Revision: 21297
http://sourceforge.net/p/jmol/code/21297
Author: hansonr
Date: 2016-12-02 13:01:31 +0000 (Fri, 02 Dec 2016)
Log Message:
-----------
Jmol.___JmolVersion="14.7.4_2016.12.02"
new feature: fully implemented CIF 2.0 reader
new feature: x = getProperty("cifInfo", "c:/temp/test.cif")
-- reads CIF file data in structured format
-- automatically uses CIF 1.0 or CIF 2.0, as needed.
Modified Paths:
--------------
trunk/Jmol/src/javajs/util/CifDataParser.java
trunk/Jmol/src/org/jmol/adapter/readers/cif/Cif2DataParser.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/PropertyManager.java
Modified: trunk/Jmol/src/javajs/util/CifDataParser.java
===================================================================
--- trunk/Jmol/src/javajs/util/CifDataParser.java 2016-12-02 05:30:58 UTC
(rev 21296)
+++ trunk/Jmol/src/javajs/util/CifDataParser.java 2016-12-02 13:01:31 UTC
(rev 21297)
@@ -857,49 +857,48 @@
/**
* CIF 1.0 only; we handle various quote types here
* @param ch
- * @return true if this character is a (starting) qyuote
+ * @return true if this character is a (starting) quote
*/
protected boolean isQuote(char ch) {
switch (ch) {
case '\'':
case '\"':
case '\1':
- case '[':
return true;
}
return false;
}
/**
- * CIF 1.0 only, with addition of SIMPLE arrays due to the fact that
- * the MagCIF format includes one data value of that type even though it is
not a CIF 2.0 file.
+ * CIF 1.0 only.
*
- * This is just a rudimentary hack to allow simple [....] in magCIF files.
- * See Cif2DataParser for the real thing.
*
* @param ch current character being pointed to
* @return a String data object
*/
protected Object getQuotedStringOrObject(char ch) {
int ichStart = ich;
- boolean isArray = (ch == '[');
- char chClosingQuote = (isArray ? ']' : ch);
+ char chClosingQuote = ch;
boolean wasQuote = false;
while (++ich < cch) {
ch = str.charAt(ich);
- // CIF 1.0 rules require that the closing ' or "" be followed by space
or tab
+ // CIF 1.0 rules require that the closing ' or "" be followed by space
or tab or EOL
if (wasQuote && (ch == ' ' || ch == '\t'))
break;
wasQuote = (ch == chClosingQuote);
}
- if (ich == cch || isArray) {
- if (wasQuote && !isArray) // close quote was last char of string
- return str.substring(ichStart + 1, ich - 1);
- // reached the end of the string without finding closing ', or we have
[...]
- return str.substring(ichStart, ich);
+ int pt1 = ichStart + 1;
+ int pt2 = ich - 1;
+ if (ich == cch && !wasQuote) {
+ // reached the end of the string without finding closing '
+ // so take the whole thing. Probably a bad CIF file.
+ pt1--;
+ pt2++;
+ } else {
+ // throw away the last white character
+ ++ich;
}
- ++ich; // throw away the last white character
- return str.substring(ichStart + 1, ich - 2);
+ return str.substring(pt1, pt2);
}
Modified: trunk/Jmol/src/org/jmol/adapter/readers/cif/Cif2DataParser.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/cif/Cif2DataParser.java
2016-12-02 05:30:58 UTC (rev 21296)
+++ trunk/Jmol/src/org/jmol/adapter/readers/cif/Cif2DataParser.java
2016-12-02 13:01:31 UTC (rev 21297)
@@ -3,8 +3,6 @@
import java.util.Hashtable;
import java.util.Map;
-import org.jmol.util.Logger;
-
import javajs.util.CifDataParser;
import javajs.util.Lst;
import javajs.util.PT;
@@ -158,8 +156,17 @@
//
//
-
+
/**
+ * There is no need to convert to unicode in CIF 2.0.
+ *
+ */
+ @Override
+ public String toUnicode(String data) {
+ return data;
+ }
+
+ /**
* Includes all possible operator tokens
*/
@Override
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2016-12-02 05:30:58 UTC
(rev 21296)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2016-12-02 13:01:31 UTC
(rev 21297)
@@ -47,16 +47,13 @@
-- sets the echo offset to a specific screen pixel offset
-- TODO not saved in state
-Jmol.___JmolVersion="14.7.4_2016.12.01"
+Jmol.___JmolVersion="14.7.4_2016.12.02"
new feature: fully implemented CIF 2.0 reader
new feature: x = getProperty("cifInfo", "c:/temp/test.cif")
-- reads CIF file data in structured format
-- automatically uses CIF 1.0 or CIF 2.0, as needed.
-
-new feature: CIF reader allows for nonstandard [ .... ] array notation in CIF
1.0 files
- -- returned as an unaltered string for CIF 1.x; JSON string in CIF 2.x
JmolVersion="14.7.4_2016.11.28"
Modified: trunk/Jmol/src/org/jmol/viewer/PropertyManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/PropertyManager.java 2016-12-02 05:30:58 UTC
(rev 21296)
+++ trunk/Jmol/src/org/jmol/viewer/PropertyManager.java 2016-12-02 13:01:31 UTC
(rev 21297)
@@ -174,7 +174,7 @@
"domainInfo" , atomExpression, "{visible}",
"validationInfo" , atomExpression, "{visible}",
"service" , "<hashTable>", "",
- "CIFInfo" , "<filename>", "_modelFile",
+ "CIFInfo" , "<filename>", "",
};
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