*/
package jalview.ext.jmol;
-import jalview.api.FeatureRenderer;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SequenceI;
-import jalview.gui.IProgressIndicator;
-import jalview.gui.StructureViewer.ViewerType;
-import jalview.io.DataSourceType;
-import jalview.io.StructureFile;
-import jalview.structure.AtomSpec;
-import jalview.structure.StructureCommand;
-import jalview.structure.StructureCommandI;
-import jalview.structure.StructureSelectionManager;
-import jalview.structures.models.AAStructureBindingModel;
-
import java.awt.Container;
import java.awt.event.ComponentEvent;
import java.awt.event.ComponentListener;
import org.jmol.c.CBK;
import org.jmol.viewer.Viewer;
+import jalview.api.FeatureRenderer;
+import jalview.bin.Cache;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.gui.IProgressIndicator;
+import jalview.gui.StructureViewer.ViewerType;
+import jalview.io.DataSourceType;
+import jalview.io.StructureFile;
+import jalview.structure.AtomSpec;
+import jalview.structure.StructureCommand;
+import jalview.structure.StructureCommandI;
+import jalview.structure.StructureSelectionManager;
+import jalview.structures.models.AAStructureBindingModel;
+
public abstract class JalviewJmolBinding extends AAStructureBindingModel
implements JmolStatusListener, JmolSelectionListener,
ComponentListener
return getViewerTitle("Jmol", true);
}
- public void closeViewer()
+ private String jmolScript(String script)
{
- // remove listeners for all structures in viewer
- getSsm().removeStructureViewerListener(this, this.getStructureFiles());
- jmolViewer.dispose();
- lastCommand = null;
- jmolViewer = null;
- releaseUIResources();
+ Cache.log.debug(">>Jmol>> " + script);
+ String s = jmolViewer.scriptWait(script);
+ Cache.log.debug("<<Jmol<< " + s);
+
+ return s;
}
@Override
jmolHistory(false);
if (lastCommand == null || !lastCommand.equals(cmd))
{
- jmolViewer.evalStringQuiet(cmd + "\n");
+ jmolScript(cmd + "\n");
}
jmolHistory(true);
lastCommand = cmd;
@Override
public synchronized String[] getStructureFiles()
{
- List<String> mset = new ArrayList<>();
if (jmolViewer == null)
{
return new String[0];
{
int modelCount = jmolViewer.ms.mc;
String filePath = null;
+ List<String> mset = new ArrayList<>();
for (int i = 0; i < modelCount; ++i)
{
+ /*
+ * defensive check for null as getModelFileName can return null
+ * even when model count ms.mc is > 0
+ */
filePath = jmolViewer.ms.getModelFileName(i);
- if (!mset.contains(filePath))
+ if (filePath != null && !mset.contains(filePath))
{
mset.add(filePath);
}
}
- modelFileNames = mset.toArray(new String[mset.size()]);
+ if (!mset.isEmpty())
+ {
+ modelFileNames = mset.toArray(new String[mset.size()]);
+ }
}
return modelFileNames;
{
if (resetLastRes.length() > 0)
{
- jmolViewer.evalStringQuiet(resetLastRes.toString());
+ jmolScript(resetLastRes.toString());
resetLastRes.setLength(0);
}
for (AtomSpec atom : atoms)
public void highlightAtom(int atomIndex, int pdbResNum, String chain,
String pdbfile)
{
- if (modelFileNames == null)
- {
- return;
- }
-
- // look up file model number for this pdbfile
- int mdlNum = 0;
- // may need to adjust for URLencoding here - we don't worry about that yet.
- while (mdlNum < modelFileNames.length
- && !pdbfile.equals(modelFileNames[mdlNum]))
- {
- mdlNum++;
- }
- if (mdlNum == modelFileNames.length)
+ String modelId = getModelIdForFile(pdbfile);
+ if (modelId.isEmpty())
{
return;
}
jmolHistory(false);
+ StringBuilder selection = new StringBuilder(32);
StringBuilder cmd = new StringBuilder(64);
- cmd.append("select ").append(String.valueOf(pdbResNum)); // +modelNum
-
- resetLastRes.append("select ").append(String.valueOf(pdbResNum)); // +modelNum
-
- cmd.append(":");
- resetLastRes.append(":");
+ selection.append("select ").append(String.valueOf(pdbResNum));
+ selection.append(":");
if (!chain.equals(" "))
{
- cmd.append(chain);
- resetLastRes.append(chain);
- }
- {
- cmd.append(" /").append(String.valueOf(mdlNum + 1));
- resetLastRes.append("/").append(String.valueOf(mdlNum + 1));
+ selection.append(chain);
}
- cmd.append(";wireframe 100;" + cmd.toString() + " and not hetero;");
+ selection.append(" /").append(modelId);
- resetLastRes.append(";wireframe 0;" + resetLastRes.toString()
- + " and not hetero; spacefill 0;");
+ cmd.append(selection).append(";wireframe 100;").append(selection)
+ .append(" and not hetero;").append("spacefill 200;select none");
- cmd.append("spacefill 200;select none");
+ resetLastRes.append(selection).append(";wireframe 0;").append(selection)
+ .append(" and not hetero; spacefill 0;");
- jmolViewer.evalStringQuiet(cmd.toString());
+ jmolScript(cmd.toString());
jmolHistory(true);
-
}
private boolean debug = true;
private void jmolHistory(boolean enable)
{
- jmolViewer.evalStringQuiet("History " + ((debug || enable) ? "on" : "off"));
+ jmolScript("History " + ((debug || enable) ? "on" : "off"));
}
public void loadInline(String string)
{
/**
* this implements the toggle label behaviour copied from the original
- * structure viewer, MCView
+ * structure viewer, mc_view
*/
if (strData != null)
{
if (!atomsPicked.contains(picked))
{
- jmolViewer.evalStringQuiet("select " + picked + ";label %n %r:%c");
+ jmolScript("select " + picked + ";label %n %r:%c");
atomsPicked.addElement(picked);
}
else
// see JAL-623 - need method of matching pasted data up
{
pdb = getSsm().setMapping(getSequence()[pe], getChains()[pe],
- pdbfile, DataSourceType.PASTE,
- getIProgressIndicator());
+ pdbfile, DataSourceType.PASTE, getIProgressIndicator());
getPdbEntry(modelnum).setFile("INLINE" + pdb.getId());
matches = true;
foundEntry = true;
// }
if (!isLoadingFromArchive())
{
- jmolViewer.evalStringQuiet(
+ jmolScript(
"model *; select backbone;restrict;cartoon;wireframe off;spacefill off");
}
// register ourselves as a listener and notify the gui that it needs to
public void showHelp()
{
- showUrl("http://jmol.sourceforge.net/docs/JmolUserGuide/", "jmolHelp");
+ showUrl("http://wiki.jmol.org"
+ // BH 2018 "http://jmol.sourceforge.net/docs/JmolUserGuide/"
+ , "jmolHelp");
}
/**
*/
public abstract void showConsole(boolean show);
+ public static Viewer getJmolData(JmolParser jmolParser)
+ {
+ return (Viewer) JmolViewer.allocateViewer(null, null, null, null, null,
+ "-x -o -n", jmolParser);
+ }
+
/**
+ *
+ *
+ *
* @param renderPanel
* @param jmolfileio
* - when true will initialise jmol's file IO system (should be false
* @param consolePanel
* - panel to contain Jmol console
* @param buttonsToShow
- * - buttons to show on the console, in ordr
+ * - buttons to show on the console, in order
*/
public void allocateViewer(Container renderPanel, boolean jmolfileio,
String htmlName, URL documentBase, URL codeBase,
String commandOptions, final Container consolePanel,
String buttonsToShow)
{
+
+ System.err.println("Allocating Jmol Viewer: " + commandOptions);
+
if (commandOptions == null)
{
commandOptions = "";
jmolViewer.setJmolStatusListener(this); // extends JmolCallbackListener
- console = createJmolConsole(consolePanel, buttonsToShow);
+ try
+ {
+ console = createJmolConsole(consolePanel, buttonsToShow);
+ } catch (Throwable e)
+ {
+ System.err.println("Could not create Jmol application console. "
+ + e.getMessage());
+ e.printStackTrace();
+ }
if (consolePanel != null)
{
consolePanel.addComponentListener(this);
protected abstract JmolAppConsoleInterface createJmolConsole(
Container consolePanel, String buttonsToShow);
+ // BH 2018 -- Jmol console is not working due to problems with styled
+ // documents.
+
protected org.jmol.api.JmolAppConsoleInterface console = null;
@Override
{
if (modelFileNames[i].equalsIgnoreCase(pdbFile))
{
- return String.valueOf(i);
+ return String.valueOf(i + 1);
}
}
return "";
{
return String.valueOf(pdbfnum + 1);
}
+
+ /**
+ * Returns ".spt" - the Jmol session file extension
+ *
+ * @return
+ * @see https://chemapps.stolaf.edu/jmol/docs/#writemodel
+ */
+ @Override
+ public String getSessionFileExtension()
+ {
+ return ".spt";
+ }
}
git://source.jalview.org / jalview.git / blobdiff