Revision: 21246
http://sourceforge.net/p/jmol/code/21246
Author: hansonr
Date: 2016-09-19 01:10:23 +0000 (Mon, 19 Sep 2016)
Log Message:
-----------
Jmol.___JmolVersion="14.7.3_2016.09.18"
new feature: show chemical formula reads formula from CIF
bug fix: write MENU broken for non-English language (UTF-8 strings not
correctly encoded using base64)
bug fix: write PNGJ should not store "#_DOCACHE_" in PNGJ file
bug fix: JSmol echo image loading from PNGJ can fail
bug fix: load "" after pasting in structure to load fails
Modified Paths:
--------------
trunk/Jmol/src/javajs/util/SB.java
trunk/Jmol/src/org/jmol/scriptext/CmdExt.java
trunk/Jmol/src/org/jmol/viewer/FileManager.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/OutputManager.java
Modified: trunk/Jmol/src/javajs/util/SB.java
===================================================================
--- trunk/Jmol/src/javajs/util/SB.java 2016-09-15 03:14:17 UTC (rev 21245)
+++ trunk/Jmol/src/javajs/util/SB.java 2016-09-19 01:10:23 UTC (rev 21246)
@@ -1,6 +1,8 @@
package javajs.util;
+import java.nio.charset.Charset;
+
import javajs.J2SIgnoreImport;
/**
@@ -12,7 +14,7 @@
*
*/
-@J2SIgnoreImport({java.lang.StringBuilder.class})
+@J2SIgnoreImport({java.lang.StringBuilder.class,
java.nio.charset.Charset.class})
public class SB {
private java.lang.StringBuilder sb;
@@ -308,19 +310,33 @@
}
/**
- * simple byte conversion not allowing for unicode.
- * Used for base64 conversion and allows for offset
- * @param off
- * @param len or -1 for full length (then off must = 0)
+ * simple byte conversion properly implementing UTF-8. * Used for base64
+ * conversion and allows for offset
+ *
+ * @param off
+ * @param len
+ * or -1 for full length (then off must = 0)
* @return byte[]
*/
public byte[] toBytes(int off, int len) {
- if (len < 0)
- len = length() - off;
- byte[] b = new byte[len];
- for (int i = off + len, j = i - off; --i >= off;)
- b[--j] = (byte) charAt(i);
- return b;
+ if (len == 0)
+ return new byte[0];
+ Charset cs;
+ /**
+ *
+ * just a string in JavaScript
+ *
+ * @j2sNative
+ *
+ * cs = "UTF-8";
+ *
+ */
+ {
+ cs = Charset.forName("UTF-8");
+ }
+ return (len > 0 ? substring2(off, off + len)
+ : off == 0 ? toString()
+ : substring2(off, length() - off)).getBytes(cs);
}
public void replace(int start, int end, String str) {
Modified: trunk/Jmol/src/org/jmol/scriptext/CmdExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/scriptext/CmdExt.java 2016-09-15 03:14:17 UTC
(rev 21245)
+++ trunk/Jmol/src/org/jmol/scriptext/CmdExt.java 2016-09-19 01:10:23 UTC
(rev 21246)
@@ -4244,52 +4244,61 @@
+ filterLen);
if (chk)
return;
- try {
- if (tok != T.smiles) {
- msg = vwr.ms.getModelDataBaseName(vwr.bsA());
- // this does not work for NCI, because, for example, "$menthol"
returns an enantiomer, but menthol/smiles uses nonstereo option
- // but we don't want to be generating our own SMILES here, do we?
- // what is the solution?
- if (msg != null && (msg.startsWith("$") || msg.startsWith(":"))) {
- msg = msg.substring(1);
+ String param2 = eval.optParameterAsString(2);
+ if (tok == T.chemical && "formula".equals(param2)) {
+ msg = (String) vwr.ms.getInfo(vwr.am.cmi, "formula");
+ // cif files will have formula already
+ if (msg != null)
+ msg = PT.rep(msg, " ", "");
+ }
+ if (msg == null) {
+ try {
+ if (tok != T.smiles) {
+ msg = vwr.ms.getModelDataBaseName(vwr.bsA());
+ // this does not work for NCI, because, for example, "$menthol"
returns an enantiomer, but menthol/smiles uses nonstereo option
+ // but we don't want to be generating our own SMILES here, do we?
+ // what is the solution?
+ if (msg != null && (msg.startsWith("$") || msg.startsWith(":"))) {
+ msg = msg.substring(1);
+ } else {
+ msg = null;
+ }
+ } else if (param2.equalsIgnoreCase("true")) {
+ msg = vwr.getBioSmiles(null);
+ filter = null;
+ } else if (filter != null) {
+ msg = vwr.getSmilesOpt(null, -1, -1, JC.SMILES_TYPE_SMILES, filter
+ + "///");
+ filter = null;
+ }
+ if (msg == null)
+ msg = (tok == T.smiles ? vwr.getSmiles(null) : vwr
+ .getOpenSmiles(null));
+ } catch (Exception ex) {
+ msg = ex.getMessage();
+ }
+ switch (tok) {
+ case T.smiles:
+ break;
+ case T.drawing:
+ if (msg.length() > 0) {
+ vwr.fm.loadImage(vwr.setLoadFormat("_" + msg, '2', false), "\1"
+ + msg, false);
+ return;
+ }
+ msg = "Could not show drawing -- Either insufficient atoms are
selected or the model is a PDB file.";
+ break;
+ case T.chemical:
+ len = 3;
+ if (msg.length() > 0) {
+ msg = vwr.getChemicalInfo(msg, param2);
+ if (msg.indexOf("FileNotFound") >= 0)
+ msg = "?";
} else {
- msg = null;
+ msg = "Could not show name -- Either insufficient atoms are
selected or the model is a PDB file.";
}
- } else if (eval.optParameterAsString(2).equalsIgnoreCase("true")) {
- msg = vwr.getBioSmiles(null);
- filter = null;
- } else if (filter != null) {
- msg = vwr.getSmilesOpt(null, -1, -1, JC.SMILES_TYPE_SMILES, filter
- + "///");
- filter = null;
}
- if (msg == null)
- msg = (tok == T.smiles ? vwr.getSmiles(null) : vwr
- .getOpenSmiles(null));
- } catch (Exception ex) {
- msg = ex.getMessage();
}
- switch (tok) {
- case T.smiles:
- break;
- case T.drawing:
- if (msg.length() > 0) {
- vwr.fm.loadImage(vwr.setLoadFormat("_" + msg, '2', false),
- "\1" + msg, false);
- return;
- }
- msg = "Could not show drawing -- Either insufficient atoms are
selected or the model is a PDB file.";
- break;
- case T.chemical:
- len = 3;
- if (msg.length() > 0) {
- msg = vwr.getChemicalInfo(msg, getToken(2).value.toString());
- if (msg.indexOf("FileNotFound") >= 0)
- msg = "?";
- } else {
- msg = "Could not show name -- Either insufficient atoms are selected
or the model is a PDB file.";
- }
- }
break;
case T.spacegroup:
case T.symop:
Modified: trunk/Jmol/src/org/jmol/viewer/FileManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/FileManager.java 2016-09-15 03:14:17 UTC
(rev 21245)
+++ trunk/Jmol/src/org/jmol/viewer/FileManager.java 2016-09-19 01:10:23 UTC
(rev 21246)
@@ -882,7 +882,8 @@
}
if (!vwr.isJS && image != null && bytes != null)
nameOrError = ";base64," + Base64.getBase64(bytes).toString();
- if (!vwr.isJS || isPopupImage && nameOrError == null)
+ if (!vwr.isJS || isPopupImage && nameOrError == null
+ || !isPopupImage && image != null)
return vwr.loadImageData(image, nameOrError, echoName, null);
return isAsynchronous;
// JSmol will call that from awtjs2d.Platform.java asynchronously
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2016-09-15 03:14:17 UTC
(rev 21245)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2016-09-19 01:10:23 UTC
(rev 21246)
@@ -47,8 +47,13 @@
-- sets the echo offset to a specific screen pixel offset
-- TODO not saved in state
-Jmol.___JmolVersion="14.7.2_2016.09.14"
+Jmol.___JmolVersion="14.7.3_2016.09.18"
+new feature: show chemical formula reads formula from CIF
+
+bug fix: write MENU broken for non-English language (UTF-8 strings not
correctly encoded using base64)
+bug fix: write PNGJ should not store "#_DOCACHE_" in PNGJ file
+bug fix: JSmol echo image loading from PNGJ can fail
bug fix: load "" after pasting in structure to load fails
JmolVersion="14.7.2_2016.09.12"
Modified: trunk/Jmol/src/org/jmol/viewer/OutputManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/OutputManager.java 2016-09-15 03:14:17 UTC
(rev 21245)
+++ trunk/Jmol/src/org/jmol/viewer/OutputManager.java 2016-09-19 01:10:23 UTC
(rev 21246)
@@ -934,6 +934,7 @@
.replaceAllCharacters(name, "/:?\"'=&", "_") : FileManager
.stripPath(name));
newName = PT.replaceAllCharacters(newName, "[]", "_");
+ newName = PT.rep(newName, "#_DOCACHE_", "");
boolean isSparDir = (fm.spardirCache != null && fm.spardirCache
.containsKey(name));
if (isLocal && name.indexOf("|") < 0 && !isSparDir) {
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