12427,7 +12427,7 @@
return addX(sb.toString());
}
- private boolean evaluateData(Token[] args) throws ScriptException {
+ private boolean evaluateData(Token[] args) {
if (args.length == 0 || args.length > 2)
return false;
if (isSyntaxCheck)
@@ -12485,7 +12485,7 @@
return addX(getBitsetIdent(Token.bsSelect(x1), format, x1.value, true));
}
- private boolean evaluateWithin(Token[] args) throws ScriptException {
+ private boolean evaluateWithin(Token[] args) {
if (args.length < 1)
return false;
int i = args.length;
@@ -13072,7 +13072,7 @@
return true;
}
- private boolean evaluateBoundBox(Token x2) throws ScriptException {
+ private boolean evaluateBoundBox(Token x2) {
if (x2.tok != Token.bitset)
return false;
if (isSyntaxCheck)
@@ -13176,8 +13176,13 @@
return null;
}
- void stackOverflow() throws ScriptException {
- evalError(GT._("too many parentheses"));
+ void stackOverflow() {
+ oStack = (Token[]) ArrayUtil.doubleLength(oStack);
+ xStack = (Token[]) ArrayUtil.doubleLength(xStack);
+ maxLevel *= 2;
+ return;
+ //
+ //evalError(GT._("too many parentheses"));
}
}
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-07-10 18:17:08 UTC (rev 9580)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-07-10 19:07:02 UTC (rev 9581)
@@ -2,6 +2,7 @@
# add it on line starting with # below the "version=..." line
version=11.5.46_dev
+# bug fix: array size limited
# new feature: quaternion({atom expression}) -- returns calculated
# frame based on quaternionFrame setting.
# bug fix: drawhover not in state
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|
|
From: <ha...@us...> - 2008-07-15 14:06:13
|
Revision: 9594
http://jmol.svn.sourceforge.net/jmol/?rev=9594&view=rev
Author: hansonr
Date: 2008-07-15 07:05:48 -0700 (Tue, 15 Jul 2008)
Log Message:
-----------
11.5.47 VERSION
# bug fix: 11.5.46 broke standard "spin x 30"
# new feature: draw ARC {pt1} {pt2} {ptref} {theta0, nDegrees, fractionalOffset}
# new feature: draw ARROW ARC {pt1} {pt2} {ptref} {theta0, nDegrees, fractionalOffset}
#
# draws a circular arc or arrow around an axis defined by {pt1} and {pt2}
# using {ptref} as a starting point (looking down the axis, angles
# are measured in a clockwise manner, starting with the projected position
# of {ptref} in a plane perpendicular to the axis. This is similar (but opposite)
# to the way dihedral angles are indicated.
# theta0 is the the offset angle from 0
# nDegrees is the number of degrees of arc to draw
# fractionalOffset is the fraction of the distance from {pt1} to {pt2} for the
# plane containing the arc.
#
# new feature: draw RAMACHANDRAN
# draws phi and psi angles in the form of draw ARROW ARC
# new feature: write RAMACHANDRAN draw
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/viewer/Eval.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/viewer/Eval.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Eval.java 2008-07-15 13:33:46 UTC (rev 9593)
+++ trunk/Jmol/src/org/jmol/viewer/Eval.java 2008-07-15 14:05:48 UTC (rev 9594)
@@ -4988,8 +4988,8 @@
// rotate axisangle {0 1 0} 10
// rotate x 10 (atoms) # point-centered
// rotate x 10 $object # point-centered
- viewer.rotateAxisAngleAtCenter(points[0], rotAxis, degrees, endDegrees,
- isSpin, bsAtoms);
+ viewer.rotateAxisAngleAtCenter(nPoints == 1 ? new Point3f(points[0]) : null,
+ rotAxis, degrees, endDegrees, isSpin, bsAtoms);
return;
}
// rotate MOLECULAR
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-07-15 13:33:46 UTC (rev 9593)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-07-15 14:05:48 UTC (rev 9594)
@@ -1,8 +1,9 @@
# Developers: to add a description of changes you have made,
# add it on line starting with # below the "version=..." line
-version=11.5.47_dev
+version=11.5.47
+# bug fix: 11.5.46 broke standard "spin x 30"
# new feature: draw ARC {pt1} {pt2} {ptref} {theta0, nDegrees, fractionalOffset}
# new feature: draw ARROW ARC {pt1} {pt2} {ptref} {theta0, nDegrees, fractionalOffset}
#
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ha...@us...> - 2008-07-15 17:48:40
|
Revision: 9596
http://jmol.svn.sourceforge.net/jmol/?rev=9596&view=rev
Author: hansonr
Date: 2008-07-15 10:48:35 -0700 (Tue, 15 Jul 2008)
Log Message:
-----------
11.5.47 VERSION (b)
# bug fix: 11.5.46 broke standard "spin x 30" (b)
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/viewer/Eval.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/viewer/Eval.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Eval.java 2008-07-15 15:54:38 UTC (rev 9595)
+++ trunk/Jmol/src/org/jmol/viewer/Eval.java 2008-07-15 17:48:35 UTC (rev 9596)
@@ -4977,20 +4977,21 @@
return;
if (degrees == Float.MIN_VALUE)
degrees = 10;
- if (nPoints == 0)
- points[0] = new Point3f();
if (isSelected && bsAtoms == null)
bsAtoms = viewer.getSelectionSet();
if (nPoints < 2) {
+
if (!isMolecular) {
// fixed-frame rotation
// rotate x 10 # Chime-like
// rotate axisangle {0 1 0} 10
// rotate x 10 (atoms) # point-centered
// rotate x 10 $object # point-centered
- viewer.rotateAxisAngleAtCenter(nPoints == 1 ? new Point3f(points[0]) : null,
+ viewer.rotateAxisAngleAtCenter(points[0],
rotAxis, degrees, endDegrees, isSpin, bsAtoms);
return;
+ } else if (nPoints == 0) {
+ points[0] = new Point3f();
}
// rotate MOLECULAR
// rotate MOLECULAR (atom1)
@@ -5001,7 +5002,7 @@
}
if (points[0].distance(points[1]) == 0) {
points[1] = new Point3f(points[0]);
- points[1].y += 1.0;
+ points[1].y -= 1.0;
}
viewer.rotateAboutPointsInternal(points[0], points[1], degrees, endDegrees,
isSpin, bsAtoms);
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-07-15 15:54:38 UTC (rev 9595)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2008-07-15 17:48:35 UTC (rev 9596)
@@ -5,7 +5,7 @@
# bug fix: Removed stray semicolons from header script comments in webexport templates. They
# were causing WYSIWG web editors to corrupt the code scripts.
-# bug fix: 11.5.46 broke standard "spin x 30"
+# bug fix: 11.5.46 broke standard "spin x 30" (b)
# new feature: draw ARC {pt1} {pt2} {ptref} {theta0, nDegrees, fractionalOffset}
# new feature: draw ARROW ARC {pt1} {pt2} {ptref} {theta0, nDegrees, fractionalOffset}
#
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