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;
import java.awt.Color;
import java.net.BindException;
import java.util.ArrayList;
+import java.util.Hashtable;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
private static final String ALPHACARBON = "CA";
+ private List<String> chainNames = new ArrayList<String>();
+
+ private Hashtable<String, String> chainFile = new Hashtable<String, String>();
+
/*
* Object through which we talk to Chimera
*/
private String lastCommand;
- private boolean loadedInline;
-
- /**
- * current set of model filenames loaded
- */
- String[] modelFileNames = null;
-
String lastHighlightCommand;
- private List<String> lastReply;
-
/*
* incremented every time a load notification is successfully handled -
* lightweight mechanism for other threads to detect when they can start
*/
private long loadNotifiesHandled = 0;
+ private Thread chimeraMonitor;
+
/**
* Open a PDB structure file in Chimera and set up mappings from Jalview.
*
* @param protocol
*/
public JalviewChimeraBinding(StructureSelectionManager ssm,
- PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains,
- String protocol)
+ PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String protocol)
+ {
+ super(ssm, pdbentry, sequenceIs, protocol);
+ 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()
{
- super(ssm, pdbentry, sequenceIs, chains, protocol);
- viewer = new ChimeraManager(
- new ext.edu.ucsf.rbvi.strucviz2.StructureManager(true));
+ 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();
}
/**
boolean first = true;
for (String chain : toshow)
{
+ int modelNumber = getModelNoForChain(chain);
+ String showChainCmd = modelNumber == -1 ? "" : modelNumber + ":."
+ + chain.split(":")[1];
if (!first)
{
cmd.append(",");
}
- cmd.append(":.").append(chain);
+ cmd.append(showChainCmd);
first = false;
}
* window, but it looks more helpful not to (easier to relate chains to the
* whole)
*/
- final String command = "~display #*; ~ribbon #*; ribbon "
+ final String command = "~display #*; ~ribbon #*; ribbon :"
+ cmd.toString();
sendChimeraCommand(command, false);
}
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
{
return new String[0];
}
- // if (modelFileNames == null)
- // {
- // Collection<ChimeraModel> chimodels = viewer.getChimeraModels();
- // _modelFileNameMap = new int[chimodels.size()];
- // int j = 0;
- // for (ChimeraModel chimodel : chimodels)
- // {
- // String mdlName = chimodel.getModelName();
- // }
- // modelFileNames = new String[j];
- // // System.arraycopy(mset, 0, modelFileNames, 0, j);
- // }
return chimeraMaps.keySet().toArray(
modelFileNames = new String[chimeraMaps.size()]);
}
/**
- * 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' positions 44 and 46)
- * show #0:44,46.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 cmd = new StringBuilder(128);
boolean first = true;
boolean found = false;
{
if (first)
{
- cmd.append("show #").append(cms.get(0).getModelNumber())
+ cmd.append("rlabel #").append(cms.get(0).getModelNumber())
.append(":");
}
else
cmd.append(",");
}
first = false;
- cmd.append(cms.get(0).getModelNumber()).append(":");
cmd.append(pdbResNum);
if (!chain.equals(" "))
{
String command = cmd.toString();
/*
- * Avoid repeated commands for the same residue
+ * avoid repeated commands for the same residue
*/
if (command.equals(lastHighlightCommand))
{
return;
}
- viewerCommandHistory(false);
+ /*
+ * unshow the label for the previous residue
+ */
+ if (lastHighlightCommand != null)
+ {
+ viewer.sendChimeraCommand("~" + lastHighlightCommand, false);
+ }
if (found)
{
- viewer.sendChimeraCommand(command.toString(), false);
+ viewer.sendChimeraCommand(command, false);
}
- viewerCommandHistory(true);
this.lastHighlightCommand = command;
}
}
/**
- * Returns a list of chains mapped in this viewer. Note this list is not
- * currently scoped per structure.
- *
- * @return
- */
- public List<String> getChainNames()
- {
- List<String> names = new ArrayList<String>();
- String[][] allNames = getChains();
- if (allNames != null)
- {
- for (String[] chainsForPdb : allNames)
- {
- if (chainsForPdb != null)
- {
- for (String chain : chainsForPdb)
- {
- if (chain != null && !names.contains(chain))
- {
- names.add(chain);
- }
- }
- }
- }
- }
- return names;
- }
-
- /**
* Send a 'focus' command to Chimera to recentre the visible display
*/
public void focusView()
sm.highlightStructure(this, seq, positions);
}
}
+
+ @Override
+ public List<String> getChainNames()
+ {
+ return chainNames;
+ }
+
+ public Hashtable<String, String> getChainFile()
+ {
+ return chainFile;
+ }
+
+ public List<ChimeraModel> getChimeraModelByChain(String chain)
+ {
+ return chimeraMaps.get(chainFile.get(chain));
+ }
+
+ public int getModelNoForChain(String chain)
+ {
+ List<ChimeraModel> foundModels = getChimeraModelByChain(chain);
+ if (foundModels != null && !foundModels.isEmpty())
+ {
+ return foundModels.get(0).getModelNumber();
+ }
+ return -1;
+ }
}
git://source.jalview.org / jalview.git / blobdiff