import java.io.File;
import java.net.URL;
import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.StringTokenizer;
import java.util.Vector;
+import javax.swing.SwingUtilities;
+
import org.jmol.adapter.smarter.SmarterJmolAdapter;
import org.jmol.api.JmolAppConsoleInterface;
import org.jmol.api.JmolSelectionListener;
import org.jmol.c.CBK;
import org.jmol.viewer.Viewer;
+import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureRenderer;
-import jalview.bin.Cache;
+import jalview.api.FeatureSettingsModelI;
+import jalview.api.SequenceRenderer;
+import jalview.bin.Console;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
+import jalview.gui.AppJmol;
import jalview.gui.IProgressIndicator;
import jalview.gui.StructureViewer.ViewerType;
import jalview.io.DataSourceType;
import jalview.structure.StructureCommandI;
import jalview.structure.StructureSelectionManager;
import jalview.structures.models.AAStructureBindingModel;
+import jalview.ws.dbsources.Pdb;
+import javajs.util.BS;
public abstract class JalviewJmolBinding extends AAStructureBindingModel
implements JmolStatusListener, JmolSelectionListener,
setStructureCommands(new JmolCommands());
/*
* viewer = JmolViewer.allocateViewer(renderPanel, new SmarterJmolAdapter(),
- * "jalviewJmol", ap.av.applet .getDocumentBase(),
- * ap.av.applet.getCodeBase(), "", this);
+ * "jalviewJmol", ap.av.applet .getDocumentBase(), ap.av.applet.getCodeBase(),
+ * "", this);
*
* jmolpopup = JmolPopup.newJmolPopup(viewer, true, "Jmol", true);
*/
private String jmolScript(String script)
{
- Cache.log.debug(">>Jmol>> " + script);
- String s = jmolViewer.scriptWait(script);
- Cache.log.debug("<<Jmol<< " + s);
+ return jmolScript(script, false);
+ }
+
+ private String jmolScript(String script, boolean useScriptWait)
+ {
+ Console.debug(">>Jmol>> " + script);
+ String s;
+ if (useScriptWait)
+ {
+ s = jmolViewer.scriptWait(script);
+ }
+ else
+ {
+ s = jmolViewer.evalStringQuiet(script); // scriptWait(script); BH
+ }
+ Console.debug("<<Jmol<< " + s);
return s;
}
public void createImage(String file, String type, int quality)
{
- System.out.println("JMOL CREATE IMAGE");
+ jalview.bin.Console.outPrintln("JMOL CREATE IMAGE");
}
@Override
public String createImage(String fileName, String type,
Object textOrBytes, int quality)
{
- System.out.println("JMOL CREATE IMAGE");
+ jalview.bin.Console.outPrintln("JMOL CREATE IMAGE");
return null;
}
@Override
public String eval(String strEval)
{
- // System.out.println(strEval);
+ // jalview.bin.Console.outPrintln(strEval);
// "# 'eval' is implemented only for the applet.";
return null;
}
// End StructureListener
// //////////////////////////
-
+
+ ////////////////////////////
+ // HETATM get
+ //
+
+ @Override
+ public List<String> getHetatmNames()
+ {
+ HashMap<String,String> hetlist=new HashMap();
+ for (int mc=0;mc<jmolViewer.ms.mc; mc++)
+ {
+ Map<String,String> hets = jmolViewer.ms.getHeteroList(mc);
+ if (hets!=null)
+ {
+ hetlist.putAll(hets);
+ }
+ }
+ return Arrays.asList(hetlist.keySet().toArray(new String[0]));
+ }
+ //
+ ////////////////////////////
+
@Override
public float[][] functionXY(String functionName, int x, int y)
{
for (int i = 0; i < modelCount; ++i)
{
/*
- * defensive check for null as getModelFileName can return null
- * even when model count ms.mc is > 0
+ * defensive check for null as getModelFileName can return null even when model
+ * count ms.mc is > 0
*/
filePath = jmolViewer.ms.getModelFileName(i);
if (filePath != null && !mset.contains(filePath))
jmolScript(resetLastRes.toString());
resetLastRes.setLength(0);
}
+ StringBuilder highlightCommands=null;
for (AtomSpec atom : atoms)
{
- highlightAtom(atom.getAtomIndex(), atom.getPdbResNum(),
+ StringBuilder thisAtom = highlightAtom(atom.getAtomIndex(), atom.getPdbResNum(),
atom.getChain(), atom.getPdbFile());
+ if (thisAtom!=null) {
+ if (highlightCommands==null)
+ {
+ highlightCommands=thisAtom;
+ } else {
+ highlightCommands.append(thisAtom);
+ }
+ }
}
+ if (highlightCommands!=null)
+ {
+ jmolHistory(false);
+ jmolScript(highlightCommands.toString());
+ jmolHistory(true);
+ }
+ // Highlight distances between atoms with a 'measure' command - not yet
+ // working
+ // if (atoms.size() >= 2)
+ // {
+ // StringBuilder sb = new StringBuilder();
+ // for (int a = 0; a < atoms.size(); a++)
+ // {
+ // AtomSpec speca = atoms.get(a);
+ // String a_model = getModelIdForFile(speca.getPdbFile());
+ // for (int b = a + 1; b < atoms.size(); b++)
+ // {
+ // AtomSpec specb = atoms.get(b);
+ // String b_model = getModelIdForFile(speca.getPdbFile());
+ // sb.append("measure ALL (" + speca.getAtomIndex() + " and */"
+ // + a_model + ") (" + specb.getAtomIndex() + " and */"
+ // + b_model + ");");
+ // }
+ // }
+ // jmolHistory(false, useScriptWait);
+ // jmolScript(sb.toString(), useScriptWait);
+ // jmolHistory(true, useScriptWait);
+ // }
+
}
+
}
// jmol/ssm only
- public void highlightAtom(int atomIndex, int pdbResNum, String chain,
+ private StringBuilder highlightAtom(int atomIndex, int pdbResNum, String chain,
String pdbfile)
{
String modelId = getModelIdForFile(pdbfile);
if (modelId.isEmpty())
{
- return;
+ return null;
}
- jmolHistory(false);
-
StringBuilder selection = new StringBuilder(32);
StringBuilder cmd = new StringBuilder(64);
selection.append("select ").append(String.valueOf(pdbResNum));
resetLastRes.append(selection).append(";wireframe 0;").append(selection)
.append(" and not hetero; spacefill 0;");
- jmolScript(cmd.toString());
- jmolHistory(true);
+ return cmd;
}
private boolean debug = true;
private void jmolHistory(boolean enable)
{
- jmolScript("History " + ((debug || enable) ? "on" : "off"));
+ jmolHistory(enable, false);
+ }
+
+ private void jmolHistory(boolean enable, boolean useScriptWait)
+ {
+ jmolScript("History " + ((debug || enable) ? "on" : "off"),
+ useScriptWait);
}
public void loadInline(String string)
}
/*
- * highlight position on alignment(s); if some text is returned,
- * show this as a second line on the structure hover tooltip
+ * highlight position on alignment(s); if some text is returned, show this as a
+ * second line on the structure hover tooltip
*/
String label = getSsm().mouseOverStructure(pdbResNum, chainId,
pdbfilename);
lastMessage = strInfo;
if (data != null)
{
- System.err.println("Ignoring additional hover info: " + data
+ jalview.bin.Console.errPrintln("Ignoring additional hover info: " + data
+ " (other info: '" + strInfo + "' pos " + atomIndex + ")");
}
mouseOverStructure(atomIndex, strInfo);
/*
* { if (history != null && strStatus != null &&
- * !strStatus.equals("Script completed")) { history.append("\n" + strStatus);
- * } }
+ * !strStatus.equals("Script completed")) { history.append("\n" + strStatus); }
+ * }
*/
public void notifyAtomPicked(int atomIndex, String strInfo,
*/
if (strData != null)
{
- System.err.println("Ignoring additional pick data string " + strData);
+ jalview.bin.Console.errPrintln("Ignoring additional pick data string " + strData);
}
int chainSeparator = strInfo.indexOf(":");
int p = 0;
@Override
public void notifyCallback(CBK type, Object[] data)
{
+ /*
+ * ensure processed in AWT thread to avoid risk of deadlocks
+ */
+ SwingUtilities.invokeLater(new Runnable()
+ {
+
+ @Override
+ public void run()
+ {
+ processCallback(type, data);
+ }
+ });
+ }
+
+ /**
+ * Processes one callback notification from Jmol
+ *
+ * @param type
+ * @param data
+ */
+ protected void processCallback(CBK type, Object[] data)
+ {
try
{
switch (type)
(data == null) ? ((String) null) : (String) data[1]);
break;
case ERROR:
- // System.err.println("Ignoring error callback.");
+ // jalview.bin.Console.errPrintln("Ignoring error callback.");
break;
case SYNC:
case RESIZE:
case CLICK:
default:
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Unhandled callback " + type + " " + data[1].toString());
break;
}
} catch (Exception e)
{
- System.err.println("Squashed Jmol callback handler error:");
+ jalview.bin.Console.errPrintln("Squashed Jmol callback handler error:");
e.printStackTrace();
}
}
modelFileNames = null;
boolean notifyLoaded = false;
String[] modelfilenames = getStructureFiles();
+ if (modelfilenames == null)
+ {
+ // Jmol is still loading files!
+ return;
+ }
// first check if we've lost any structures
if (oldmodels != null && oldmodels.length > 0)
{
FeatureRenderer fr = getFeatureRenderer(null);
if (fr != null)
{
- fr.featuresAdded();
+ FeatureSettingsModelI colours = new Pdb().getFeatureColourScheme();
+ ((AppJmol) getViewer()).getAlignmentPanel().av
+ .applyFeaturesStyle(colours);
}
refreshGUI();
loadNotifiesHandled++;
public abstract void sendConsoleEcho(String strEcho); /*
* { showConsole(true);
*
- * history.append("\n" +
- * strEcho); }
+ * history.append("\n" + strEcho); }
*/
// /End JmolStatusListener
public void setCallbackFunction(String callbackType,
String callbackFunction)
{
- System.err.println("Ignoring set-callback request to associate "
+ jalview.bin.Console.errPrintln("Ignoring set-callback request to associate "
+ callbackType + " with function " + callbackFunction);
}
String buttonsToShow)
{
- System.err.println("Allocating Jmol Viewer: " + commandOptions);
+ jalview.bin.Console.errPrintln("Allocating Jmol Viewer: " + commandOptions);
if (commandOptions == null)
{
console = createJmolConsole(consolePanel, buttonsToShow);
} catch (Throwable e)
{
- System.err.println("Could not create Jmol application console. "
+ jalview.bin.Console.errPrintln("Could not create Jmol application console. "
+ e.getMessage());
e.printStackTrace();
}
{
return ".spt";
}
+
+ @Override
+ public void selectionChanged(BS arg0)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public SequenceRenderer getSequenceRenderer(AlignmentViewPanel avp)
+ {
+ return new jalview.gui.SequenceRenderer(avp.getAlignViewport());
+ }
+
+ @Override
+ public String getHelpURL()
+ {
+ return "http://wiki.jmol.org"; // BH 2018
+ }
}
git://source.jalview.org / jalview.git / blobdiff