[Jmol-commits] SF.net SVN: jmol:[18629] trunk/Jmol/src/org

[<ha...@us...>]

Revision: 18629
          http://sourceforge.net/p/jmol/code/18629
Author:   hansonr
Date:     2013-08-29 15:52:02 +0000 (Thu, 29 Aug 2013)
Log Message:
-----------
___JmolVersion="13.3.5_dev_2013.08.29"

new feature: show NMR taps into NMRDB directly
 -- for now, application only

Modified Paths:
--------------
    trunk/Jmol/src/org/jmol/util/Escape.java
    trunk/Jmol/src/org/jmol/viewer/StateCreator.java
    trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/StatusListener.java

Modified: trunk/Jmol/src/org/jmol/util/Escape.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/Escape.java	2013-08-29 10:35:11 UTC (rev 18628)
+++ trunk/Jmol/src/org/jmol/util/Escape.java	2013-08-29 15:52:02 UTC (rev 18629)
@@ -1035,7 +1035,7 @@
       String s = Parser.getQuotedStringNext(data, next);
       if (s == null)
         return null;
-      v.addLast(s);
+      v.addLast(TextFormat.simpleReplace(s, "\\\"", "\""));
       while (next[0] < data.length() && data.charAt(next[0]) != '"')
         next[0]++;
     }    

Modified: trunk/Jmol/src/org/jmol/viewer/StateCreator.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/StateCreator.java	2013-08-29 10:35:11 UTC (rev 18628)
+++ trunk/Jmol/src/org/jmol/viewer/StateCreator.java	2013-08-29 15:52:02 UTC (rev 18629)
@@ -108,6 +108,8 @@
     this.viewer = viewer;
   }
 
+  public static String SIMULATION_PROTOCOL = "http://SIMULATION/";
+
   public Object getWrappedState(String fileName, String[] scripts,
                                 boolean isImage, boolean asJmolZip, int width,
                                 int height) {
@@ -2125,9 +2127,21 @@
     if (disableSend)
       sm.setSyncDriver(StatusManager.SYNC_DISABLE);
     if (script.indexOf("Mouse: ") != 0) {
+      if (script.startsWith("Peaks: [")) {
+        // JSpecView simulation
+        String[] list = Escape.unescapeStringArray(script.substring(7));
+        JmolList<String> peaks = new JmolList<String>();
+        for (int i = 0; i < list.length; i++)
+          peaks.addLast(list[i]);
+        viewer.getModelSet().setModelAuxiliaryInfo(
+            viewer.getCurrentModelIndex(), "jdxAtomSelect_1HNMR", peaks);
+        return;
+      }
       if (script.startsWith("Select: ")) {
         // from JSpecView peak pick
         String filename = Parser.getQuotedAttribute(script, "file");
+        if (filename.startsWith(SIMULATION_PROTOCOL + "MOL="))
+          filename = null; // from our sending; don't reload
         String modelID = Parser.getQuotedAttribute(script, "model");
         String baseModel = Parser.getQuotedAttribute(script, "baseModel");
         String atoms = Parser.getQuotedAttribute(script, "atoms");
@@ -2135,10 +2149,9 @@
         String script2 = Parser.getQuotedAttribute(script, "script");
         boolean isNIH = (modelID != null && modelID.startsWith("$"));
         if (isNIH)
-          filename = (modelID.substring(1).equals(
-              viewer.getParameter("_smilesstring")) ? null : modelID);
-        String id = (isNIH || modelID == null ? null : (filename == null ? ""
-            : filename + "#")
+          filename = (String) viewer.setLoadFormat(modelID, '$', false);
+        String id = (modelID == null ? null : (filename == null ? "" : filename
+            + "#")
             + modelID);
         if ("".equals(baseModel))
           id += ".baseModel";
@@ -2147,6 +2160,7 @@
           return; // file was found, or no file was indicated, but not this model -- ignore
         script = (modelIndex == -1 && filename != null ? script = "load "
             + Escape.eS(filename) : "");
+        script = TextFormat.simpleReplace(script, SIMULATION_PROTOCOL, "");
         if (id != null)
           script += ";model " + Escape.eS(id);
         if (atoms != null)

Modified: trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/StatusListener.java
===================================================================
--- trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/StatusListener.java	2013-08-29 10:35:11 UTC (rev 18628)
+++ trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/StatusListener.java	2013-08-29 15:52:02 UTC (rev 18629)
@@ -376,6 +376,7 @@
       jSpecViewFrame.setLocation(jmol.frame.getLocation().x + 10, jmol.frame
           .getLocation().y + 100);
       jSpecViewFrame.register("Jmol", this);
+      viewer.setBooleanProperty("_jspecview", true);
       if (peaks.length() == 0) {
         doLoadCheck = true;
       }
@@ -397,9 +398,12 @@
         if (data == null)
           return;
         peaks = "hidden true; load CHECK MOL "
-            + Escape.eS("id='~" + model + "';" + data) + ";hidden false";
+            + Escape.eS("id='~" + model + "';" + data) + ";hidden false #SYNC_PEAKS";
       }
     }
+    if (!jSpecViewFrame.isVisible() && peaks.contains("<PeakData"))
+      return;
+
     if (!jSpecViewFrame.isVisible()) {
     //    && !peaks.toLowerCase().startsWith("hidden")) {
       jSpecViewFrame.awaken(true);

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