Revision: 21079
http://sourceforge.net/p/jmol/code/21079
Author: hansonr
Date: 2016-04-30 13:34:51 +0000 (Sat, 30 Apr 2016)
Log Message:
-----------
JSpecView.jar for 13C Simulation
Modified Paths:
--------------
branches/v14_4/Jmol/srcjsv/jspecview/application/AboutDialog.java
branches/v14_4/Jmol/srcjsv/jspecview/application/AppToolBar.java
branches/v14_4/Jmol/srcjsv/jspecview/application/ApplicationMenu.java
branches/v14_4/Jmol/srcjsv/jspecview/application/MainFrame.java
branches/v14_4/Jmol/srcjsv/jspecview/common/JSVFileManager.java
branches/v14_4/Jmol/srcjsv/jspecview/common/JSViewer.java
branches/v14_4/Jmol/srcjsv/jspecview/common/Spectrum.java
branches/v14_4/Jmol/srcjsv/jspecview/java/AwtPlatform.java
branches/v14_4/Jmol/srcjsv/jspecview/js2d/JsPlatform.java
branches/v14_4/Jmol/srcjsv/jspecview/source/AnIMLReader.java
branches/v14_4/Jmol/srcjsv/jspecview/source/JDXReader.java
Modified: branches/v14_4/Jmol/srcjsv/jspecview/application/AboutDialog.java
===================================================================
--- branches/v14_4/Jmol/srcjsv/jspecview/application/AboutDialog.java
2016-04-30 13:33:42 UTC (rev 21078)
+++ branches/v14_4/Jmol/srcjsv/jspecview/application/AboutDialog.java
2016-04-30 13:34:51 UTC (rev 21079)
@@ -1,4 +1,4 @@
-/* Copyright (c) 2002-2014 The University of the West Indies
+/* Copyright (c) 2002-2016 The University of the West Indies
*
* Contact: robert.lancash...@uwimona.edu.jm
*
@@ -39,8 +39,8 @@
import jspecview.common.JSVersion;
/**
- * The <code>About Dialog</code> class is the <i>help | about</i> window for
the
- * JSpecView.
+ * The <code>About Dialog</code> class is the <i>help | about</i> window for
JSpecView.
+ * @author Bob Hanson
* @author Debbie-Ann Facey
* @author Khari A. Bryan
* @author Prof. Robert J. Lancashire
@@ -120,7 +120,7 @@
txt = drawMessage(message, "Arial", Font.BOLD, 12);
p.add(txt);
- message = "Copyright (c) 2014, Department of Chemistry\nUniversity of the
West Indies, Mona Campus\nJAMAICA";
+ message = "Copyright (c) 2016, Department of Chemistry\nUniversity of the
West Indies, Mona Campus\nJAMAICA";
txt = drawMessage(message, "Arial", Font.PLAIN, 12);
p.add(txt);
Modified: branches/v14_4/Jmol/srcjsv/jspecview/application/AppToolBar.java
===================================================================
--- branches/v14_4/Jmol/srcjsv/jspecview/application/AppToolBar.java
2016-04-30 13:33:42 UTC (rev 21078)
+++ branches/v14_4/Jmol/srcjsv/jspecview/application/AppToolBar.java
2016-04-30 13:34:51 UTC (rev 21079)
@@ -114,7 +114,7 @@
@Override
public void actionPerformed(ActionEvent e) {
if (script.equals("open"))
- vwr.openFileFromDialog(false, false, false, null);
+ vwr.openFileFromDialog(false, false, null, null);
else if (script.equals("about"))
new AboutDialog(mainFrame);
else
Modified: branches/v14_4/Jmol/srcjsv/jspecview/application/ApplicationMenu.java
===================================================================
--- branches/v14_4/Jmol/srcjsv/jspecview/application/ApplicationMenu.java
2016-04-30 13:33:42 UTC (rev 21078)
+++ branches/v14_4/Jmol/srcjsv/jspecview/application/ApplicationMenu.java
2016-04-30 13:34:51 UTC (rev 21079)
@@ -125,21 +125,28 @@
InputEvent.CTRL_MASK, new ActionListener() {
@Override
public void actionPerformed(ActionEvent
e) {
- viewer.openFileFromDialog(true, false, false, null);
+ viewer.openFileFromDialog(true, false, null, null);
}
});
- JMenuItem openSimulationMenuItem = setMenuItem(null, 'I', "Add
Simulation...", 73,
+ JMenuItem openSimulationH1MenuItem = setMenuItem(null, 'H', "Add H1
Simulation...", 72,
InputEvent.CTRL_MASK, new ActionListener() {
@Override
public void actionPerformed(ActionEvent
e) {
- viewer.openFileFromDialog(true, false, true, null);
+ viewer.openFileFromDialog(true, false, "H1", null);
}
});
+ JMenuItem openSimulationC13MenuItem = setMenuItem(null, 'C', "Add C13
Simulation...", 67,
+ InputEvent.CTRL_MASK, new ActionListener() {
+ @Override
+ public void actionPerformed(ActionEvent e) {
+ viewer.openFileFromDialog(true, false, "C13", null);
+ }
+ });
JMenuItem openURLMenuItem = setMenuItem(null, 'U', "Add URL...", 85,
InputEvent.CTRL_MASK, new ActionListener() {
@Override
public void actionPerformed(ActionEvent
e) {
- viewer.openFileFromDialog(true, true, false, null);
+ viewer.openFileFromDialog(true, true, null, null);
}
});
@@ -408,7 +415,8 @@
setProcessingMenu(processingMenu);
fileMenu.add(openFileMenuItem);
- fileMenu.add(openSimulationMenuItem);
+ fileMenu.add(openSimulationH1MenuItem);
+ fileMenu.add(openSimulationC13MenuItem);
fileMenu.add(openURLMenuItem);
fileMenu.add(openRecentMenu);
// application does not need append
Modified: branches/v14_4/Jmol/srcjsv/jspecview/application/MainFrame.java
===================================================================
--- branches/v14_4/Jmol/srcjsv/jspecview/application/MainFrame.java
2016-04-30 13:33:42 UTC (rev 21078)
+++ branches/v14_4/Jmol/srcjsv/jspecview/application/MainFrame.java
2016-04-30 13:34:51 UTC (rev 21079)
@@ -1051,7 +1051,7 @@
@Override
public void siSetLoaded(String fileName, String filePath) {
appMenu.setCloseMenuItem(fileName);
- setTitle("JSpecView - " +
(filePath.startsWith(JSVFileManager.SIMULATION_PROTOCOL) ? "SIMULATION" :
filePath));
+ setTitle("JSpecView - " +
(filePath.startsWith(JSVFileManager.SIMULATION_PROTOCOL) ?
JSVFileManager.getSimulationType(filePath) + " SIMULATION" : filePath));
appMenu.setSourceEnabled(true);
}
Modified: branches/v14_4/Jmol/srcjsv/jspecview/common/JSVFileManager.java
===================================================================
--- branches/v14_4/Jmol/srcjsv/jspecview/common/JSVFileManager.java
2016-04-30 13:33:42 UTC (rev 21078)
+++ branches/v14_4/Jmol/srcjsv/jspecview/common/JSVFileManager.java
2016-04-30 13:34:51 UTC (rev 21079)
@@ -46,7 +46,7 @@
// ALL STATIC METHODS
public final static String SIMULATION_PROTOCOL = "http://SIMULATION/";;
- // possibly http://SIMULATION/MOL=...\n....\n....\n....
+ // possibly http://SIMULATION/H1/MOL=...\n....\n....\n....
public static URL appletDocumentBase;
@@ -57,7 +57,6 @@
}
public static String jsDocumentBase = "";
- public static Map<String, String> htCorrelationCache = new
Hashtable<String, String>();
/**
@@ -206,39 +205,55 @@
* involve mol=..., we want to abbreviate those names for display
*
* @param name actual path name to simulation
+ * @param type "H1" or "C13"
* @return actual name or hashed name
*/
- public static String getAbbrSimulationFileName(String name) {
- String filename = getAbbreviatedSimulationName(name, true);
- if (name.indexOf("MOL=") >= 0) {
- String data = htCorrelationCache.get(name);
- if (data != null)
- htCorrelationCache.put(filename, data);
- }
+ public static String getAbbrSimulationFileName(String name, String
type) {
+ if (type == null)
+ type = getSimulationType(name);
+ String filename = getAbbreviatedSimulationName(name, type,
true);
+ if (name.indexOf("MOL=") >= 0)
+ cachePut(name, cacheGet(type + name));
return filename;
}
- static String getAbbreviatedSimulationName(String name, boolean
addProtocol) {
+ static String getAbbreviatedSimulationName(String name, String type,
boolean addProtocol) {
return (name.indexOf("MOL=") >= 0 ? (addProtocol ?
SIMULATION_PROTOCOL : "") + "MOL="
+ getSimulationHash(name) : name);
}
private static String getSimulationHash(String name) {
- return "" + Math.abs(name.substring(name.indexOf("V2000") +
1).hashCode());
+ String code = "" +
Math.abs(name.substring(name.indexOf("V2000") + 1).hashCode());
+ if (Logger.debugging)
+ System.out.println("JSVFileManager hash for " + name +
" = " + code);
+ return code;
}
- public static String getSimulationFileData(String name) {
- return htCorrelationCache.get(name.startsWith("MOL=") ? name.substring(4)
:
- getAbbreviatedSimulationName(name, false));
+ public static String getSimulationFileData(String name, String type) {
+ return cacheGet(name.startsWith("MOL=") ? name.substring(4) :
+ getAbbreviatedSimulationName(name, type, false));
}
- private static BufferedReader getSimulationReader(String name) {
- String data = htCorrelationCache.get(name);
- if (data == null) {
- data =
getNMRSimulationJCampDX(name.substring(SIMULATION_PROTOCOL.length()));
- if (data != null)
- htCorrelationCache.put(name, data);
- }
+ private static Map<String, String> htCorrelationCache = new
Hashtable<String, String>();
+
+ public static void cachePut(String name, String data) {
+ if (Logger.debugging)
+ Logger.debug("JSVFileManager cachePut " + data + " for
" + name);
+ if (data != null)
+ htCorrelationCache.put(name, data);
+ }
+
+ public static String cacheGet(String key) {
+ String data = htCorrelationCache.get(key);
+ if (Logger.debugging)
+ Logger.info("JSVFileManager cacheGet " + data + " for
" + key);
+ return data;
+ }
+
+ private static BufferedReader getSimulationReader(String name) {
+ String data = cacheGet(name);
+ if (data == null)
+ cachePut(name, data =
getNMRSimulationJCampDX(name.substring(SIMULATION_PROTOCOL.length())));
return getBufferedReaderForData(data);
}
@@ -399,8 +414,9 @@
}
- private static String nciResolver =
"http://cactus.nci.nih.gov/chemical/structure/%FILE/file?format=sdf&get3d=True";;
- private static String nmrdbServer =
"http://www.nmrdb.org/tools/jmol/predict.php?POST?molfile=";;
+ private static String nciResolver =
"https://cactus.nci.nih.gov/chemical/structure/%FILE/file?format=sdf&get3d=True";;
+ private static String nmrdbServerH1 =
"http://www.nmrdb.org/tools/jmol/predict.php?POST?molfile=";;
+ private static String nmrdbServerC13 =
"http://www.nmrdb.org/service/jsmol13c?POST?molfile=";;
/**
* Accepts either $chemicalname or MOL=molfiledata Queries NMRDB or
NIH+NMRDB
@@ -413,8 +429,12 @@
* @return jcamp data
*/
private static String getNMRSimulationJCampDX(String name) {
+ System.out.println("JSVFileManager getNMRSimulationJCampDX for
" + name);
String key = "" + getSimulationHash(name);
- String jcamp = htCorrelationCache.get(key);
+ String type = getSimulationType(name);
+ if (name.startsWith(type))
+ name = name.substring(type.length() + 1);
+ String jcamp = cacheGet(key);
if (jcamp != null)
return jcamp;
boolean isInline = name.startsWith("MOL=");
@@ -422,38 +442,48 @@
String src = (isInline ? null : PT.rep(nciResolver, "%FILE",
PT.escapeUrl(name)));
if ((molFile = (isInline ? PT.rep(name.substring(4), "\\n",
"\n")
- : getFileAsString(src))) == null)
- Logger.info("no data returned");
- String json = getFileAsString(nmrdbServer + molFile);
- htCorrelationCache.put("json", json);
- Logger.debug(json);
+ : getFileAsString(src))) == null ||
molFile.indexOf("<html") >= 0) {
+ Logger.error("no MOL data returned by NCI");
+ return null;
+ }
+ String url = (type.equals("H1") ? nmrdbServerH1 :
nmrdbServerC13);
+ String json = getFileAsString(url + molFile);
+ cachePut("json", json);
if (json.indexOf("\"error\":") >= 0)
return null;
json = PT.rep(json, "\\r\\n", "\n");
json = PT.rep(json, "\\t", "\t");
json = PT.rep(json, "\\n", "\n");
String jsonMolFile = getQuotedJSONAttribute(json, "molfile",
null);
- htCorrelationCache.put("mol", jsonMolFile);
+ if (jsonMolFile == null) {
+ System.out.println("JSVFileManager: no MOL file
returned from EPFL");
+ jsonMolFile = molFile;
+ }
+ cachePut("mol", jsonMolFile);
/**
* @j2sNative
*
- * if (!isInline)
Jmol.Cache.put("http://SIMULATION/"; + name + "#molfile",
jsonMolFile.getBytes());
+ * if (!isInline)
Jmol.Cache.put("http://SIMULATION/"; + type + "/" + name + "#molfile",
jsonMolFile.getBytes());
*
*/
{
// JAVA only
+ System.out.println("type/name: " + type + "/" + name);
System.out.println("molFile is \n" + molFile);
System.out.println("jsonMolFile is \n" + jsonMolFile);
viewer.syncScript("JSVSTR:" + jsonMolFile);
}
String xml = getQuotedJSONAttribute(json, "xml", null);
- xml = PT.rep(xml, "<Signals>", "<Signals src=" +
PT.esc(PT.rep(nmrdbServer,"?POST?molfile=","")) + ">");
+ xml = PT.rep(xml, "<Signals>", "<Signals src=" +
PT.esc(PT.rep(nmrdbServerH1,"?POST?molfile=","")) + ">");
xml = PT.rep(xml, "</", "\n</");
xml = PT.rep(xml, "><", ">\n<");
xml = PT.rep(xml, "\\\"", "\"");
- htCorrelationCache.put("xml", xml);
+ cachePut("xml", xml);
jcamp = getQuotedJSONAttribute(json, "jcamp", null);
- jcamp = "##TITLE=" + (isInline ? "JMOL SIMULATION" : name) +
"\n"
+ if (jcamp.equals("value"))
+ jcamp =
getQuotedJSONAttribute(json.substring(json.indexOf("jcamp") + 4), "value",
null);
+
+ jcamp = "##TITLE=" + (isInline ? "JMOL SIMULATION/" + type :
name) + "\n"
+ jcamp.substring(jcamp.indexOf("\n##") + 1);
int pt = molFile.indexOf("\n");
pt = molFile.indexOf("\n", pt + 1);
@@ -462,7 +492,7 @@
+ molFile.substring(pt + 1);
pt = 0;
pt = jcamp.indexOf("##.");
- String id = getAbbreviatedSimulationName(name, false);
+ String id = getAbbreviatedSimulationName(name, type, false);
int pt1 = id.indexOf("id='");
if (isInline && pt1 > 0)
id = id.substring(pt1 + 4, (id + "'").indexOf("'", pt1
+ 4));
@@ -470,8 +500,8 @@
+ "<ModelData id=" + PT.esc(id) + "
type=\"MOL\" src=" + PT.esc(src)
+ ">\n" + molFile + "</ModelData>\n</Models>\n"
+ "##$SIGNALS=\n" + xml
+ "\n" + jcamp.substring(pt);
- htCorrelationCache.put("jcamp", jcamp);
- htCorrelationCache.put(key, jcamp);
+ cachePut("jcamp", jcamp);
+ cachePut(key, jcamp);
return jcamp;
}
@@ -537,7 +567,7 @@
if (isURL(fileName)) {
try {
if (fileName.startsWith(SIMULATION_PROTOCOL))
- return
getAbbrSimulationFileName(fileName);
+ return
getAbbrSimulationFileName(fileName, null);
String name = (new URL((URL) null, fileName,
null)).getFile();
return name.substring(name.lastIndexOf('/') +
1);
} catch (IOException e) {
@@ -564,6 +594,10 @@
appletDocumentBase = documentBase;
}
+ public static String getSimulationType(String filePath) {
+ return (filePath.indexOf("C13/") >= 0 ? "C13" : "H1");
+ }
+
}
// a nice idea, but never implemented; not relevant to JavaScript
Modified: branches/v14_4/Jmol/srcjsv/jspecview/common/JSViewer.java
===================================================================
--- branches/v14_4/Jmol/srcjsv/jspecview/common/JSViewer.java 2016-04-30
13:33:42 UTC (rev 21078)
+++ branches/v14_4/Jmol/srcjsv/jspecview/common/JSViewer.java 2016-04-30
13:34:51 UTC (rev 21079)
@@ -972,7 +972,7 @@
}
if (key != null && key.startsWith("DATA_")) {
// mol, json, xml, jcamp -- most recent only
- map.put(key, "" +
JSVFileManager.htCorrelationCache.get(key.substring(5)));
+ map.put(key, "" +
JSVFileManager.cacheGet(key.substring(5)));
return map;
}
@@ -1361,20 +1361,25 @@
if (script == null)
script = defaultLoadScript;
if (filename.equals("?")) {
- openFileFromDialog(isAppend, false, false, script);
+ openFileFromDialog(isAppend, false, null, script);
return;
}
if (filename.equals("http://?";)) {
- openFileFromDialog(isAppend, true, false, null);
+ openFileFromDialog(isAppend, true, null, null);
return;
}
- if (filename.equals("$?")) {
- openFileFromDialog(isAppend, true, true, null);
+ if (filename.equals("$?") || filename.equals("$H1?")) {
+ openFileFromDialog(isAppend, true, "H1", null);
return;
}
- boolean isMOL = filename.equalsIgnoreCase("MOL");
- if (isMOL)
- filename = JSVFileManager.SIMULATION_PROTOCOL + "MOL="
+ if (filename.equals("$C13?")) {
+ openFileFromDialog(isAppend, true, "C13", null);
+ return;
+ }
+ boolean isH1 = filename.equalsIgnoreCase("MOL") ||
filename.equalsIgnoreCase("H1");
+ boolean isC13 = filename.equalsIgnoreCase("C13");
+ if (isH1 || isC13)
+ filename = JSVFileManager.SIMULATION_PROTOCOL + (isH1 ?
"H1/" : "C13/") + "MOL="
+ PT.trimQuotes(tokens.get(++pt));
if (!isCheck && !isAppend) {
if (filename.equals("\"\"") && currentSource != null)
@@ -1383,7 +1388,8 @@
}
filename = PT.trimQuotes(filename);
if (filename.startsWith("$")) {
- isMOL = true;
+ if (!filename.startsWith("$H1") &&
!filename.startsWith("$C13"))
+ filename = "$H1/" + filename.substring(3);
filename = JSVFileManager.SIMULATION_PROTOCOL +
filename.substring(1);
}
int firstSpec = (pt + 1 < tokens.size() ?
Integer.valueOf(tokens.get(++pt))
@@ -1867,15 +1873,15 @@
}
public void openFileFromDialog(boolean isAppend, boolean isURL,
- boolean isSimulation, String script) {
+ String simulationType, String script) {
String url = null;
- if (isSimulation) {
+ if (simulationType != null) {
url = fileHelper.getUrlFromDialog(
"Enter the name or identifier of a
compound", recentSimulation);
if (url == null)
return;
recentSimulation = url;
- load((isAppend ? "APPEND " : "") + "\"$" + url + "\"",
script);
+ load((isAppend ? "APPEND " : "") + "\"$" +
simulationType + "/" + url + "\"", script);
} else if (isURL) {
url = fileHelper.getUrlFromDialog("Enter the URL of a
JCAMP-DX File",
recentURL == null ? recentOpenURL :
recentURL);
Modified: branches/v14_4/Jmol/srcjsv/jspecview/common/Spectrum.java
===================================================================
--- branches/v14_4/Jmol/srcjsv/jspecview/common/Spectrum.java 2016-04-30
13:33:42 UTC (rev 21078)
+++ branches/v14_4/Jmol/srcjsv/jspecview/common/Spectrum.java 2016-04-30
13:34:51 UTC (rev 21079)
@@ -242,6 +242,14 @@
String type = (peakList == null || peakList.size() == 0 ?
getQualifiedDataType() :
peakList.get(0).getType());
+ if (type != null && type.startsWith("NMR")) {
+ if (nucleusY != null && !nucleusY.equals("?")) {
+ type = "2D" + type;
+ } else {
+ type = nucleusX + type;
+ }
+
+ }
return (type != null && type.length() > 0 ? type + " " : "")
+ getTitle();
}
Modified: branches/v14_4/Jmol/srcjsv/jspecview/java/AwtPlatform.java
===================================================================
--- branches/v14_4/Jmol/srcjsv/jspecview/java/AwtPlatform.java 2016-04-30
13:33:42 UTC (rev 21078)
+++ branches/v14_4/Jmol/srcjsv/jspecview/java/AwtPlatform.java 2016-04-30
13:34:51 UTC (rev 21079)
@@ -313,5 +313,10 @@
return null;
}
+ @Override
+ public boolean forceAsyncLoad(String filename) {
+ return false;
+ }
+
}
Modified: branches/v14_4/Jmol/srcjsv/jspecview/js2d/JsPlatform.java
===================================================================
--- branches/v14_4/Jmol/srcjsv/jspecview/js2d/JsPlatform.java 2016-04-30
13:33:42 UTC (rev 21078)
+++ branches/v14_4/Jmol/srcjsv/jspecview/js2d/JsPlatform.java 2016-04-30
13:34:51 UTC (rev 21079)
@@ -75,8 +75,7 @@
* we must use Object[] here to hide [HTMLUnknownElement] and [Attribute]
from Java2Script
* @j2sNative
*
- * if (method == "localName")return jsObject[0]["nodeName"];
- * return (args == null ? jsObject[0][method] :
jsObject[0][method](args[0]));
+ * return (method == null ? null : method == "localName" ?
jsObject[0]["nodeName"] : args == null ? jsObject[0][method] :
jsObject[0][method](args[0]));
*
*
*/
@@ -386,4 +385,10 @@
return null;
}
+ @Override
+ public boolean forceAsyncLoad(String filename) {
+ // TODO Auto-generated method stub
+ return false;
+ }
+
}
Modified: branches/v14_4/Jmol/srcjsv/jspecview/source/AnIMLReader.java
===================================================================
--- branches/v14_4/Jmol/srcjsv/jspecview/source/AnIMLReader.java
2016-04-30 13:33:42 UTC (rev 21078)
+++ branches/v14_4/Jmol/srcjsv/jspecview/source/AnIMLReader.java
2016-04-30 13:34:51 UTC (rev 21079)
@@ -220,7 +220,6 @@
}
private void getYValues() throws Exception {
- BC bc = new BC();
String vectorType = parser.getAttrValueLC("type");
if (vectorType.length() == 0)
vectorType = parser.getAttrValueLC("vectorType");
Modified: branches/v14_4/Jmol/srcjsv/jspecview/source/JDXReader.java
===================================================================
--- branches/v14_4/Jmol/srcjsv/jspecview/source/JDXReader.java 2016-04-30
13:33:42 UTC (rev 21078)
+++ branches/v14_4/Jmol/srcjsv/jspecview/source/JDXReader.java 2016-04-30
13:34:51 UTC (rev 21079)
@@ -103,6 +103,7 @@
filePath = PT.trimQuotes(filePath);
isSimulation = (filePath != null &&
filePath.startsWith(JSVFileManager.SIMULATION_PROTOCOL));
if (isSimulation) {
+ //TODO: H1 vs. C13 here?
nmrMaxY = (Float.isNaN(nmrNormalization) ? 10000 : nmrNormalization);
//filePath = JSVFileManager.getAbbrSimulationFileName(filePath);
}
@@ -301,7 +302,7 @@
}
}
if (acdMolFile != null)
- JSVFileManager.htCorrelationCache.put("mol",
acdMolFile);
+ JSVFileManager.cachePut("mol", acdMolFile);
}
if (!Float.isNaN(nmrMaxY))
spectrum.doNormalize(nmrMaxY);
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