*/
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.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.ext.rbvi.chimera.JalviewChimeraBinding;
+import jalview.gui.AlignmentPanel;
import jalview.gui.Desktop;
import jalview.gui.StructureViewer.ViewerType;
import jalview.io.DataSourceType;
/**
*
- * 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.
*
public static class SuperposeData
{
public String filename;
-
+
public String pdbId;
-
+
public String chain = "";
-
+
public boolean isRna;
-
+
/*
* The pdb residue number (if any) mapped to columns of the alignment
*/
public int[] pdbResNo; // or use SparseIntArray?
-
+
public String modelId;
-
+
/**
* Constructor
*
chains = newchains;
return chainmaps > 0;
}
+
public StructureSelectionManager getSsm()
{
return ssm;
}
}
}
+
@Override
public abstract void highlightAtoms(List<AtomSpec> atoms);
* @return
*/
protected int findSuperposableResidues(AlignmentI alignment,
- BitSet matched, AAStructureBindingModel.SuperposeData[] structures)
+ BitSet matched,
+ AAStructureBindingModel.SuperposeData[] structures)
{
int refStructure = -1;
String[] files = getStructureFiles();
* Calculate the superposable alignment columns ('matched'), and the
* corresponding structure residue positions (structures.pdbResNo)
*/
- int refStructure = findSuperposableResidues(alignment,
- matched, structures);
+ int refStructure = findSuperposableResidues(alignment, matched,
+ structures);
/*
* require at least 4 positions to be able to execute superposition
int nmatched = matched.cardinality();
if (nmatched < MIN_POS_TO_SUPERPOSE)
{
- String msg = MessageManager.formatMessage("label.insufficient_residues",
- nmatched);
+ String msg = MessageManager
+ .formatMessage("label.insufficient_residues", nmatched);
error += view.getViewName() + ": " + msg + "; ";
continue;
}
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;
}
return error;
}
- private AtomSpecModel getAtomSpec(AAStructureBindingModel.SuperposeData superposeData,
+ private AtomSpecModel getAtomSpec(
+ AAStructureBindingModel.SuperposeData superposeData,
BitSet matched)
{
AtomSpecModel model = new AtomSpecModel();
// TODO: JAL-628 colour chains distinctly across all visible models
- executeCommand(commandGenerator.colourByChain(), false,
- COLOURING_STRUCTURES);
+ executeCommand(false, COLOURING_STRUCTURES,
+ commandGenerator.colourByChain());
}
/**
{
return;
}
-
+
/*
* build a map of {Residue3LetterCode, Color}
*/
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)
{
+ 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
+
+ /*
+ * fire and forget
+ */
+ String threadName = msg == null ? "StructureCommand" : msg;
+ new Thread(new Runnable()
{
- /*
- * 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()
+ @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)
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
AlignmentI al = viewport.getAlignment();
Map<Object, AtomSpecModel> colourMap = new LinkedHashMap<>();
Color lastColour = null;
-
+
for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
{
final String modelId = getModelIdForFile(files[pdbfnum]);
StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
-
+
if (mapping == null || mapping.length < 1)
{
continue;
}
-
+
int startPos = -1, lastPos = -1;
String lastChain = "";
for (int s = 0; s < sequence[pdbfnum].length; s++)
continue;
}
int pos = mapping[m].getPDBResNum(asp.findPosition(r));
-
+
if (pos < 1 || pos == lastPos)
{
continue;
}
-
+
Color colour = sr.getResidueColour(seq, r, finder);
-
+
/*
* darker colour for hidden regions
*/
{
colour = Color.GRAY;
}
-
+
final String chain = mapping[m].getChain();
-
+
/*
* Just keep incrementing the end position for this colour range
* _unless_ colour, PDB model or chain has changed, or there is a
{
if (startPos != -1)
{
- addAtomSpecRange(colourMap, lastColour, modelId,
- startPos, lastPos, lastChain);
+ addAtomSpecRange(colourMap, lastColour, modelId, startPos,
+ lastPos, lastChain);
}
startPos = pos;
}
}
/**
- * Helper method to add one contiguous range to the AtomSpec model for the given
- * value (creating the model if necessary). As used by Jalview, {@code value} is
+ * Helper method to add one contiguous range to the AtomSpec model for the
+ * given value (creating the model if necessary). As used by Jalview,
+ * {@code value} is
* <ul>
* <li>a colour, when building a 'colour structure by sequence' command</li>
* <li>a feature value, when building a 'set Chimera attributes from features'
* @param chain
*/
public static final void addAtomSpecRange(Map<Object, AtomSpecModel> map,
- Object value,
- String model, int startPos, int endPos, String chain)
+ Object value, String model, int startPos, int endPos,
+ String chain)
{
/*
* Get/initialize map of data for the colour
atomSpec = new AtomSpecModel();
map.put(value, atomSpec);
}
-
+
atomSpec.addRange(model, startPos, endPos, chain);
}
saveSession(f);
} catch (IOException e)
{
- Cache.log.error(String.format("Error saving %s session: %s",
- prefix, e.toString()));
+ Console.error(String.format("Error saving %s session: %s", prefix,
+ e.toString()));
}
return f;
*/
protected void saveSession(File f)
{
- StructureCommandI cmd = commandGenerator
- .saveSession(f.getPath());
+ StructureCommandI cmd = commandGenerator.saveSession(f.getPath());
if (cmd != null)
{
executeCommand(cmd, false);
externalViewerMonitor = null;
}
+ stopListening();
+
if (forceClose)
{
StructureCommandI cmd = getCommandGenerator().closeViewer();
{
return theMap;
}
-
+
AlignViewportI viewport = viewPanel.getAlignViewport();
List<String> visibleFeatures = fr.getDisplayedFeatureTypes();
-
+
/*
* if alignment is showing features from complement, we also transfer
* these features to the corresponding mapped structure residues
{
return theMap;
}
-
+
AlignmentI alignment = viewPanel.getAlignment();
SequenceI[][] seqs = getSequence();
{
String modelId = getModelIdForFile(files[pdbfnum]);
StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
-
+
if (mapping == null || mapping.length < 1)
{
continue;
}
-
+
for (int seqNo = 0; seqNo < seqs[pdbfnum].length; seqNo++)
{
for (int m = 0; m < mapping.length; m++)
}
/**
- * Scans visible features in mapped positions of the CDS/peptide complement, and
- * adds any found to the map of attribute values/structure positions
+ * Scans visible features in mapped positions of the CDS/peptide complement,
+ * and adds any found to the map of attribute values/structure positions
*
* @param complementRenderer
* @param structureMapping
for (SequenceFeature sf : mf.features)
{
String type = sf.getType();
-
+
/*
* Don't copy features which originated from Chimera
*/
{
continue;
}
-
+
/*
* record feature 'value' (score/description/type) as at the
* corresponding structure position
*/
List<int[]> mappedRanges = structureMapping
.getPDBResNumRanges(seqPos, seqPos);
-
+
if (!mappedRanges.isEmpty())
{
String value = sf.getDescription();
for (SequenceFeature sf : sfs)
{
String type = sf.getType();
-
+
/*
* Don't copy features which originated from Chimera
*/
{
continue;
}
-
+
List<int[]> mappedRanges = mapping.getPDBResNumRanges(sf.getBegin(),
sf.getEnd());
-
+
if (!mappedRanges.isEmpty())
{
String value = sf.getDescription();
{
externalViewerMonitor = new Thread(new Runnable()
{
-
+
@Override
public void run()
{
});
externalViewerMonitor.start();
}
+
+ /**
+ * If supported by the external structure viewer, sends it commands to notify
+ * model or selection changes to the specified URL (where Jalview has started
+ * a listener)
+ *
+ * @param uri
+ */
+ protected void startListening(String uri)
+ {
+ List<StructureCommandI> commands = getCommandGenerator()
+ .startNotifications(uri);
+ if (commands != null)
+ {
+ executeCommands(commands, false, null);
+ }
+ }
+
+ /**
+ * If supported by the external structure viewer, sends it commands to stop
+ * notifying model or selection changes
+ */
+ protected void stopListening()
+ {
+ List<StructureCommandI> commands = getCommandGenerator()
+ .stopNotifications();
+ if (commands != null)
+ {
+ executeCommands(commands, false, null);
+ }
+ }
+
+ /**
+ * If supported by the structure viewer, queries it for all residue attributes
+ * with the given attribute name, and creates features on corresponding
+ * residues of the alignment. Returns the number of features added.
+ *
+ * @param attName
+ * @param alignmentPanel
+ * @return
+ */
+ public int copyStructureAttributesToFeatures(String attName,
+ AlignmentPanel alignmentPanel)
+ {
+ StructureCommandI cmd = getCommandGenerator()
+ .getResidueAttributes(attName);
+ if (cmd == null)
+ {
+ return 0;
+ }
+ List<String> residueAttributes = executeCommand(cmd, true);
+
+ int featuresAdded = createFeaturesForAttributes(attName,
+ residueAttributes);
+ if (featuresAdded > 0)
+ {
+ alignmentPanel.getFeatureRenderer().featuresAdded();
+ }
+ return featuresAdded;
+ }
+
+ /**
+ * Parses {@code residueAttributes} and creates sequence features on any
+ * mapped alignment residues. Returns the number of features created.
+ * <p>
+ * {@code residueAttributes} is the reply from the structure viewer to a
+ * command to list any residue attributes for the given attribute name. Syntax
+ * and parsing of this is viewer-specific.
+ *
+ * @param attName
+ * @param residueAttributes
+ * @return
+ */
+ protected int createFeaturesForAttributes(String attName,
+ List<String> residueAttributes)
+ {
+ return 0;
+ }
}
git://source.jalview.org / jalview.git / blobdiff