Revision: 20155
http://sourceforge.net/p/jmol/code/20155
Author: hansonr
Date: 2014-12-05 04:03:24 +0000 (Fri, 05 Dec 2014)
Log Message:
-----------
Jmol.___JmolVersion="14.3.11_2014.12.04"
new feature: "....".split("",true) // CSV split of string to array of arrays
new feature: [...].split("",true) // CSV split of array to array of arrays
new feature: "...".split("\t",true) // tab split of string to array of arrays
new feature: [...].split("\t",true) // tab split of array to array of arrays
new feature: [...][...].join("",true) // CSV join to array of lines
new feature: [...][...].join("\t",true) // tab join to array of lines
-- example:
x = load("test.csv").lines.split("",true) //from CSV
print x.join("",true) // back to CSV
print x.join("\t",true) // to tab-separated
new feature: [...][...].col(n)
-- extracts nth column from an array of arrays
-- example:
x = load("test.csv").lines.split("",true).col(3) //3rd column from CSV
Modified Paths:
--------------
trunk/Jmol/src/javajs/util/PT.java
trunk/Jmol/src/org/jmol/script/ScriptEval.java
trunk/Jmol/src/org/jmol/script/T.java
trunk/Jmol/src/org/jmol/scriptext/MathExt.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/javajs/util/PT.java
===================================================================
--- trunk/Jmol/src/javajs/util/PT.java 2014-12-02 13:02:46 UTC (rev 20154)
+++ trunk/Jmol/src/javajs/util/PT.java 2014-12-05 04:03:24 UTC (rev 20155)
@@ -548,21 +548,55 @@
return getQuotedStringNext(line, next);
}
+ /**
+ *
+ * @param line
+ * @param next passes [current pointer]
+ * @return quoted string -- does NOT unescape characters
+ */
public static String getQuotedStringNext(String line, int[] next) {
- String value = line;
int i = next[0];
- if (i < 0 || (i = value.indexOf("\"", i)) < 0)
+ if (i < 0 || (i = line.indexOf("\"", i)) < 0)
return "";
- next[0] = ++i;
- value = value.substring(i);
- i = -1;
- while (++i < value.length() && value.charAt(i) != '"')
- if (value.charAt(i) == '\\')
+ int pt = i + 1;
+ int len = line.length();
+ while (++i < len && line.charAt(i) != '"')
+ if (line.charAt(i) == '\\')
i++;
- next[0] += i + 1;
- return value.substring(0, i);
+ next[0] = i + 1;
+ return line.substring(pt, i);
}
+ /**
+ * CSV format -- escaped quote is "" WITHIN "..."
+ *
+ *
+ * @param line
+ * @param next int[2] filled with [ptrQuote1, ptrAfterQuote2]
+ * @return unescaped string or null
+ */
+ public static String getCSVString(String line, int[] next) {
+ int i = next[1];
+ if (i < 0 || (i = line.indexOf("\"", i)) < 0)
+ return null;
+ int pt = next[0] = i;
+ int len = line.length();
+ boolean escaped = false;
+ boolean haveEscape = false;
+ while (++i < len
+ && (line.charAt(i) != '"' || (escaped = (i + 1 < len && line.charAt(i
+ 1) == '"'))))
+ if (escaped) {
+ escaped = false;
+ haveEscape = true;
+ i++;
+ }
+ if (i >= len)
+ return null; // unmatched
+ next[1] = i + 1;
+ String s = line.substring(pt + 1, i);
+ return (haveEscape ? rep(rep(s, "\"\"", "\0"), "\0","\"") : s);
+ }
+
public static boolean isOneOf(String key, String semiList) {
if (semiList.length() == 0)
return false;
@@ -581,11 +615,8 @@
}
/**
- * Does a clean replace of strFrom in str with strTo. This method has far
- * faster performance than just String.replace() when str does not contain
- * strFrom, but is about 15% slower when it does. (Note that
- * String.replace(CharSeq, CharSeq) was introduced in Java 1.5. Finally
- * getting around to using it in Jmol!)
+ * Does a clean ITERATIVE replace of strFrom in str with strTo.
+ * Thus, rep("Testttt", "tt","t") becomes "Test".
*
* @param str
* @param strFrom
Modified: trunk/Jmol/src/org/jmol/script/ScriptEval.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptEval.java 2014-12-02 13:02:46 UTC
(rev 20154)
+++ trunk/Jmol/src/org/jmol/script/ScriptEval.java 2014-12-05 04:03:24 UTC
(rev 20155)
@@ -8585,9 +8585,9 @@
if (key.startsWith("_"))
invArg();
if (key.indexOf("/") >= 0)
- contextVariables.put(key, t = SV.newI(0));
+ contextVariables.put(key.toLowerCase(), t = SV.newI(0));
else
- t = vwr.g.getOrSetNewVariable(key, true);
+ t = vwr.g.getOrSetNewVariable(key, true);
}
return t;
}
Modified: trunk/Jmol/src/org/jmol/script/T.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/T.java 2014-12-02 13:02:46 UTC (rev
20154)
+++ trunk/Jmol/src/org/jmol/script/T.java 2014-12-05 04:03:24 UTC (rev
20155)
@@ -742,10 +742,8 @@
public final static int div = 0 | 1 << 9 | mathfunc | mathproperty;
public final static int dot = 1 | 1 << 9 | mathfunc | mathproperty;
- public final static int join = 2 | 1 << 9 | mathfunc | mathproperty;
public final static int mul = 3 | 1 << 9 | mathfunc | mathproperty;
public final static int mul3 = 4 | 1 << 9 | mathfunc | mathproperty;
- public final static int split = 6 | 1 << 9 | mathfunc | mathproperty;
public final static int sub = 7 | 1 << 9 | mathfunc | mathproperty;
public final static int trim = 8 | 1 << 9 | mathfunc | mathproperty;
public final static int volume = 9 | 1 << 9 | mathfunc | mathproperty
| floatproperty;
@@ -755,7 +753,7 @@
// xxx(a,b)
public final static int cross = 1 | 2 << 9 | mathfunc;
- public final static int load = 2 | 2 << 9 | mathfunc | scriptCommand;
+ public final static int load = 3 | 2 << 9 | mathfunc | scriptCommand;
public final static int random = 4 | 2 << 9 | mathfunc;
public final static int script = 5 | 2 << 9 | mathfunc | scriptCommand;
public final static int substructure = 6 | 2 << 9 | mathfunc | intproperty |
strproperty;
@@ -775,7 +773,9 @@
public final static int add = 1 | 2 << 9 | mathfunc | mathproperty;
public final static int distance = 2 | 2 << 9 | mathfunc | mathproperty;
public final static int push = 3 | 2 << 9 | mathfunc | mathproperty
| scriptCommand | noArgs; //internal only;
-
+ public final static int join = 4 | 2 << 9 | mathfunc | mathproperty;
+ public final static int split = 5 | 2 << 9 | mathfunc | mathproperty;
+
// xxx(a,b,c)
public final static int hkl = 1 | 3 << 9 | mathfunc;
Modified: trunk/Jmol/src/org/jmol/scriptext/MathExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/scriptext/MathExt.java 2014-12-02 13:02:46 UTC
(rev 20154)
+++ trunk/Jmol/src/org/jmol/scriptext/MathExt.java 2014-12-05 04:03:24 UTC
(rev 20155)
@@ -1124,7 +1124,8 @@
/**
* array.add(x) array.add(sep, x) array.sub(x) array.mul(x) array.mul3(x)
- * array.div(x) array.push() array.pop()
+ * array.div(x) array.push() array.pop() array.split("")
+ * array.split("\t",true)
*
* @param mp
* @param tok
@@ -1140,13 +1141,16 @@
SV x2;
switch (tok) {
case T.push:
- return (len == 2 && mp.addX(x1.pushPop(args[1], args[0])) || len == 1 &&
mp.addX(x1.pushPop(args[0], null)));
+ return (len == 2 && mp.addX(x1.pushPop(args[1], args[0])) || len == 1
+ && mp.addX(x1.pushPop(args[0], null)));
case T.pop:
- return (len == 1 && mp.addX(x1.pushPop(null, args[0])) || len == 0 &&
mp.addX(x1.pushPop(null, null)));
+ return (len == 1 && mp.addX(x1.pushPop(null, args[0])) || len == 0
+ && mp.addX(x1.pushPop(null, null)));
case T.add:
if (len != 1 && len != 2)
return false;
break;
+ case T.split:
case T.join:
break;
default:
@@ -1156,14 +1160,89 @@
String[] sList1 = null, sList2 = null, sList3 = null;
if (len == 2) {
- // [xxxx].add("\t", [...])
+ // [...].add("\t", [...])
+ // [...].split("\t", true) [split individual elements as strings]
+ // [...].split("", true) [CSV split]
+ // [...][...].join("x", true) [2D-array line join]
+ // [...][...].join("", true) [CSV join]
int itab = (args[0].tok == T.string ? 0 : 1);
String tab = SV.sValue(args[itab]);
- sList1 = (isArray1 ? SV.strListValue(x1) : PT.split(SV.sValue(x1),
- "\n"));
+ if (len == 2) {
+ Lst<SV> l = x1.getList();
+ boolean isCSV = (tab.length() == 0);
+ if (isCSV)
+ tab = ",";
+ if (tok == T.join) {
+ SV[] s2 = new SV[l.size()];
+ for (int i = l.size(); --i >= 0;) {
+ Lst<SV> a = l.get(i).getList();
+ if (a == null)
+ s2[i] = l.get(i);
+ else {
+ SB sb = new SB();
+ for (int j = 0, n = a.size(); j < n; j++) {
+ if (j > 0)
+ sb.append(tab);
+ SV sv = a.get(j);
+ sb.append(isCSV && sv.tok == T.string ? "\"" + PT.rep(
+ (String) sv.value, "\"", "\"\"") + "\""
+ : "" + sv.asString());
+ }
+ s2[i] = SV.newS(sb.toString());
+ }
+ }
+ return mp.addXAV(s2);
+ }
+ SV[] sa = new SV[l.size()];
+ if (isCSV)
+ tab = "\0";
+ int[] next = new int[2];
+ for (int i = l.size(); --i >= 0;) {
+ String line = l.get(i).asString();
+ if (isCSV) {
+ next[1] = 0;
+ next[0] = 0;
+ int last = 0;
+ while (true) {
+ String s = PT.getCSVString(line, next);
+ if (s == null) {
+ line = line.substring(0, last)
+ + line.substring(last).replace(',', '\0');
+ break;
+ }
+ line = line.substring(0, last)
+ + line.substring(last, next[0]).replace(',', '\0') + s
+ + line.substring(next[1]);
+ next[1] = last = next[0] + s.length();
+ }
+ }
+ String[] linaa = line.split(tab);
+ Lst<SV> la = new Lst<SV>();
+ for (int j = 0, n = linaa.length; j < n; j++) {
+ String s = linaa[j];
+ if (s.indexOf(".") < 0)
+ try {
+ la.addLast(SV.newI(Integer.parseInt(s)));
+ continue;
+ } catch (Exception e) {
+ }
+ else
+ try {
+ la.addLast(SV.getVariable(Float.valueOf(Float.parseFloat(s))));
+ continue;
+ } catch (Exception ee) {
+ }
+ la.addLast(SV.newS(s));
+ }
+ sa[i] = SV.getVariableList(la);
+ }
+ return mp.addXObj(SV.getVariable(sa));
+ }
+
+ sList1 = (isArray1 ? SV.strListValue(x1) : PT.split(SV.sValue(x1),
"\n"));
x2 = args[1 - itab];
- sList2 = (x2.tok == T.varray ? SV.strListValue(x2) :
PT.split(SV.sValue(x2),
- "\n"));
+ sList2 = (x2.tok == T.varray ? SV.strListValue(x2) : PT.split(
+ SV.sValue(x2), "\n"));
sList3 = new String[len = Math.max(sList1.length, sList2.length)];
for (int i = 0; i < len; i++)
sList3[i] = (i >= sList1.length ? "" : sList1[i]) + tab
@@ -1230,7 +1309,7 @@
SV[] olist = new SV[len];
if (isArray1 && isAll) {
- Lst<SV> llist = new Lst<SV>();
+ Lst<SV> llist = new Lst<SV>();
return mp.addXList(addAllLists(x1.getList(), llist));
}
SV a = (isScalar1 ? x1 : null);
@@ -1926,6 +2005,17 @@
m4.getColumn(n, f);
return mp.addXAF(f);
}
+ case T.varray:
+ // column of a[][]
+ Lst<SV> l1 = x1.getList();
+ Lst<SV> l2 = new Lst<SV>();
+ for (int i = 0, len = l1.size(); i < len; i++) {
+ Lst<SV> l3 = l1.get(i).getList();
+ if (l3 == null)
+ return mp.addXStr("");
+ l2.addLast(n < l3.size() ? l3.get(n) : SV.newS(""));
+ }
+ return mp.addXList(l2);
}
return false;
@@ -2086,17 +2176,31 @@
private boolean evaluateString(ScriptMathProcessor mp, int tok, SV[] args)
throws ScriptException {
- if (args.length > 1)
- return false;
SV x = mp.getX();
- if (x.tok == T.varray && tok != T.split && tok != T.trim) {
+ String sArg = (args.length > 0 ? SV.sValue(args[0]) : tok == T.trim ? ""
+ : "\n");
+ switch (args.length) {
+ case 0:
+ case 1:
+ break;
+ case 2:
+ if (x.tok == T.varray)
+ break;
+ if (tok == T.split) {
+ x = SV.getVariable(PT.split(PT.rep((String) x.value, "\n\r",
"\n").replace('\r', '\n'), "\n"));
+ break;
+ }
+ //$FALL-THROUGH$
+ default:
+ return false;
+ }
+
+ if (x.tok == T.varray && tok != T.trim && (tok != T.split || args.length
== 2)) {
mp.addX(x);
return evaluateList(mp, tok, args);
}
- String s = (tok == T.split && x.tok == T.bitset || tok == T.trim
- && x.tok == T.varray ? null : SV.sValue(x));
- String sArg = (args.length == 1 ? SV.sValue(args[0]) : tok == T.trim ? ""
- : "\n");
+ String s = (tok == T.split && x.tok == T.bitset
+ || tok == T.trim && x.tok == T.varray ? null : SV.sValue(x));
switch (tok) {
case T.split:
if (x.tok == T.bitset) {
@@ -2110,7 +2214,7 @@
bs.and(bsSelected);
s += Escape.eBS(bs);
}
- }
+ }
return mp.addXAS(PT.split(s, sArg));
case T.join:
if (s.length() > 0 && s.charAt(s.length() - 1) == '\n')
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2014-12-02 13:02:46 UTC
(rev 20154)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2014-12-05 04:03:24 UTC
(rev 20155)
@@ -17,6 +17,7 @@
Jmol.___JmolVersion="14.3.11_2014.12.02"
+bug fix: for (x in yUpperCase) fails
bug fix: draw SYMOP fails for incommensurate space groups
bug fix: incommensurate magnetic CIF reading does not apply magnetic spin
operation to spin modulations
bug fix: CIF reader can cycle infinitely if loop_ keywords are not followed by
any data
@@ -29,6 +30,8 @@
new feature: readers for ESS input types: CFILE, VFILE, MOPAC, NWChem,
Gaussian, GAMESS, Orca, PQS
-- CFILE and VFILE require CFI:: and VFI:: (or C:: and V::)
-- MOPAC requires MND::
+ -- any of these could also use ZMATRIX:: or INPUT::
+
bug fix: dynamicMeasurements deprecated in 14.1.1 but
not left in as a valid token to allow use
@@ -45,6 +48,8 @@
released as 14.3.10
+(note - these were not fixed in 14.2)
+
bug fix: SPIN BRANCH {atomno=2} {atomno=1} does not work
code: scriptExt.IsoExt splits CmdExt into two parts
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