import java.util.HashMap;
import java.util.LinkedHashMap;
import java.util.List;
+import java.util.Locale;
import java.util.Map;
import javax.swing.SwingUtilities;
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.ColumnSelection;
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.MappedFeatures;
import jalview.datamodel.PDBEntry;
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.StructureCommandsI.AtomSpecType;
import jalview.structure.StructureListener;
import jalview.structure.StructureMapping;
import jalview.structure.StructureSelectionManager;
/**
*
- * A base class to hold common function for protein structure model binding.
- * Initial version created by refactoring JMol and Chimera binding models, but
- * other structure viewers could in principle be accommodated in future.
+ * 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.
*
* @author gmcarstairs
*
public String chain = "";
+ /**
+ * is the mapped sequence not protein ?
+ */
public boolean isRna;
/*
protected boolean colourBySequence = true;
+ /**
+ * true if all sequences appear to be nucleotide
+ */
private boolean nucleotide;
private boolean finishedInit = false;
structures[pdbfnum].chain = chain;
}
structures[pdbfnum].pdbId = mapping.getPdbId();
- structures[pdbfnum].isRna = theSequence.getRNA() != null;
+ structures[pdbfnum].isRna = !theSequence.isProtein();
/*
* move on to next pdb file (ignore sequences for other chains
if (waiting)
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Timed out waiting for structure viewer to load file "
+ notLoaded);
return false;
{
AlignmentI alignment = view.getAlignment();
HiddenColumns hiddenCols = alignment.getHiddenColumns();
-
/*
* 'matched' bit i will be set for visible alignment columns i where
* all sequences have a residue with a mapping to their PDB structure
*/
- BitSet matched = new BitSet();
final int width = alignment.getWidth();
- for (int m = 0; m < width; m++)
+ BitSet matched = new BitSet();
+ ColumnSelection cs = view.getAlignViewport().getColumnSelection();
+ // restrict to active column selection, if there is one
+ if (cs != null && cs.hasSelectedColumns()
+ && cs.getSelected().size() >= 4)
{
- if (hiddenCols == null || hiddenCols.isVisible(m))
+ for (int s : cs.getSelected())
{
- matched.set(m);
+ matched.set(s);
+ }
+ }
+ else
+ {
+ for (int m = 0; m < width; m++)
+ {
+ if (hiddenCols == null || hiddenCols.isVisible(m))
+ {
+ matched.set(m);
+ }
}
}
-
AAStructureBindingModel.SuperposeData[] structures = new AAStructureBindingModel.SuperposeData[files.length];
for (int f = 0; f < files.length; f++)
{
// todo better way to ensure synchronous than setting getReply true!!
executeCommands(commandGenerator.showBackbone(), true, null);
+ AtomSpecType backbone = structures[refStructure].isRna
+ ? AtomSpecType.PHOSPHATE
+ : AtomSpecType.ALPHA;
+ List<AtomSpecModel> models = new ArrayList<AtomSpecModel>();
+ models.add(refAtoms);
/*
* superpose each (other) structure to the reference in turn
*/
{
AtomSpecModel atomSpec = getAtomSpec(structures[i], matched);
List<StructureCommandI> commands = commandGenerator
- .superposeStructures(refAtoms, atomSpec);
+ .superposeStructures(refAtoms, atomSpec, backbone);
List<String> replies = executeCommands(commands, true, null);
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;
}
}
+ models.add(atomSpec);
}
}
+ List<StructureCommandI> finalView = commandGenerator
+ .centerViewOn(models);
+ if (finalView != null && finalView.size() > 0)
+ {
+ executeCommands(finalView, false, "Centered on Superposition");
+ }
}
-
return error;
}
// 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,
+ public List<String> executeCommands(List<StructureCommandI> commands,
boolean getReply, String msg)
{
+ 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
*/
- final JalviewStructureDisplayI theViewer = getViewer();
- final long handle = msg == null ? 0 : theViewer.startProgressBar(msg);
+ List<String> response = new ArrayList<>();
try
{
- return executeCommand(cmd, getReply);
+ for (StructureCommandI cmd : cmds)
+ {
+ List<String> replies = executeCommand(cmd, true);
+ if (replies != null)
+ {
+ response.addAll(replies);
+ }
+ }
+ return response;
} finally
{
if (msg != null)
}
}
}
- else
- {
- /*
- * asynchronous (new thread) execution if no reply needed
- */
- final JalviewStructureDisplayI theViewer = getViewer();
- final long handle = msg == null ? 0 : theViewer.startProgressBar(msg);
- SwingUtilities.invokeLater(new Runnable()
+ /*
+ * fire and forget
+ */
+ String threadName = msg == null ? "StructureCommand" : msg;
+ new Thread(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. If a progress message is
- * provided, it is shown first, and removed after all commands have been run.
- *
- * @param commands
- * @param getReply
- * @param msg
- */
- protected List<String> executeCommands(List<StructureCommandI> commands,
- boolean getReply, String msg)
- {
- /*
- * show progress message if specified
- */
- final JalviewStructureDisplayI theViewer = getViewer();
- final long handle = msg == null ? 0 : theViewer.startProgressBar(msg);
-
- List<String> response = getReply ? new ArrayList<>() : null;
- try
- {
- for (StructureCommandI cmd : commands)
- {
- List<String> replies = executeCommand(cmd, getReply, null);
- if (getReply && replies != null)
- {
- response.addAll(replies);
- }
- }
- return response;
- } finally
- {
- if (msg != null)
- {
- theViewer.stopProgressBar(null, handle);
}
- }
+ }, threadName).start();
+ return null;
}
/**
List<StructureCommandI> colourBySequenceCommands = commandGenerator
.colourBySequence(colourMap);
- executeCommands(colourBySequenceCommands, false, null);
+ executeCommands(colourBySequenceCommands, false, COLOURING_STRUCTURES);
}
/**
*/
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)
@Override
public void updateColours(Object source)
{
+ if (getViewer() == null)
+ {
+ // can happen if a viewer was not instantiated or cleaned up and is still
+ // registered - mostly during tests
+ return;
+ }
AlignmentViewPanel ap = (AlignmentViewPanel) source;
// ignore events from panels not used to colour this view
if (!getViewer().isUsedForColourBy(ap))
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()));
}
return f;
}
+
+ /**
+ * Use restoreSession when you want to restore a previously saved sesssion to
+ * the running viewer instance.
+ *
+ * @param absolutePath
+ */
+ public void restoreSession(String absolutePath)
+ {
+ String prefix = getViewerType().toString();
+ try {
+
+ StructureCommandI cmd = commandGenerator.restoreSession(absolutePath);
+ if (cmd != null)
+ {
+ executeCommand(cmd, false);
+ }
+ } catch (Throwable e)
+ {
+ Console.error(String.format("Error restoring %s session: %s", prefix,
+ e.toString()));
+ }
+
+ }
+
/**
* Saves the structure viewer session to the given file
*