import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureRenderer;
import jalview.api.SequenceRenderer;
+import jalview.api.structures.JalviewStructureDisplayI;
import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
private String lastCommand;
- private boolean loadedInline;
-
- /**
- * current set of model filenames loaded
- */
- String[] modelFileNames = null;
-
- String lastMousedOverAtomSpec;
-
- private List<String> lastReply;
+ String lastHighlightCommand;
/*
* incremented every time a load notification is successfully handled -
*/
private long loadNotifiesHandled = 0;
+ private Thread chimeraMonitor;
+
/**
* Open a PDB structure file in Chimera and set up mappings from Jalview.
*
String protocol)
{
super(ssm, pdbentry, sequenceIs, chains, protocol);
- viewer = new ChimeraManager(
- new ext.edu.ucsf.rbvi.strucviz2.StructureManager(true));
+ viewer = new ChimeraManager(new StructureManager(true));
+ }
+
+ /**
+ * Starts a thread that waits for the Chimera process to finish, so that we
+ * can then close the associated resources. This avoids leaving orphaned
+ * Chimera viewer panels in Jalview if the user closes Chimera.
+ */
+ protected void startChimeraProcessMonitor()
+ {
+ final Process p = viewer.getChimeraProcess();
+ chimeraMonitor = new Thread(new Runnable()
+ {
+
+ @Override
+ public void run()
+ {
+ try
+ {
+ p.waitFor();
+ JalviewStructureDisplayI display = getViewer();
+ if (display != null)
+ {
+ display.closeViewer(false);
+ }
+ } catch (InterruptedException e)
+ {
+ // exit thread if Chimera Viewer is closed in Jalview
+ }
+ }
+ });
+ chimeraMonitor.start();
}
/**
lastCommand = null;
viewer = null;
+ if (chimeraMonitor != null)
+ {
+ chimeraMonitor.interrupt();
+ }
releaseUIResources();
}
/**
* Launch Chimera, unless an instance linked to this object is already
- * running. Returns true if chimera is successfully launched, or already
+ * running. Returns true if Chimera is successfully launched, or already
* running, else false.
*
* @return
*/
public boolean launchChimera()
{
- if (!viewer.isChimeraLaunched())
- {
- return viewer.launchChimera(StructureManager.getChimeraPaths());
- }
if (viewer.isChimeraLaunched())
{
return true;
}
- log("Failed to launch Chimera!");
- return false;
+
+ boolean launched = viewer.launchChimera(StructureManager
+ .getChimeraPaths());
+ if (launched)
+ {
+ startChimeraProcessMonitor();
+ }
+ else
+ {
+ log("Failed to launch Chimera!");
+ }
+ return launched;
}
/**
if (lastCommand == null || !lastCommand.equals(command))
{
// trim command or it may never find a match in the replyLog!!
- lastReply = viewer.sendChimeraCommand(command.trim(), logResponse);
+ List<String> lastReply = viewer.sendChimeraCommand(command.trim(),
+ logResponse);
if (logResponse && debug)
{
log("Response from command ('" + command + "') was:\n" + lastReply);
// End StructureListener
// //////////////////////////
- public Color getColour(int atomIndex, int pdbResNum, String chain,
- String pdbfile)
- {
- if (getModelNum(pdbfile) < 0)
- {
- return null;
- }
- log("get model / residue colour attribute unimplemented");
- return null;
- }
-
/**
* returns the current featureRenderer that should be used to colour the
* structures
}
/**
- * map from string to applet
- */
- public Map getRegistryInfo()
- {
- // TODO Auto-generated method stub
- return null;
- }
-
- /**
* returns the current sequenceRenderer that should be used to colour the
* structures
*
AlignmentViewPanel alignment);
/**
- * Construct and send a command to highlight zero, one or more atoms.
- *
- * <pre>
- * Done by generating a command like (to 'highlight' position 44)
- * show #0:44.C
- * </pre>
+ * Construct and send a command to highlight zero, one or more atoms. We do
+ * this by sending an "rlabel" command to show the residue label at that
+ * position.
*/
@Override
public void highlightAtoms(List<AtomSpec> atoms)
{
- if (atoms == null)
+ if (atoms == null || atoms.size() == 0)
{
return;
}
- StringBuilder atomSpecs = new StringBuilder();
+
+ StringBuilder cmd = new StringBuilder(128);
boolean first = true;
+ boolean found = false;
for (AtomSpec atom : atoms)
{
List<ChimeraModel> cms = chimeraMaps.get(pdbfile);
if (cms != null && !cms.isEmpty())
{
- /*
- * Formatting as #0:34.A,#1:33.A doesn't work as desired, so instead we
- * concatenate multiple 'show' commands
- */
- atomSpecs.append(first ? "" : ",");
+ if (first)
+ {
+ cmd.append("rlabel #").append(cms.get(0).getModelNumber())
+ .append(":");
+ }
+ else
+ {
+ cmd.append(",");
+ }
first = false;
- atomSpecs.append(cms.get(0).getModelNumber());
- atomSpecs.append(":" + pdbResNum);
+ cmd.append(pdbResNum);
if (!chain.equals(" "))
{
- atomSpecs.append("." + chain);
+ cmd.append(".").append(chain);
}
+ found = true;
}
}
- String atomSpec = atomSpecs.toString();
+ String command = cmd.toString();
/*
- * Avoid repeated commands for the same residue
+ * avoid repeated commands for the same residue
*/
- if (atomSpec.equals(lastMousedOverAtomSpec))
+ if (command.equals(lastHighlightCommand))
{
return;
}
- StringBuilder command = new StringBuilder(32);
- viewerCommandHistory(false);
- if (atomSpec.length() > 0)
+ /*
+ * unshow the label for the previous residue
+ */
+ if (lastHighlightCommand != null)
{
- command.append("show #").append(atomSpec);
- viewer.sendChimeraCommand(command.toString(), false);
+ viewer.sendChimeraCommand("~" + lastHighlightCommand, false);
}
- viewerCommandHistory(true);
- this.lastMousedOverAtomSpec = atomSpec;
+ if (found)
+ {
+ viewer.sendChimeraCommand(command, false);
+ }
+ this.lastHighlightCommand = command;
}
/**
{
sendChimeraCommand("focus", false);
}
+
+ /**
+ * Send a 'show' command for all atoms in the currently selected columns
+ *
+ * TODO: pull up to abstract structure viewer interface
+ *
+ * @param vp
+ */
+ public void highlightSelection(AlignmentViewPanel vp)
+ {
+ List<Integer> cols = vp.getAlignViewport().getColumnSelection()
+ .getSelected();
+ AlignmentI alignment = vp.getAlignment();
+ StructureSelectionManager sm = getSsm();
+ for (SequenceI seq : alignment.getSequences())
+ {
+ /*
+ * convert selected columns into sequence positions
+ */
+ int[] positions = new int[cols.size()];
+ int i = 0;
+ for (Integer col : cols)
+ {
+ positions[i++] = seq.findPosition(col);
+ }
+ sm.highlightStructure(this, seq, positions);
+ }
+ }
}
git://source.jalview.org / jalview.git / blobdiff