*/
package jalview.structures.models;
+import java.util.Locale;
+
import java.awt.Color;
import java.io.File;
import java.io.IOException;
import jalview.api.SequenceRenderer;
import jalview.api.StructureSelectionManagerProvider;
import jalview.api.structures.JalviewStructureDisplayI;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.MappedFeatures;
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;
/**
*
- * A base class to hold common function for protein structure model binding.
+ * A base class to hold common function for 3D structure model binding.
* Initial version created by refactoring JMol and Chimera binding models, but
* other structure viewers could in principle be accommodated in future.
*
}
}
}
+
@Override
public abstract void highlightAtoms(List<AtomSpec> atoms);
for (String reply : replies)
{
// return this error (Chimera only) to the user
- if (reply.toLowerCase().contains("unequal numbers of atoms"))
+ if (reply.toLowerCase(Locale.ROOT).contains("unequal numbers of atoms"))
{
error += "; " + reply;
}
// 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). WARNING: if you
+ * are sending commands that need to execute before later calls to
+ * executeCommand (e.g. mouseovers, which clean up after previous ones) then
+ * set getReply true to ensure that commands are not executed out of order.
+ *
+ * @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);
+ if (replies != null)
+ {
+ 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());
}
/**
}
/**
- * Returns the FeatureRenderer for the given alignment view, or null if
- * feature display is turned off in the view.
+ * Returns the FeatureRenderer for the given alignment view
*
* @param avp
* @return
{
return null;
}
- return ap.getAlignViewport().isShowSequenceFeatures()
- ? ap.getFeatureRenderer()
- : null;
+ return ap.getFeatureRenderer();
}
protected void setStructureCommands(StructureCommandsI cmd)
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
saveSession(f);
} catch (IOException e)
{
- Cache.log.error(String.format("Error saving %s session: %s", prefix,
+ Console.error(String.format("Error saving %s session: %s", prefix,
e.toString()));
}
git://source.jalview.org / jalview.git / blobdiff