Revision: 20761
http://sourceforge.net/p/jmol/code/20761
Author: hansonr
Date: 2015-09-09 03:46:44 +0000 (Wed, 09 Sep 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.3.16_2015.09.08"
code: Efficient JSON parser javajs.util.JSONParser
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/smarter/SmarterJmolAdapter.java
trunk/Jmol/src/org/jmol/modelsetbio/BioModel.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/Viewer.java
Added Paths:
-----------
trunk/Jmol/src/javajs/util/JSJSONParser.java
trunk/Jmol/src/javajs/util/JSONException.java
Added: trunk/Jmol/src/javajs/util/JSJSONParser.java
===================================================================
--- trunk/Jmol/src/javajs/util/JSJSONParser.java
(rev 0)
+++ trunk/Jmol/src/javajs/util/JSJSONParser.java 2015-09-09 03:46:44 UTC
(rev 20761)
@@ -0,0 +1,316 @@
+package javajs.util;
+
+import java.util.HashMap;
+import java.util.Map;
+
+
+
+/**
+ * a very simple JSON parser for JSON objects that are compatible with
JavaScript
+ * A gross simplification of https://github.com/douglascrockford/JSON-java
+ *
+ * A SUBSET of JSON with similarly to window.JSON.parse():
+ *
+ * -- requires quoted strings for keys and values
+ *
+ * -- does not allow /xxx/ objects
+ *
+ *
+ */
+public class JSJSONParser {
+
+ private String str;
+ private int index;
+ private int len;
+
+ public JSJSONParser () {
+ // for reflection
+ }
+
+ /**
+ * requires { "key":"value", "key":"value",....}
+ *
+ * @param str
+ *
+ * @return Map or null
+ */
+ @SuppressWarnings("unchecked")
+ public Map<String, Object> parseMap(String str) {
+ index = 0;
+ this.str = str;
+ len = str.length();
+ if (getChar() != '{')
+ return null;
+ returnChar();
+ return (Map<String, Object>) getValue(false);
+ }
+
+ /**
+ * Could return Integer, Double, Boolean, String, Map<String, Object>,
Lst<Object>, or null
+ *
+ * @param str
+ * @return a object equivalent to the JSON string str
+ *
+ */
+ public Object parse(String str) {
+ index = 0;
+ this.str = str;
+ len = str.length();
+ return getValue(false);
+ }
+
+ private char next() {
+ return (index < len ? str.charAt(index++) : '\0');
+ }
+
+ private void returnChar() {
+ index--;
+ }
+
+ /**
+ * Get the next char in the string, skipping whitespace.
+ *
+ * @throws JSONException
+ * @return one character, or 0 if there are no more characters.
+ */
+ private char getChar() throws JSONException {
+ for (;;) {
+ char c = next();
+ if (c == 0 || c > ' ') {
+ return c;
+ }
+ }
+ }
+
+ /**
+ * only allowing the following values:
+ *
+ * {...} object
+ *
+ * [...] array
+ *
+ * Integer
+ *
+ * Double
+ *
+ * "quoted string"
+ *
+ *
+ * @param isKey if we should allow {...} and [...]
+ * @return a subclass of Object
+ * @throws JSONException
+ */
+ private Object getValue(boolean isKey) throws JSONException {
+ int i = index;
+ char c = getChar();
+ switch (c) {
+ case '\0':
+ return null;
+ case '"':
+ case '\'':
+ return getString(c);
+ case '{':
+ if (!isKey)
+ return getObject();
+ c = 0;
+ break;
+ case '[':
+ if (!isKey)
+ return getArray();
+ c = 0;
+ break;
+ default:
+ // standard syntax is assumed; not checking all possible invalid keys
+ // for example, "-" is not allowed in JavaScript, which is what this is
for
+ returnChar();
+ while (c >= ' ' && "[,]{:}'\"".indexOf(c) < 0)
+ c = next();
+ returnChar();
+ if (isKey && c != ':')
+ c = 0;
+ break;
+ }
+ if (isKey && c == 0)
+ throw new JSONException("invalid key");
+
+ String string = str.substring(i, index);
+
+ // check for the only valid simple words: true, false, null (lower case)
+ // and in this case, only for
+
+ if (!isKey) {
+ if (string.equals("true")) {
+ return Boolean.TRUE;
+ }
+ if (string.equals("false")) {
+ return Boolean.FALSE;
+ }
+ if (string.equals("null")) {
+ return null;
+ }
+ }
+ // only numbers from here on:
+
+ c = string.charAt(0);
+ if (c >= '0' && c <= '9' || c == '-')
+ try {
+ if (string.indexOf('.') < 0 && string.indexOf('e') < 0
+ && string.indexOf('E') < 0)
+ return new Integer(string);
+ // not allowing infinity or NaN
+ Double d = Double.valueOf(string);
+ if (!d.isInfinite() && !d.isNaN())
+ return d;
+ } catch (Exception e) {
+ }
+ // not a valid number
+ throw new JSONException("invalid value");
+ }
+
+ private String getString(char quote) throws JSONException {
+ char c;
+ SB sb = null;
+ int i0 = index;
+ for (;;) {
+ int i1 = index;
+ switch (c = next()) {
+ case '\0':
+ case '\n':
+ case '\r':
+ throw syntaxError("Unterminated string");
+ case '\\':
+ switch (c = next()) {
+ case '"':
+ case '\'':
+ case '\\':
+ case '/':
+ break;
+ case 'b':
+ c = '\b';
+ break;
+ case 't':
+ c = '\t';
+ break;
+ case 'n':
+ c = '\n';
+ break;
+ case 'f':
+ c = '\f';
+ break;
+ case 'r':
+ c = '\r';
+ break;
+ case 'u':
+ int i = index;
+ index += 4;
+ try {
+ c = (char) Integer.parseInt(str.substring(i, index), 16);
+ } catch (Exception e) {
+ throw syntaxError("Substring bounds error");
+ }
+ break;
+ default:
+ throw syntaxError("Illegal escape.");
+ }
+ break;
+ default:
+ if (c == quote)
+ return (sb == null ? str.substring(i0, i1) : sb.toString());
+ break;
+ }
+ if (index > i1 + 1) {
+ if (sb == null) {
+ sb = new SB();
+ sb.append(str.substring(i0, i1));
+ }
+ }
+ if (sb != null)
+ sb.appendC(c);
+ }
+ }
+
+ private Object getObject() {
+ Map<String, Object> map = new HashMap<String, Object>();
+ String key = null;
+ switch (getChar()) {
+ case '}':
+ return map;
+ case 0:
+ throw new JSONException("invalid object");
+ }
+ returnChar();
+ boolean isKey = false;
+ for (;;) {
+ if ((isKey = !isKey) == true)
+ key = getValue(true).toString();
+ else
+ map.put(key, getValue(false));
+ switch (getChar()) {
+ case '}':
+ return map;
+ case ':':
+ if (isKey)
+ continue;
+ isKey = true;
+ //$FALL-THROUGH$
+ case ',':
+ if (!isKey)
+ continue;
+ //$FALL-THROUGH$
+ default:
+ throw syntaxError("Expected ',' or ':' or '}'");
+ }
+ }
+ }
+
+ private Object getArray() {
+ Lst<Object> l = new Lst<Object>();
+ switch (getChar()) {
+ case ']':
+ return l;
+ case 0:
+ throw new JSONException("invalid array");
+ }
+ returnChar();
+ boolean isNull = false;
+ for (;;) {
+ if (isNull) {
+ l.addLast(null);
+ isNull = false;
+ } else {
+ l.addLast(getValue(false));
+ }
+ switch (getChar()) {
+ case ',':
+ switch (getChar()) {
+ case ']':
+ // terminal ,
+ return l;
+ case ',':
+ // empty value
+ isNull = true;
+ //$FALL-THROUGH$
+ default:
+ returnChar();
+ }
+ continue;
+ case ']':
+ return l;
+ default:
+ throw syntaxError("Expected ',' or ']'");
+ }
+ }
+ }
+
+ /**
+ * Make a JSONException to signal a syntax error.
+ *
+ * @param message
+ * The error message.
+ * @return A JSONException object, suitable for throwing
+ */
+ public JSONException syntaxError(String message) {
+ return new JSONException(message + " for " + str.substring(0,
Math.min(index, len)));
+ }
+
+}
Property changes on: trunk/Jmol/src/javajs/util/JSJSONParser.java
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+text/plain
\ No newline at end of property
Added: trunk/Jmol/src/javajs/util/JSONException.java
===================================================================
--- trunk/Jmol/src/javajs/util/JSONException.java
(rev 0)
+++ trunk/Jmol/src/javajs/util/JSONException.java 2015-09-09 03:46:44 UTC
(rev 20761)
@@ -0,0 +1,8 @@
+package javajs.util;
+
+public class JSONException extends RuntimeException {
+ public JSONException(String message) {
+ super(message);
+ }
+
+}
Property changes on: trunk/Jmol/src/javajs/util/JSONException.java
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+text/plain
\ No newline at end of property
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/SmarterJmolAdapter.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/SmarterJmolAdapter.java
2015-09-08 06:25:42 UTC (rev 20760)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/SmarterJmolAdapter.java
2015-09-09 03:46:44 UTC (rev 20761)
@@ -31,10 +31,13 @@
import org.jmol.api.JmolFilesReaderInterface;
import javajs.api.GenericBinaryDocument;
+import javajs.api.Interface;
import javajs.util.Lst;
import org.jmol.script.SV;
import org.jmol.util.Logger;
+
+import javajs.util.JSJSONParser;
import javajs.util.P3;
import javajs.util.PT;
import javajs.util.Rdr;
@@ -46,7 +49,6 @@
import java.util.Map;
-
public class SmarterJmolAdapter extends JmolAdapter {
/**************************************************************
@@ -207,7 +209,7 @@
// hack to determine type:
String type = (f.contains("version\":\"DSSR") ? "dssr" : f
.contains("/outliers/") ? "validation" : "domains");
- SV x = vwr.evaluateExpressionAsVariable(f);
+ SV x = vwr.parseJSON(f);
if (x != null && x.getMap() != null)
htParams.put(type, x);
continue;
Modified: trunk/Jmol/src/org/jmol/modelsetbio/BioModel.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelsetbio/BioModel.java 2015-09-08 06:25:42 UTC
(rev 20760)
+++ trunk/Jmol/src/org/jmol/modelsetbio/BioModel.java 2015-09-09 03:46:44 UTC
(rev 20761)
@@ -1324,7 +1324,7 @@
Object annotv = cache.get(key);
if (annotv == null && ann != null) {
annotv = (ann instanceof SV || ann instanceof Hashtable ? ann
- : vwr.evaluateExpressionAsVariable(ann));
+ : vwr.parseJSON((String) ann));
cache.put(key, annotv);
}
return (annotv instanceof SV || annotv instanceof Hashtable ? annotv :
null);
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-09-08 06:25:42 UTC
(rev 20760)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-09-09 03:46:44 UTC
(rev 20761)
@@ -58,8 +58,12 @@
TODO: image off stops JSmol
-Jmol.___JmolVersion="14.3.16_2015.09.06"
+Jmol.___JmolVersion="14.3.16_2015.09.08"
+code: Efficient JSON parser javajs.util.JSONParser
+
+JmolVersion="14.3.16_2015.09.06"
+
new feature: 3DNA DSSR JSON mode
--
http://x3dna.bio.columbia.edu/dssr/report.php?id=1ehz&opts=--more%20--json=ebi-no-str-id
-- uses unit ids
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2015-09-08 06:25:42 UTC (rev
20760)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2015-09-09 03:46:44 UTC (rev
20761)
@@ -45,6 +45,7 @@
import javajs.awt.Font;
import javajs.util.CU;
import javajs.util.DF;
+import javajs.util.JSJSONParser;
import javajs.util.Lst;
import javajs.util.M3;
import javajs.util.M4;
@@ -9345,7 +9346,7 @@
jmolpopup.jpiUpdateComputedMenus();
}
- JmolChimeMessenger jcm;
+ private JmolChimeMessenger jcm;
public JmolChimeMessenger getChimeMessenger() {
return (jcm == null ? jcm = ((JmolChimeMessenger) Interface.getInterface(
@@ -9357,4 +9358,11 @@
false));
}
+ private JSJSONParser jsonParser;
+
+ public SV parseJSON(String ann) {
+ if (jsonParser == null)
+ jsonParser = ((JSJSONParser)
Interface.getInterface("javajs.util.JSJSONParser", this, "script"));
+ return SV.getVariable(jsonParser.parseMap(ann));
+ }
}
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