Revision: 18627
http://sourceforge.net/p/jmol/code/18627
Author: hansonr
Date: 2013-08-29 10:32:22 +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/adapter/readers/more/JcampdxReader.java
trunk/Jmol/src/org/jmol/api/JmolViewer.java
trunk/Jmol/src/org/jmol/modelset/ModelCollection.java
trunk/Jmol/src/org/jmol/modelset/ModelLoader.java
trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java
trunk/Jmol/src/org/jmol/util/ModulationSet.java
trunk/Jmol/src/org/jmol/viewer/JC.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/PropertyManager.java
trunk/Jmol/src/org/jmol/viewer/StateCreator.java
trunk/Jmol/src/org/jmol/viewer/Viewer.java
trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/StatusListener.java
Modified: trunk/Jmol/src/org/jmol/adapter/readers/more/JcampdxReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/more/JcampdxReader.java
2013-08-28 06:42:53 UTC (rev 18626)
+++ trunk/Jmol/src/org/jmol/adapter/readers/more/JcampdxReader.java
2013-08-29 10:32:22 UTC (rev 18627)
@@ -26,10 +26,12 @@
import java.io.BufferedReader;
import java.io.StringReader;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
+
import org.jmol.util.JmolList;
-
-
-
import org.jmol.util.TextFormat;
import org.jmol.adapter.readers.molxyz.MolReader;
@@ -96,7 +98,7 @@
public class JcampdxReader extends MolReader {
- private String modelID;
+ private String thisModelID;
private AtomSetCollection models;
private String modelIdList = "";
private JmolList<String> peakData = new JmolList<String>();
@@ -152,7 +154,9 @@
if (label.equals("##$MODELS"))
return readModels();
if (label.equals("##$PEAKS"))
- return readPeaks();
+ return (readPeaks(false) > 0);
+ if (label.equals("##$SIGNALS"))
+ return (readPeaks(true) > 0);
return true;
}
@@ -180,7 +184,7 @@
// load xxx.jdx 0 will mean "load only the base model(s)"
models = null;
line = "";
- modelID = "";
+ thisModelID = "";
boolean isFirst = true;
while (true) {
int model0 = atomSetCollection.getCurrentAtomSetIndex();
@@ -208,11 +212,11 @@
private void updateModelIDs(int model0, boolean isFirst) {
int n = atomSetCollection.getAtomSetCount();
if (isFirst && n == model0 + 2) {
- atomSetCollection.setAtomSetAuxiliaryInfo("modelID", modelID);
+ atomSetCollection.setAtomSetAuxiliaryInfo("modelID", thisModelID);
return;
}
for (int pt = 0, i = model0; ++i < n;) {
- atomSetCollection.setAtomSetAuxiliaryInfoForSet("modelID", modelID + "."
+ atomSetCollection.setAtomSetAuxiliaryInfoForSet("modelID", thisModelID +
"."
+ (++pt), i);
}
}
@@ -223,10 +227,10 @@
}
private AtomSetCollection getModelAtomSetCollection() throws Exception {
- lastModel = modelID;
- modelID = getAttribute(line, "id");
+ lastModel = thisModelID;
+ thisModelID = getAttribute(line, "id");
// read model only once for a given ID
- String key = ";" + modelID + ";";
+ String key = ";" + thisModelID + ";";
if (modelIdList.indexOf(key) >= 0) {
discardLinesUntilContains("</ModelData>");
return null;
@@ -276,7 +280,7 @@
for (int i = a.getAtomCount(); --i >= 0;)
atoms[i].scaleVector(vibScale);
}
- Logger.info("jdx model=" + modelID + " type=" + a.getFileTypeName());
+ Logger.info("jdx model=" + thisModelID + " type=" + a.getFileTypeName());
return a;
}
@@ -312,23 +316,170 @@
}
}
- private boolean readPeaks() throws Exception {
- if (line.indexOf("<Peaks") < 0)
- discardLinesUntilContains2("<Peaks", "##");
- if (line.indexOf("<Peaks") < 0)
- return false;
- String type = getAttribute(line, "type").toUpperCase();
- if (type.equals("HNMR"))
- type = "1HNMR";
- else if (type.equals("CNMR"))
- type = "13CNMR";
- while (readLine() != null && !(line = line.trim()).startsWith("</Peaks>"))
- if (line.startsWith("<PeakData"))
- peakData.addLast("<PeakData file=" + peakFilePath + " index=\"" +
(++peakIndex[0]) + "\"" + " type=\"" + type + "\" " + line.substring(9).trim());
- return true;
+ String piUnitsX, piUnitsY;
+
+ /**
+ * read a <Peaks> or <Signals> block See similar method in
+ * JSpecViewLib/src/jspecview/source/FileReader.java
+ *
+ * @param isSignals
+ * @return true if successful
+ * @throws Exception
+ */
+ private int readPeaks(boolean isSignals) throws Exception {
+ JcampdxReader reader = this;
+ Object spectrum = null;
+
+ try {
+ String tag1 = (isSignals ? "Signals" : "Peaks");
+ String tag2 = (isSignals ? "<Signal" : "<PeakData");
+ String line = discardUntil(reader, tag1);
+ if (line.indexOf("<" + tag1) < 0)
+ line = discardUntil(reader, "<" + tag1);
+ if (line.indexOf("<" + tag1) < 0)
+ return 0;
+
+ String file = getPeakFilePath();
+ String model = getQuotedAttribute(line, "model");
+ model = " model=" + escape(model == null ? thisModelID : model);
+ String type = getQuotedAttribute(line, "type");
+ if ("HNMR".equals(type))
+ type = "1HNMR";
+ else if ("CNMR".equals(type))
+ type = "13CNMR";
+ type = (type == null ? "" : " type=" + escape(type));
+ piUnitsX = getQuotedAttribute(line, "xLabel");
+ piUnitsY = getQuotedAttribute(line, "yLabel");
+ Map<String, Object[]> htSets = new Hashtable<String, Object[]>();
+ List<Object[]> list = new ArrayList<Object[]>();
+ while ((line = reader.readLine()) != null
+ && !(line = line.trim()).startsWith("</" + tag1)) {
+ if (line.startsWith(tag2)) {
+ info(line);
+ String title = getQuotedAttribute(line, "title");
+ if (title == null) {
+ title = (type == "1HNMR" ? "atom%S%: %ATOMS%; integration:
%NATOMS%" : "");
+ title = " title=" + escape(title);
+ } else {
+ title = "";
+ }
+ String stringInfo = "<PeakData "
+ + file
+ + " index=\"%INDEX%\""
+ + title
+ + type
+ + (getQuotedAttribute(line, "model") == null ? model
+ : "") + " " + line.substring(tag2.length()).trim();
+ String atoms = getQuotedAttribute(stringInfo, "atoms");
+ if (atoms != null)
+ stringInfo = simpleReplace(stringInfo, "atoms=\""
+ + atoms + "\"", "atoms=\"%ATOMS%\"");
+ String key = ((int) (parseFloatStr(getQuotedAttribute(line, "xMin"))
* 100))
+ + "_"
+ + ((int) (parseFloatStr(getQuotedAttribute(line,
+ "xMax")) * 100));
+ Object[] o = htSets.get(key);
+ if (o == null) {
+ o = new Object[] { stringInfo,
+ (atoms == null ? null : new BS()) };
+ htSets.put(key, o);
+ list.add(o);
+ }
+ BS bs = (BS) o[1];
+ if (bs != null) {
+ atoms = atoms.replace(',', ' ');
+ bs.or(unescapeBitSet("({" + atoms + "})"));
+ }
+ }
+ }
+ int nH = 0;
+ int n = list.size();
+ for (int i = 0; i < n; i++) {
+ Object[] o = list.get(i);
+ String stringInfo = (String) o[0];
+ stringInfo = simpleReplace(stringInfo, "%INDEX%", ""
+ + getPeakIndex());
+ BS bs = (BS) o[1];
+ if (bs != null) {
+ String s = "";
+ for (int j = bs.nextSetBit(0); j >= 0; j = bs.nextSetBit(j + 1))
+ s += "," + (j + 1);
+ int na = bs.cardinality();
+ nH += na;
+ stringInfo = simpleReplace(stringInfo, "%ATOMS%", s
+ .substring(1));
+ stringInfo = simpleReplace(stringInfo, "%S%",
+ (na == 1 ? "" : "s"));
+ stringInfo = simpleReplace(stringInfo, "%NATOMS%", ""
+ + na);
+ }
+ info("Jmol using " + stringInfo);
+ add(peakData, stringInfo);
+ }
+ setSpectrumPeaks(spectrum, peakData, nH);
+ return n;
+ } catch (Exception e) {
+ return 0;
+ }
}
+ private void info(String s) {
+ Logger.info(s);
+ }
+
+ private BS unescapeBitSet(String s) {
+ return Escape.uB(s);
+ }
+
+ private String simpleReplace(String s, String sfrom, String sto) {
+ return TextFormat.simpleReplace(s, sfrom, sto);
+ }
+
+ private String escape(String s) {
+ return Escape.eS(s);
+ }
+
+ private String getQuotedAttribute(String s, String attr) {
+ return Parser.getQuotedAttribute(s, attr);
+ }
+
/**
+ * @param o1
+ * @param o2
+ * @param nH
+ */
+ private void setSpectrumPeaks(Object o1, Object o2,
+ int nH) {
+ // only in JSpecView
+ }
+
+ private void add(JmolList<String> peakData, String info) {
+ peakData.addLast(info);
+ }
+
+ private String getPeakFilePath() {
+ return " file=" + Escape.eS(peakFilePath);
+ }
+
+
+ /**
+ * @param ignored
+ * @param tag
+ * @return line
+ * @throws Exception
+ */
+ private String discardUntil(Object ignored, String tag) throws Exception {
+ return discardLinesUntilContains2("<" + tag, "##");
+ }
+
+ /**
+ * @return index
+ */
+ private int getPeakIndex() {
+ return ++peakIndex[0];
+ }
+
+ /**
* integrate the <PeakAssignment> records into the associated models, and
delete unreferenced n.m models
*/
@SuppressWarnings("unchecked")
@@ -341,10 +492,10 @@
for (int p = 0; p < n; p++) {
line = peakData.get(p);
String type = getAttribute(line, "type");
- modelID = getAttribute(line, "model");
- int i = findModelById(modelID);
+ thisModelID = getAttribute(line, "model");
+ int i = findModelById(thisModelID);
if (i < 0) {
- Logger.warn("cannot find model " + modelID + " required for " + line);
+ Logger.warn("cannot find model " + thisModelID + " required for " +
line);
continue;
}
addType(i, type);
@@ -372,9 +523,9 @@
}
n = atomSetCollection.getAtomSetCount();
for (int i = n; --i >= 0;) {
- modelID = (String) atomSetCollection
+ thisModelID = (String) atomSetCollection
.getAtomSetAuxiliaryInfoValue(i, "modelID");
- if (havePeaks && !bsModels.get(i) && modelID.indexOf(".") >= 0) {
+ if (havePeaks && !bsModels.get(i) && thisModelID.indexOf(".") >= 0) {
atomSetCollection.removeAtomSet(i);
n--;
}
Modified: trunk/Jmol/src/org/jmol/api/JmolViewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/api/JmolViewer.java 2013-08-28 06:42:53 UTC (rev
18626)
+++ trunk/Jmol/src/org/jmol/api/JmolViewer.java 2013-08-29 10:32:22 UTC (rev
18627)
@@ -618,6 +618,7 @@
*/
abstract public String runScript(String script);
abstract public int modelGetLastVibrationIndex(int i, int tok);
+ abstract public String extractMolData(String what);
}
Modified: trunk/Jmol/src/org/jmol/modelset/ModelCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelCollection.java 2013-08-28
06:42:53 UTC (rev 18626)
+++ trunk/Jmol/src/org/jmol/modelset/ModelCollection.java 2013-08-29
10:32:22 UTC (rev 18627)
@@ -197,6 +197,10 @@
return (String) getModelAuxiliaryInfoValue(modelIndex, "fileName");
}
+ public String getModelFileType(int modelIndex) {
+ return (String) getModelAuxiliaryInfoValue(modelIndex, "fileType");
+ }
+
public void setFrameTitle(BS bsFrames, Object title) {
if (title instanceof String) {
for (int i = bsFrames.nextSetBit(0); i >= 0; i = bsFrames
@@ -1010,10 +1014,6 @@
return models[modelIndex].nInsertions;
}
- public String getModelFileType(int modelIndex) {
- return (String) getModelAuxiliaryInfoValue(modelIndex, "fileType");
- }
-
public static int modelFileNumberFromFloat(float fDotM) {
//only used in the case of select model = someVariable
//2.1 and 2.10 will be ambiguous and reduce to 2.1
@@ -3397,13 +3397,14 @@
String fname = null;
for (int i = 0; i < modelCount; i++) {
String mid = (String) getModelAuxiliaryInfoValue(i, "modelID");
- if (mid == null && (mid = getModelTitle(i)) == null)
+ String mnum = (id.startsWith("~") ? "~" + getModelNumberDotted(i) :
null);
+ if (mnum == null && mid == null && (mid = getModelTitle(i)) == null)
continue;
if (haveFile) {
fname = getModelFileName(i) + "#";
mid = fname + mid;
}
- if (id.equalsIgnoreCase(mid))
+ if (id.equalsIgnoreCase(mid) || id.equalsIgnoreCase(mnum))
return (isBaseModel ? viewer.getJDXBaseModelIndex(i) : i);
if (fname != null && id.startsWith(fname))
errCode = -2;
Modified: trunk/Jmol/src/org/jmol/modelset/ModelLoader.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelLoader.java 2013-08-28 06:42:53 UTC
(rev 18626)
+++ trunk/Jmol/src/org/jmol/modelset/ModelLoader.java 2013-08-29 10:32:22 UTC
(rev 18627)
@@ -686,6 +686,7 @@
}
Model[] models = modelSet.models;
for (int i = baseModelCount; i < modelCount; ++i) {
+ modelSet.setModelAuxiliaryInfo(i, "fileType", modelSet.modelSetTypeName);
if (fileHeader != null)
modelSet.setModelAuxiliaryInfo(i, "fileHeader", fileHeader);
int filenumber = modelNumbers[i] / 1000000;
Modified: trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2013-08-28 06:42:53 UTC
(rev 18626)
+++ trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2013-08-29 10:32:22 UTC
(rev 18627)
@@ -14646,9 +14646,12 @@
if (optParameterAsString(2).equalsIgnoreCase("1H")) {
len = 3;
if (!chk)
- msg = viewer.getNMRPredict(viewer.getModelExtract("selected", true,
false, "V2000"));
+ msg = viewer.getNMRPredict(false);
+ break;
}
- break;
+ if (!chk)
+ viewer.getNMRPredict(true);
+ return;
case T.smiles:
case T.drawing:
case T.chemical:
@@ -14665,13 +14668,6 @@
}
msg = "Could not show drawing -- Either insufficient atoms are
selected or the model is a PDB file.";
break;
- case T.nmr:
- if (msg.length() > 0) {
- viewer.showNMR(msg);
- return;
- }
- msg = "Could not show nmr -- Either insufficient atoms are selected or
the model is a PDB file.";
- break;
case T.chemical:
len = 3;
String info = null;
Modified: trunk/Jmol/src/org/jmol/util/ModulationSet.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/ModulationSet.java 2013-08-28 06:42:53 UTC
(rev 18626)
+++ trunk/Jmol/src/org/jmol/util/ModulationSet.java 2013-08-29 10:32:22 UTC
(rev 18627)
@@ -30,16 +30,35 @@
V3 x456;
/**
- * A collection of modulations for a specific atom.
+ * A collection of modulations for a specific atom.
*
+ * We treat the set of modulation vectors q1,q2,q3,... as
+ * a matrix Q with row 1 = q1, row 2 = q2, etc. Then we
+ * have Qr = [q1.r, q2.r, q3.r,...].
+ *
+ * Similarly, we express the x1' - xn' aspects of the operators
+ * as the matrix Gamma_I (epsilons) and s_I (shifts). However,
+ * since we are only considering up to n = 3, we can express these
+ * together as a 4x4 matrix just for storage.
+ *
+ * Then for X defined as [x4,x5,x6...] (column vector, really)
+ * we have:
+ *
+ * X' = Gamma_I * X + s_I
+ *
+ * and
+ *
+ * X = Gamma_I^-1(X' - S_I)
+ *
+ * not figured out for composite structures
+ *
* @param id
* @param r
- * @param vocc0
* @param modDim
* @param mods
* @param gammaE
* @param gammaIS
- * @param q123
+ * @param q123w
* @param qlen
*
*
Modified: trunk/Jmol/src/org/jmol/viewer/JC.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/JC.java 2013-08-28 06:42:53 UTC (rev
18626)
+++ trunk/Jmol/src/org/jmol/viewer/JC.java 2013-08-29 10:32:22 UTC (rev
18627)
@@ -1292,7 +1292,7 @@
"ligand", "http://www.rcsb.org/pdb/files/ligand/%FILE.cif";,
"mp", "http://www.materialsproject.org/materials/%FILE/cif";,
"nci", "http://cactus.nci.nih.gov/chemical/structure/%FILE";,
- "nmr", "http://www.nmrdb.org/predictor?smiles=";,
+ "nmr", "http://www.nmrdb.org/predictor?POST?molfile=";,
"nmrdb", "http://www.nmrdb.org/service/predictor?POST?molfile=";,
"pdb", "http://www.rcsb.org/pdb/files/%FILE.pdb.gz";,
"pubchem",
"http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/%FILE/SDF?record_type=3d";
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-08-28 06:42:53 UTC
(rev 18626)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-08-29 10:32:22 UTC
(rev 18627)
@@ -11,8 +11,13 @@
# The quotes above look odd for a parameter file, but they are
# important for the JavaScript version of Jmol.
-___JmolVersion="13.3.4"
+___JmolVersion="13.3.5_dev_2013.08.29"
+new feature: show NMR taps into NMRDB directly
+ -- for now, application only
+
+JmolVersion="13.3.4"
+
bug fix: select 1-5 broken
JmolVersion="13.3.4_dev_2013.08.21"
Modified: trunk/Jmol/src/org/jmol/viewer/PropertyManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/PropertyManager.java 2013-08-28 06:42:53 UTC
(rev 18626)
+++ trunk/Jmol/src/org/jmol/viewer/PropertyManager.java 2013-08-29 10:32:22 UTC
(rev 18627)
@@ -1156,6 +1156,7 @@
sb.append("\nid").append(s).append(Escape.eS(id));
sb.append("\ntitle").append(s).append(Escape.eS(ms.getModelTitle(i)));
sb.append("\nname").append(s).append(Escape.eS(ms.getModelName(i)));
+ sb.append("\ntype").append(s).append(Escape.eS(ms.getModelFileType(i)));
}
return sb.toString();
}
Modified: trunk/Jmol/src/org/jmol/viewer/StateCreator.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/StateCreator.java 2013-08-28 06:42:53 UTC
(rev 18626)
+++ trunk/Jmol/src/org/jmol/viewer/StateCreator.java 2013-08-29 10:32:22 UTC
(rev 18627)
@@ -2126,6 +2126,7 @@
sm.setSyncDriver(StatusManager.SYNC_DISABLE);
if (script.indexOf("Mouse: ") != 0) {
if (script.startsWith("Select: ")) {
+ // from JSpecView peak pick
String filename = Parser.getQuotedAttribute(script, "file");
String modelID = Parser.getQuotedAttribute(script, "model");
String baseModel = Parser.getQuotedAttribute(script, "baseModel");
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2013-08-28 06:42:53 UTC (rev
18626)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2013-08-29 10:32:22 UTC (rev
18627)
@@ -515,7 +515,6 @@
fileManager = new FileManager(this);
definedAtomSets = new Hashtable<String, Object>();
setJmolStatusListener(statusListener);
-
if (isApplet) {
Logger.info("viewerOptions: \n" + Escape.escapeMap(viewerOptions));
jsDocumentBase = appletDocumentBase;
@@ -3185,15 +3184,11 @@
@Override
public int getModelNumber(int modelIndex) {
- if (modelIndex < 0)
- return modelIndex;
- return modelSet.getModelNumber(modelIndex);
+ return (modelIndex < 0 ? modelIndex : modelSet.getModelNumber(modelIndex));
}
public int getModelFileNumber(int modelIndex) {
- if (modelIndex < 0)
- return 0;
- return modelSet.getModelFileNumber(modelIndex);
+ return (modelIndex < 0 ? 0 : modelSet.getModelFileNumber(modelIndex));
}
@Override
@@ -5183,7 +5178,9 @@
global.setS("_modelTitle",
(modelIndex < 0 ? "" : getModelTitle(modelIndex)));
global.setS("_modelFile", (modelIndex < 0 ? ""
- : getModelFileName(modelIndex)));
+ : modelSet.getModelFileName(modelIndex)));
+ global.setS("_modelType", (modelIndex < 0 ? ""
+ : modelSet.getModelFileType(modelIndex)));
if (currentFrame == prevFrame)
return;
@@ -8574,20 +8571,34 @@
return xyzdata;
}
- public String getNMRPredict(String molFile) {
- // nmrdb cannot handle "." separator and cannot handle c=c
+ @Override
+ public String extractMolData(String what) {
+ if (what == null) {
+ int i = getCurrentModelIndex();
+ if (i < 0)
+ return null;
+ what = getModelNumberDotted(i);
+ }
+ return getModelExtract(what, true, false, "V2000");
+ }
+ public String getNMRPredict(boolean openURL) {
+ String molFile = getModelExtract("selected", true, false, "V2000");
int pt = molFile.indexOf("\n");
molFile = "Jmol " + version_date + molFile.substring(pt);
+ if (openURL) {
+ if (isApplet) {
+ //TODO -- can do this if connected
+ showUrl(global.nmrUrlFormat + molFile);
+ } else {
+ syncScript("true", "*", 0);
+ syncScript("JSpecView:", ".", 0);
+ }
+ return null;
+ }
String url = global.nmrPredictFormat + molFile;
return getFileAsString(url);
}
- public void showNMR(String smiles) {
- // nmrdb cannot handle "." separator and cannot handle c=c
- showUrl(global.nmrUrlFormat
- + Escape.escapeUrl(getChemicalInfo(smiles, '/', "smiles")));
- }
-
public void getHelp(String what) {
if (global.helpPath.indexOf("?") < 0) {
if (what.length() > 0 && what.indexOf("?") != 0)
@@ -8781,6 +8792,7 @@
}
public int getModelIndexFromId(String id) {
+ // from JSpecView peak pick and model "ID"
return modelSet.getModelIndexFromId(id);
}
Modified: trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/StatusListener.java
===================================================================
--- trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/StatusListener.java
2013-08-28 06:42:53 UTC (rev 18626)
+++ trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/StatusListener.java
2013-08-29 10:32:22 UTC (rev 18627)
@@ -74,6 +74,7 @@
private JmolViewer viewer;
private MainFrame jSpecViewFrame;
+ private boolean jSpecViewForceNew;
void setViewer(JmolViewer viewer) {
this.viewer = viewer;
}
@@ -131,6 +132,8 @@
display.status.setStatus(1, menuName);
if (jmol.frame != null)
jmol.frame.setTitle(menuName);
+// if (jSpecViewFrame != null)
+// setJSpecView("", true);
}
return;
case SCRIPT:
@@ -167,7 +170,7 @@
break;
case SYNC:
if (strInfo != null && strInfo.toLowerCase().startsWith("jspecview")) {
- setJSpecView(strInfo.substring(9).trim());
+ setJSpecView(strInfo.substring(9).trim(), false, false);
return;
}
jmol.sendNioMessage(((Integer) data[3]).intValue(), strInfo);
@@ -262,10 +265,13 @@
title = modelName;
jmol.notifyFileOpen(fullPathName == null ? null : fullPathName + (isAsync
== Boolean.TRUE ? " (*)" : ""), title);
if (jSpecViewFrame != null) {
+ jSpecViewForceNew = jSpecViewFrame.isVisible();
if (fullPathName == null) {
jSpecViewFrame.syncScript("close ALL");
- } else if (fullPathName.endsWith(".jdx"))
- jSpecViewFrame.syncScript("load CHECK " + Escape.eS(fullPathName));
+ } else {
+ setJSpecView("", true, true);
+ }
+ jSpecViewForceNew = true;
}
}
@@ -359,7 +365,7 @@
return jmol.resizeInnerPanel(data);
}
- public void setJSpecView(String peaks) {
+ public void setJSpecView(String peaks, boolean doLoadCheck, boolean
isFileLoad) {
if (!display.isRotateMode())
return;
if (peaks.startsWith(":"))
@@ -367,15 +373,35 @@
if (jSpecViewFrame == null) {
jSpecViewFrame = new MainFrame((Component) viewer.getDisplay(), this);
jSpecViewFrame.setSize(800, 500);
- jSpecViewFrame.setLocation(400, 400);
+ jSpecViewFrame.setLocation(jmol.frame.getLocation().x + 10, jmol.frame
+ .getLocation().y + 100);
jSpecViewFrame.register("Jmol", this);
if (peaks.length() == 0) {
- String s = "" + viewer.getParameter("_modelfile");
- if (s.indexOf("/") >= 0)
- peaks = "hidden false; load " + Escape.eS(s);
+ doLoadCheck = true;
}
}
- if (!jSpecViewFrame.isVisible() &&
!peaks.toLowerCase().startsWith("hidden")) {
+ if (doLoadCheck || jSpecViewForceNew) {
+ String type = "" + viewer.getParameter("_modelType");
+ if (type.equalsIgnoreCase("jcampdx")) {
+ jSpecViewForceNew = false;
+ String file = "" + viewer.getParameter("_modelFile");
+ if (file.indexOf("/") < 0)
+ return;
+ peaks = "hidden true; load CHECK " + Escape.eS(file) + ";hidden false";
+ } else if (isFileLoad && !jSpecViewForceNew) {
+ return;
+ } else {
+ jSpecViewForceNew = false;
+ String model = "" + viewer.getParameter("_modelNumber");
+ String data = viewer.extractMolData(null);
+ if (data == null)
+ return;
+ peaks = "hidden true; load CHECK MOL "
+ + Escape.eS("id='~" + model + "';" + data) + ";hidden false";
+ }
+ }
+ if (!jSpecViewFrame.isVisible()) {
+ // && !peaks.toLowerCase().startsWith("hidden")) {
jSpecViewFrame.awaken(true);
display.setViewer(viewer);
}
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