*/
public class ChimeraCommands extends StructureCommandsBase
{
+ // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/focus.html
+ private static final StructureCommand FOCUS_VIEW = new StructureCommand("focus");
+
+ // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/listen.html#listresattr
+ private static final StructureCommand LIST_RESIDUE_ATTRIBUTES = new StructureCommand("list resattr");
+
+ // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/stop.html
private static final StructureCommand CLOSE_CHIMERA = new StructureCommand("stop really");
+ // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/listen.html
private static final StructureCommand STOP_NOTIFY_SELECTION = new StructureCommand("listen stop selection");
private static final StructureCommand STOP_NOTIFY_MODELS = new StructureCommand("listen stop models");
+ // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/listen.html#listselection
private static final StructureCommand GET_SELECTION = new StructureCommand("list selection level residue");
private static final StructureCommand SHOW_BACKBONE = new StructureCommand(
private static final StructureCommandI COLOUR_BY_CHARGE = new StructureCommand(
"color white;color red ::ASP,GLU;color blue ::LYS,ARG;color yellow ::CYS");
+ // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/rainbow.html
private static final StructureCommandI COLOUR_BY_CHAIN = new StructureCommand(
"rainbow chain");
@Override
public StructureCommandI focusView()
{
- // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/focus.html
- return new StructureCommand("focus");
+ return FOCUS_VIEW;
}
@Override
@Override
public StructureCommandI closeViewer()
{
- // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/stop.html
return CLOSE_CHIMERA;
}
@Override
public List<StructureCommandI> stopNotifications()
{
- // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/listen.html
List<StructureCommandI> cmds = new ArrayList<>();
cmds.add(STOP_NOTIFY_MODELS);
cmds.add(STOP_NOTIFY_SELECTION);
return GET_SELECTION;
}
+ @Override
+ public StructureCommandI listResidueAttributes()
+ {
+ return LIST_RESIDUE_ATTRIBUTES;
+ }
+
+ @Override
+ public StructureCommandI getResidueAttributes(String attName)
+ {
+ // this alternative command
+ // list residues spec ':*/attName' attr attName
+ // doesn't report 'None' values (which is good), but
+ // fails for 'average.bfactor' (which is bad):
+ return new StructureCommand("list residues attr '" + attName + "'");
+ }
+
}
*/
public class ChimeraXCommands extends ChimeraCommands
{
+ // https://www.cgl.ucsf.edu/chimerax/docs/user/commands/info.html#resattr
+ private static final StructureCommand LIST_RESIDUE_ATTRIBUTES = new StructureCommand("info resattr");
+
+ // https://www.cgl.ucsf.edu/chimerax/docs/user/commands/exit.html
private static final StructureCommand CLOSE_CHIMERAX = new StructureCommand("exit");
+ // https://www.cgl.ucsf.edu/chimerax/docs/user/commands/info.html#notify
private static final StructureCommand STOP_NOTIFY_SELECTION = new StructureCommand("info notify stop selection jalview");
private static final StructureCommand STOP_NOTIFY_MODELS = new StructureCommand("info notify stop models jalview");
- private static final StructureCommand GET_SELECTION = new StructureCommand("info selection level residue");
+ // https://www.cgl.ucsf.edu/chimerax/docs/user/commands/info.html#selection
+ private static final StructureCommand GET_SELECTION = new StructureCommand(
+ "info selection level residue");
private static final StructureCommand SHOW_BACKBONE = new StructureCommand(
"~display all;~ribbon;show @CA|P atoms");
+ // https://www.cgl.ucsf.edu/chimerax/docs/user/commands/view.html
private static final StructureCommand FOCUS_VIEW = new StructureCommand(
"view");
@Override
public StructureCommandI focusView()
{
- // https://www.cgl.ucsf.edu/chimerax/docs/user/commands/view.html
return FOCUS_VIEW;
}
@Override
public StructureCommandI closeViewer()
{
- // https://www.cgl.ucsf.edu/chimerax/docs/user/commands/exit.html
return CLOSE_CHIMERAX;
}
@Override
public List<StructureCommandI> startNotifications(String uri)
{
- // https://www.cgl.ucsf.edu/chimerax/docs/user/commands/info.html#notify
List<StructureCommandI> cmds = new ArrayList<>();
cmds.add(new StructureCommand("info notify start models prefix ModelChanged jalview url " + uri));
cmds.add(new StructureCommand("info notify start selection jalview prefix SelectionChanged url " + uri));
@Override
public List<StructureCommandI> stopNotifications()
{
- // https://www.cgl.ucsf.edu/chimerax/docs/user/commands/info.html#notify
List<StructureCommandI> cmds = new ArrayList<>();
cmds.add(STOP_NOTIFY_MODELS);
cmds.add(STOP_NOTIFY_SELECTION);
{
return GET_SELECTION;
}
+
+ @Override
+ public StructureCommandI listResidueAttributes()
+ {
+ return LIST_RESIDUE_ATTRIBUTES;
+ }
}
}
/*
- * the following call should not be needed but is temporarily included,
- * to avoid a stack trace error in Chimera after "stop really" is sent
+ * the following call is added to avoid a stack trace error in Chimera
+ * after "stop really" is sent; Chimera > 1.14 will not need it; see also
+ * http://plato.cgl.ucsf.edu/trac/chimera/ticket/17597
*/
- if (closeChimera)
+ if (closeChimera && (getViewerType() == ViewerType.CHIMERA))
{
chimeraManager.getChimeraProcess().destroy();
}
}
/**
- * Get Chimera residues which have the named attribute, find the mapped
- * positions in the Jalview sequence(s), and set as sequence features
- *
- * @param attName
- * @param alignmentPanel
- */
- public void copyStructureAttributesToFeatures(String attName,
- AlignmentViewPanel alignmentPanel)
- {
- // todo pull up to AAStructureBindingModel (and interface?)
-
- /*
- * ask Chimera to list residues with the attribute, reporting its value
- */
- // this alternative command
- // list residues spec ':*/attName' attr attName
- // doesn't report 'None' values (which is good), but
- // fails for 'average.bfactor' (which is bad):
-
- String cmd = "list residues attr '" + attName + "'";
- List<String> residues = executeCommand(new StructureCommand(cmd), true);
-
- boolean featureAdded = createFeaturesForAttributes(attName, residues);
- if (featureAdded)
- {
- alignmentPanel.getFeatureRenderer().featuresAdded();
- }
- }
-
- /**
* Create features in Jalview for the given attribute name and structure
* residues.
*
*
* @param attName
* @param residues
- * @return
+ * @return the number of features added
*/
- protected boolean createFeaturesForAttributes(String attName,
+ protected int createFeaturesForAttributes(String attName,
List<String> residues)
{
- boolean featureAdded = false;
+ int featuresAdded = 0;
String featureGroup = getViewerFeatureGroup();
for (String residue : residues)
spec = parseAtomSpec(atomSpec);
} catch (IllegalArgumentException e)
{
- System.err.println("Problem parsing atomspec " + atomSpec);
+ Cache.log.error("Problem parsing atomspec " + atomSpec);
continue;
}
start, end, score, featureGroup);
// todo: should SequenceFeature have an explicit property for chain?
// note: repeating the action shouldn't duplicate features
- featureAdded |= seq.addSequenceFeature(sf);
+ if (seq.addSequenceFeature(sf))
+ {
+ featuresAdded++;
+ }
}
}
- return featureAdded;
+ return featuresAdded;
}
/**
*/
public List<String> getChimeraAttributes()
{
- List<String> atts = chimeraManager.getAttrList();
- Iterator<String> it = atts.iterator();
- while (it.hasNext())
+ List<String> attributes = new ArrayList<>();
+ StructureCommandI command = getCommandGenerator().listResidueAttributes();
+ final List<String> reply = executeCommand(command, true);
+ if (reply != null)
{
- if (it.next().startsWith(ChimeraCommands.NAMESPACE_PREFIX))
+ for (String inputLine : reply)
{
- /*
- * attribute added from Jalview - exclude it
- */
- it.remove();
+ String[] lineParts = inputLine.split("\\s");
+ if (lineParts.length == 2 && lineParts[0].equals("resattr"))
+ {
+ String attName = lineParts[1];
+ /*
+ * exclude attributes added from Jalview
+ */
+ if (!attName.startsWith(ChimeraCommands.NAMESPACE_PREFIX))
+ {
+ attributes.add(attName);
+ }
+ }
}
}
- return atts;
+ return attributes;
}
/**
}
/**
- * Query Chimera for its residue attribute names and add them as items off the
- * attributes menu
+ * Query the structure viewer for its residue attribute names and add them as
+ * items off the attributes menu
*
* @param attributesMenu
*/
@Override
public void actionPerformed(ActionEvent e)
{
- getChimeraAttributes(attName);
+ if (getBinding().copyStructureAttributesToFeatures(attName,
+ getAlignmentPanel()) > 0)
+ {
+ getAlignmentPanel().getFeatureRenderer().featuresAdded();
+ }
}
});
attributesMenu.add(menuItem);
}
/**
- * Read residues in Chimera with the given attribute name, and set as features
- * on the corresponding sequence positions (if any)
- *
- * @param attName
- */
- protected void getChimeraAttributes(String attName)
- {
- jmb.copyStructureAttributesToFeatures(attName, getAlignmentPanel());
- }
-
- /**
* Sends command(s) to the structure viewer to create residue attributes for
* visible Jalview features
*/
*/
public abstract class StructureCommandsBase implements StructureCommandsI
{
- private static final String CMD_SEPARATOR = ";";
public static final String NAMESPACE_PREFIX = "jv_";
+ private static final String CMD_SEPARATOR = ";";
+
/**
* Returns something that separates concatenated commands
*
{
return null;
}
+
+ @Override
+ public StructureCommandI listResidueAttributes()
+ {
+ return null;
+ }
+
+ @Override
+ public StructureCommandI getResidueAttributes(String attName)
+ {
+ return null;
+ }
}
* @return
*/
StructureCommandI getSelectedResidues();
+
+ /**
+ * Returns a command to list the unique names of residue attributes, or null
+ * if no such command is supported
+ *
+ * @return
+ */
+ StructureCommandI listResidueAttributes();
+
+ /**
+ * Returns a command to list residues with an attribute of the given name,
+ * with attribute value, or null if no such command is supported
+ *
+ * @return
+ */
+ StructureCommandI getResidueAttributes(String attName);
}
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;
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;
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;
* @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;
}
return error;
}
- private AtomSpecModel getAtomSpec(AAStructureBindingModel.SuperposeData superposeData,
+ private AtomSpecModel getAtomSpec(
+ AAStructureBindingModel.SuperposeData superposeData,
BitSet matched)
{
AtomSpecModel model = new AtomSpecModel();
{
return;
}
-
+
/*
* build a map of {Residue3LetterCode, Color}
*/
*/
final JalviewStructureDisplayI theViewer = getViewer();
final long handle = msg == null ? 0 : theViewer.startProgressBar(msg);
-
+
SwingUtilities.invokeLater(new Runnable()
{
@Override
*/
final JalviewStructureDisplayI theViewer = getViewer();
final long handle = msg == null ? 0 : theViewer.startProgressBar(msg);
-
+
List<String> response = getReply ? new ArrayList<>() : null;
try
{
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()));
+ Cache.log.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);
}
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()
{
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;
+ }
}
}
@Test(groups = "Functional")
+ public void testListResidueAttributes()
+ {
+ assertEquals(testee.listResidueAttributes(),
+ new StructureCommand("list resattr"));
+ }
+
+ @Test(groups = "Functional")
+ public void testGetResidueAttributes()
+ {
+ assertEquals(testee.getResidueAttributes("binding site"),
+ new StructureCommand("list residues attr 'binding site'"));
+ }
+
+ @Test(groups = "Functional")
public void testStartNotifications()
{
List<StructureCommandI> cmds = testee.startNotifications("to here");
assertEquals(cmds.get(0), new StructureCommand("info notify stop models jalview"));
assertEquals(cmds.get(1), new StructureCommand("info notify stop selection jalview"));
}
+
+ @Test(groups = "Functional")
+ public void testListResidueAttributes()
+ {
+ assertEquals(testee.listResidueAttributes(),
+ new StructureCommand("info resattr"));
+ }
}
git://source.jalview.org / jalview.git / commitdiff