return hasChimeraModel(modelNubmer, 0);
}
- public boolean hasChimeraModel(Integer modelNubmer, Integer subModelNumber)
+ public boolean hasChimeraModel(Integer modelNubmer,
+ Integer subModelNumber)
{
- return currentModelsMap.containsKey(ChimUtils.makeModelKey(modelNubmer,
- subModelNumber));
+ return currentModelsMap.containsKey(
+ ChimUtils.makeModelKey(modelNubmer, subModelNumber));
}
public void addChimeraModel(Integer modelNumber, Integer subModelNumber,
ChimUtils.makeModelKey(modelNumber, subModelNumber), model);
}
- public void removeChimeraModel(Integer modelNumber, Integer subModelNumber)
+ public void removeChimeraModel(Integer modelNumber,
+ Integer subModelNumber)
{
int modelKey = ChimUtils.makeModelKey(modelNumber, subModelNumber);
if (currentModelsMap.containsKey(modelKey))
if (!modelList.contains(newModel))
{
newModel.setModelName(modelName);
- sendChimeraCommand(
- "setattr M name " + modelName + " #"
- + newModel.getModelNumber(), false);
+ sendChimeraCommand("setattr M name " + modelName + " #"
+ + newModel.getModelNumber(), false);
modelList.add(newModel);
}
}
{
sendChimeraCommand("close " + model.toSpec(), false);
// currentModelNamesMap.remove(model.getModelName());
- currentModelsMap.remove(ChimUtils.makeModelKey(
- model.getModelNumber(), model.getSubModelNumber()));
+ currentModelsMap.remove(ChimUtils.makeModelKey(model.getModelNumber(),
+ model.getSubModelNumber()));
// selectionList.remove(chimeraModel);
}
else
public void startListening()
{
- sendChimeraCommand("listen start models; listen start selection", false);
+ sendChimeraCommand("listen start models; listen start selection",
+ false);
}
public void stopListening()
if (error.length() == 0)
{
this.chimeraRestPort = getPortNumber();
- System.out.println("Chimera REST API started on port "
- + chimeraRestPort);
+ System.out.println(
+ "Chimera REST API started on port " + chimeraRestPort);
// structureManager.initChimTable();
structureManager.setChimeraPathProperty(workingPath);
// TODO: [Optional] Check Chimera version and show a warning if below 1.8
* Adds command-line arguments to start the REST server
* <p>
* Method extracted for Jalview to allow override in ChimeraXManager
+ *
* @param args
*/
protected void addLaunchArguments(List<String> args)
{
int port = 0;
InputStream readChan = chimera.getInputStream();
- BufferedReader lineReader = new BufferedReader(new InputStreamReader(
- readChan));
+ BufferedReader lineReader = new BufferedReader(
+ new InputStreamReader(readChan));
StringBuilder responses = new StringBuilder();
try
{
}
} catch (Exception e)
{
- logger.error("Failed to get REST port number from " + responses
- + ": " + e.getMessage());
+ logger.error("Failed to get REST port number from " + responses + ": "
+ + e.getMessage());
} finally
{
try
}
if (port == 0)
{
- System.err
- .println("Failed to start Chimera with REST service, response was: "
+ System.err.println(
+ "Failed to start Chimera with REST service, response was: "
+ responses);
}
- logger.info("Chimera REST service listening on port " + chimeraRestPort);
+ logger.info(
+ "Chimera REST service listening on port " + chimeraRestPort);
return port;
}
String[] lineParts = inputLine.split("\\s");
if (lineParts.length == 5)
{
- ChimeraResidue residue = ChimUtils
- .getResidue(lineParts[2], model);
+ ChimeraResidue residue = ChimUtils.getResidue(lineParts[2],
+ model);
String value = lineParts[4];
if (residue != null)
{
*/
public List<String> sendChimeraCommand(String command, boolean reply)
{
- if (debug) {
+ if (debug)
+ {
System.out.println("chimeradebug>> " + command);
}
if (!isChimeraLaunched() || command == null
{
return null;
}
- // TODO do we need a maximum wait time before aborting?
- while (busy)
+ /*
+ * set a maximum wait time before trying anyway
+ * to avoid hanging indefinitely
+ */
+ int waited = 0;
+ int pause = 25;
+ while (busy && waited < 1001)
{
try
{
- Thread.sleep(25);
+ Thread.sleep(pause);
+ waited += pause;
} catch (InterruptedException q)
{
}
+ (System.currentTimeMillis() - startTime) + "ms: "
+ command);
}
-
}
}
}
/**
- * Returns "POST" as the HTTP request method to use for REST service calls to Chimera
+ * Returns "POST" as the HTTP request method to use for REST service calls to
+ * Chimera
+ *
* @return
*/
protected String getHttpRequestMethod()
import java.net.BindException;
import java.util.ArrayList;
import java.util.Collections;
-import java.util.Iterator;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
import ext.edu.ucsf.rbvi.strucviz2.StructureManager.ModelType;
import jalview.api.AlignmentViewPanel;
import jalview.bin.Cache;
-import jalview.datamodel.AlignmentI;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SearchResultMatchI;
import jalview.datamodel.SearchResultsI;
*/
if (lastHighlightCommand != null)
{
- chimeraManager.sendChimeraCommand("~" + lastHighlightCommand, false);
+ executeCommand(false, null, new StructureCommand("~" + lastHighlightCommand));
}
if (found)
{
- chimeraManager.sendChimeraCommand(command, false);
+ executeCommand(false, null, new StructureCommand(command));
}
this.lastHighlightCommand = command;
}
}
else
{
- for (StructureCommandI command : commands)
- {
- sendAsynchronousCommand(command, null);
- }
+ executeCommands(commands, false, null);
}
return commands.size();
}
String path = tmp.getAbsolutePath();
StructureCommandI command = getCommandGenerator()
.openCommandFile(path);
- sendAsynchronousCommand(command, null);
+ executeCommand(false, null, command);
} catch (IOException e)
{
System.err.println("Sending commands to Chimera via file failed with "
import jalview.datamodel.SequenceI;
import jalview.ext.rbvi.chimera.JalviewChimeraBinding;
import jalview.io.DataSourceType;
-import jalview.structure.AtomSpec;
import jalview.structure.StructureSelectionManager;
public class JalviewChimeraBindingModel extends JalviewChimeraBinding
import jalview.schemes.ResidueProperties;
import jalview.structure.AtomSpec;
import jalview.structure.AtomSpecModel;
-import jalview.structure.StructureCommand;
import jalview.structure.StructureCommandI;
import jalview.structure.StructureCommandsI;
import jalview.structure.StructureListener;
// TODO: JAL-628 colour chains distinctly across all visible models
- executeCommand(commandGenerator.colourByChain(), false,
- COLOURING_STRUCTURES);
+ executeCommand(false, COLOURING_STRUCTURES,
+ commandGenerator.colourByChain());
}
/**
public void setBackgroundColour(Color col)
{
StructureCommandI cmd = commandGenerator.setBackgroundColour(col);
- executeCommand(cmd, false, null);
+ executeCommand(false, null, cmd);
}
/**
- * Sends one command to the structure viewer. If {@code getReply} is true, the
- * command is sent synchronously, otherwise in a deferred thread.
- * <p>
- * If a progress message is supplied, this is displayed before command
- * execution, and removed afterwards.
+ * Execute one structure viewer command. If {@code getReply} is true, may
+ * optionally return one or more reply messages, else returns null.
*
* @param cmd
* @param getReply
+ */
+ protected abstract List<String> executeCommand(StructureCommandI cmd,
+ boolean getReply);
+
+ /**
+ * Executes one or more structure viewer commands
+ *
+ * @param commands
+ * @param getReply
* @param msg
- * @return
*/
- private List<String> executeCommand(StructureCommandI cmd,
+ protected List<String> executeCommands(List<StructureCommandI> commands,
boolean getReply, String msg)
{
- final JalviewStructureDisplayI theViewer = getViewer();
+ return executeCommand(getReply, msg,
+ commands.toArray(new StructureCommandI[commands.size()]));
+ }
+
+ /**
+ * Executes one or more structure viewer commands, optionally returning the
+ * reply, and optionally showing a status message while the command is being
+ * executed.
+ * <p>
+ * If a reply is wanted, the execution is done synchronously (waits),
+ * otherwise it is done in a separate thread (doesn't wait).
+ *
+ * @param getReply
+ * @param msg
+ * @param cmds
+ * @return
+ */
+ protected List<String> executeCommand(boolean getReply, String msg,
+ StructureCommandI... cmds)
+ {
+ JalviewStructureDisplayI theViewer = getViewer();
final long handle = msg == null ? 0 : theViewer.startProgressBar(msg);
+
if (getReply)
{
/*
- * synchronous (same thread) execution so reply can be returned
+ * execute and wait for reply
*/
+ List<String> response = new ArrayList<>();
try
{
- return executeCommand(cmd, true);
+ for (StructureCommandI cmd : cmds)
+ {
+ List<String> replies = executeCommand(cmd, true);
+ response.addAll(replies);
+ }
+ return response;
} finally
{
if (msg != null)
}
}
}
- else
+
+ /*
+ * fire and forget
+ */
+ String threadName = msg == null ? "StructureCommand" : msg;
+ new Thread(new Runnable()
{
- /*
- * asynchronous (new thread) execution if no reply needed
- */
- SwingUtilities.invokeLater(new Runnable()
+ @Override
+ public void run()
{
- @Override
- public void run()
+ try
{
- try
+ for (StructureCommandI cmd : cmds)
{
executeCommand(cmd, false);
- } finally
+ }
+ } finally
+ {
+ if (msg != null)
{
- if (msg != null)
+ SwingUtilities.invokeLater(new Runnable()
{
- theViewer.stopProgressBar(null, handle);
- }
+ @Override
+ public void run()
+ {
+ theViewer.stopProgressBar(null, handle);
+ }
+ });
}
}
- });
- return null;
- }
- }
-
- /**
- * Execute one structure viewer command. If {@code getReply} is true, may
- * optionally return one or more reply messages, else returns null.
- *
- * @param cmd
- * @param getReply
- */
- protected abstract List<String> executeCommand(StructureCommandI cmd,
- boolean getReply);
-
- /**
- * Executes one or more structure viewer commands
- *
- * @param commands
- * @param getReply
- * @param msg
- */
- protected List<String> executeCommands(List<StructureCommandI> commands,
- boolean getReply, String msg)
- {
- List<String> response = getReply ? new ArrayList<>() : null;
- for (StructureCommandI cmd : commands)
- {
- List<String> replies = executeCommand(cmd, getReply, msg);
- if (replies != null)
- {
- response.addAll(replies);
}
- }
- return response;
+ }, threadName).start();
+ return null;
}
/**
*/
public void focusView()
{
- executeCommand(commandGenerator.focusView(), false, null);
+ executeCommand(false, null, commandGenerator.focusView());
}
/**
protected abstract ViewerType getViewerType();
/**
- * Send a structure viewer command asynchronously in a new thread. If the
- * progress message is not null, display this message while the command is
- * executing.
- *
- * @param command
- * @param progressMsg
- */
- protected void sendAsynchronousCommand(StructureCommandI command,
- String progressMsg)
- {
- final JalviewStructureDisplayI theViewer = getViewer();
- final long handle = progressMsg == null ? 0
- : theViewer.startProgressBar(progressMsg);
- SwingUtilities.invokeLater(new Runnable()
- {
- @Override
- public void run()
- {
- try
- {
- executeCommand(command, false, null);
- } finally
- {
- if (progressMsg != null)
- {
- theViewer.stopProgressBar(null, handle);
- }
- }
- }
- });
-
- }
-
- /**
* Builds a data structure which records mapped structure residues for each
* colour. From this we can easily generate the viewer commands for colour by
* sequence. Constructs and returns a map of {@code Color} to
git://source.jalview.org / jalview.git / commitdiff