*/
package jalview.structures.models;
+import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureRenderer;
import jalview.api.SequenceRenderer;
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
+import jalview.gui.StructureViewer.ViewerType;
import jalview.io.DataSourceType;
+import jalview.io.StructureFile;
+import jalview.renderer.seqfeatures.FeatureColourFinder;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ResidueProperties;
import jalview.structure.AtomSpec;
+import jalview.structure.AtomSpecModel;
+import jalview.structure.StructureCommandI;
import jalview.structure.StructureCommandsI;
import jalview.structure.StructureListener;
import jalview.structure.StructureMapping;
import java.util.Arrays;
import java.util.BitSet;
import java.util.HashMap;
+import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
extends SequenceStructureBindingModel
implements StructureListener, StructureSelectionManagerProvider
{
+ /**
+ * Data bean class to simplify parameterisation in superposeStructures
+ */
+ 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
+ *
+ * @param width
+ * width of alignment (number of columns that may potentially
+ * participate in superposition)
+ * @param model
+ * structure viewer model number
+ */
+ public SuperposeData(int width, String model)
+ {
+ pdbResNo = new int[width];
+ modelId = model;
+ }
+ }
+
+ private static final int MIN_POS_TO_SUPERPOSE = 4;
+
private static final String COLOURING_STRUCTURES = MessageManager
.getString("status.colouring_structures");
private boolean finishedInit = false;
/**
- * current set of model filenames loaded in the Jmol instance
+ * current set of model filenames loaded in the viewer
*/
protected String[] modelFileNames = null;
public String fileLoadingError;
/**
- * Data bean class to simplify parameterisation in superposeStructures
- */
- protected class SuperposeData
- {
- /**
- * Constructor with alignment width argument
- *
- * @param width
- */
- public SuperposeData(int width)
- {
- pdbResNo = new int[width];
- }
-
- public String filename;
-
- public String pdbId;
-
- public String chain = "";
-
- public boolean isRna;
-
- /*
- * The pdb residue number (if any) mapped to each column of the alignment
- */
- public int[] pdbResNo;
- }
-
- /**
* Constructor
*
* @param ssm
*/
protected void releaseUIResources()
{
+ }
+ @Override
+ public void releaseReferences(Object svl)
+ {
}
public boolean isColourBySequence()
return colourBySequence;
}
+ /**
+ * Called when the binding thinks the UI needs to be refreshed after a
+ * structure viewer state change. This could be because structures were
+ * loaded, or because an error has occurred. Default does nothing, override as
+ * required.
+ */
+ public void refreshGUI()
+ {
+ }
+
+ /**
+ * Instruct the Jalview binding to update the pdbentries vector if necessary
+ * prior to matching the jmol view's contents to the list of structure files
+ * Jalview knows about. By default does nothing, override as required.
+ */
+ public void refreshPdbEntries()
+ {
+ }
+
public void setColourBySequence(boolean colourBySequence)
{
this.colourBySequence = colourBySequence;
* @return
*/
protected int findSuperposableResidues(AlignmentI alignment,
- BitSet matched, SuperposeData[] structures)
+ BitSet matched, AAStructureBindingModel.SuperposeData[] structures)
{
int refStructure = -1;
String[] files = getStructureFiles();
* for the same structure)
*/
s = seqCountForPdbFile;
- break;
+ break; // fixme break out of two loops here!
}
}
}
/**
* Constructs and sends a command to align structures against a reference
* structure, based on one or more sequence alignments. May optionally return
- * an error or warning message for the alignment command.
+ * an error or warning message for the alignment command(s).
*
- * @param alignments
- * an array of alignments to process
- * @param structureIndices
- * an array of corresponding reference structures (index into pdb
- * file array); if a negative value is passed, the first PDB file
- * mapped to an alignment sequence is used as the reference for
- * superposition
- * @param hiddenCols
- * an array of corresponding hidden columns for each alignment
+ * @param alignWith
+ * an array of one or more alignment views to process
* @return
*/
- public abstract String superposeStructures(AlignmentI[] alignments,
- int[] structureIndices, HiddenColumns[] hiddenCols);
+ public String superposeStructures(List<AlignmentViewPanel> alignWith)
+ {
+ String error = "";
+ String[] files = getStructureFiles();
+
+ if (!waitForFileLoad(files))
+ {
+ return null;
+ }
+ refreshPdbEntries();
+
+ for (AlignmentViewPanel view : alignWith)
+ {
+ 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++)
+ {
+ 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++)
+ {
+ structures[f] = new AAStructureBindingModel.SuperposeData(width,
+ getModelIdForFile(files[f]));
+ }
+
+ /*
+ * Calculate the superposable alignment columns ('matched'), and the
+ * corresponding structure residue positions (structures.pdbResNo)
+ */
+ 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);
+ error += view.getViewName() + ": " + msg + "; ";
+ continue;
+ }
+
+ /*
+ * get a model of the superposable residues in the reference structure
+ */
+ AtomSpecModel refAtoms = getAtomSpec(structures[refStructure],
+ matched);
+
+ /*
+ * Show all as backbone before doing superposition(s)
+ * (residues used for matching will be shown as ribbon)
+ */
+ // todo better way to ensure synchronous than setting getReply true!!
+ executeCommands(commandGenerator.showBackbone(), true, null);
+
+ /*
+ * superpose each (other) structure to the reference in turn
+ */
+ for (int i = 0; i < structures.length; i++)
+ {
+ if (i != refStructure)
+ {
+ AtomSpecModel atomSpec = getAtomSpec(structures[i], matched);
+ List<StructureCommandI> commands = commandGenerator
+ .superposeStructures(refAtoms, atomSpec);
+ 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"))
+ {
+ error += "; " + reply;
+ }
+ }
+ }
+ }
+ }
+
+ return error;
+ }
+
+ private AtomSpecModel getAtomSpec(AAStructureBindingModel.SuperposeData superposeData,
+ BitSet matched)
+ {
+ AtomSpecModel model = new AtomSpecModel();
+ int nextColumnMatch = matched.nextSetBit(0);
+ while (nextColumnMatch != -1)
+ {
+ int pdbResNum = superposeData.pdbResNo[nextColumnMatch];
+ model.addRange(superposeData.modelId, pdbResNum, pdbResNum,
+ superposeData.chain);
+ nextColumnMatch = matched.nextSetBit(nextColumnMatch + 1);
+ }
+
+ return model;
+ }
/**
* returns the current sequenceRenderer that should be used to colour the
{
colourBySequence = false;
- executeCommand(commandGenerator.colourByCharge(), false,
+ executeCommands(commandGenerator.colourByCharge(), false,
COLOURING_STRUCTURES);
}
/*
* pass to the command constructor, and send the command
*/
- String cmd = commandGenerator.colourByResidues(colours);
- executeCommand(cmd, false, COLOURING_STRUCTURES);
+ List<StructureCommandI> cmd = commandGenerator
+ .colourByResidues(colours);
+ executeCommands(cmd, false, COLOURING_STRUCTURES);
}
public void setBackgroundColour(Color col)
{
- String cmd = commandGenerator.setBackgroundColour(col);
+ StructureCommandI cmd = commandGenerator.setBackgroundColour(col);
executeCommand(cmd, false, null);
}
* @param msg
* @return
*/
- private List<String> executeCommand(String cmd, boolean getReply,
- String msg)
+ private List<String> executeCommand(StructureCommandI cmd,
+ boolean getReply, String msg)
{
if (getReply)
{
- return executeSynchronous(cmd, msg, getReply);
+ /*
+ * synchronous (same thread) execution so reply can be returned
+ */
+ final JalviewStructureDisplayI theViewer = getViewer();
+ final long handle = msg == null ? 0 : theViewer.startProgressBar(msg);
+ try
+ {
+ return executeCommand(cmd, getReply);
+ } finally
+ {
+ if (msg != null)
+ {
+ theViewer.stopProgressBar(null, handle);
+ }
+ }
}
else
{
- executeAsynchronous(cmd, msg);
+ /*
+ * 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()
+ {
+ try
+ {
+ executeCommand(cmd, false);
+ } finally
+ {
+ if (msg != null)
+ {
+ theViewer.stopProgressBar(null, handle);
+ }
+ }
+ }
+ });
return null;
}
}
/**
- * Sends the command in the current thread. If a message is supplied, this is
- * shown before the thread is started, and removed when it completes. May
- * return a reply to the command if requested.
+ * Execute one structure viewer command. If {@code getReply} is true, may
+ * optionally return one or more reply messages, else returns null.
*
* @param cmd
- * @param msg
* @param getReply
- * @return
*/
- private List<String> executeSynchronous(String cmd, String msg, boolean getReply)
+ protected abstract List<String> executeCommand(StructureCommandI cmd,
+ boolean getReply);
+
+ /**
+ * A helper method that converts list of commands to a vararg array
+ *
+ * @param commands
+ * @param getReply
+ * @param msg
+ */
+ private List<String> executeCommands(List<StructureCommandI> commands,
+ boolean getReply, String msg)
{
- final JalviewStructureDisplayI theViewer = getViewer();
- final long handle = msg == null ? 0 : theViewer.startProgressBar(msg);
- try
- {
- return executeCommand(cmd, getReply);
- } finally
- {
- if (msg != null)
- {
- theViewer.stopProgressBar(null, handle);
- }
- }
+ return executeCommands(getReply, msg,
+ commands.toArray(new StructureCommandI[commands.size()]));
}
/**
- * Sends the command in a separate thread. If a message is supplied, this is
- * shown before the thread is started, and removed when it completes. No value
- * is returned.
+ * 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 cmd
+ * @param getReply
* @param msg
+ * @param commands
+ * @return
*/
- private void executeAsynchronous(String cmd, String msg)
+ protected List<String> executeCommands(boolean getReply, String msg,
+ StructureCommandI[] commands)
{
+ // todo: tidy this up
+
+ /*
+ * show progress message if specified
+ */
final JalviewStructureDisplayI theViewer = getViewer();
final long handle = msg == null ? 0 : theViewer.startProgressBar(msg);
- SwingUtilities.invokeLater(new Runnable()
+ List<String> response = getReply ? new ArrayList<>() : null;
+ try
{
- @Override
- public void run()
+ for (StructureCommandI cmd : commands)
{
- try
+ List<String> replies = executeCommand(cmd, getReply, null);
+ if (getReply && replies != null)
{
- executeCommand(cmd, false);
- } finally
- {
- if (msg != null)
- {
- theViewer.stopProgressBar(null, handle);
- }
+ response.addAll(replies);
}
}
- });
- }
-
- protected abstract List<String> executeCommand(String command,
- boolean getReply);
-
- protected List<String> executeCommands(boolean getReply,
- String... commands)
- {
- List<String> response = null;
- for (String cmd : commands)
+ return response;
+ } finally
{
- response = executeCommand(cmd, getReply);
+ if (msg != null)
+ {
+ theViewer.stopProgressBar(null, handle);
+ }
}
- return response;
}
/**
String[] files = getStructureFiles();
SequenceRenderer sr = getSequenceRenderer(alignmentv);
+ Map<Object, AtomSpecModel> colourMap = buildColoursMap(ssm, files,
+ sequence, sr, alignmentv);
- String[] colourBySequenceCommands = commandGenerator
- .colourBySequence(getSsm(), files, getSequence(), sr,
- alignmentv);
- executeCommands(false, colourBySequenceCommands);
+ List<StructureCommandI> colourBySequenceCommands = commandGenerator
+ .colourBySequence(colourMap);
+ executeCommands(colourBySequenceCommands, false, null);
}
/**
*/
public void focusView()
{
- executeCommand(commandGenerator.focusView(), false);
+ executeCommand(commandGenerator.focusView(), false, null);
}
/**
if (tokens.length == 2)
{
String pdbFile = getFileForChain(chainId);
- int modelNo = getModelNoForFile(pdbFile);
- String model = modelNo == -1 ? "" : String.valueOf(modelNo);
+ String model = getModelIdForFile(pdbFile);
showThese.add(model + ":" + tokens[1]);
}
}
- executeCommand(commandGenerator.showChains(showThese), false);
+ executeCommands(commandGenerator.showChains(showThese), false, null);
}
/**
- * Answers the structure viewer's model number given a PDB file name. Returns
- * -1 if model number is not found.
+ * Answers the structure viewer's model id given a PDB file name. Returns an
+ * empty string if model id is not found.
*
* @param chainId
* @return
*/
- protected abstract int getModelNoForFile(String chainId);
+ protected abstract String getModelIdForFile(String chainId);
public boolean hasFileLoadingError()
{
{
return chainFile.get(chainId);
}
+
+ @Override
+ public void updateColours(Object source)
+ {
+ AlignmentViewPanel ap = (AlignmentViewPanel) source;
+ // ignore events from panels not used to colour this view
+ if (!getViewer().isUsedForColourBy(ap))
+ {
+ return;
+ }
+ if (!isLoadingFromArchive())
+ {
+ colourBySequence(ap);
+ }
+ }
+
+ public StructureCommandsI getCommandGenerator()
+ {
+ return commandGenerator;
+ }
+
+ 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
+ * {@code AtomSpecModel}, where the atomspec model holds
+ *
+ * <pre>
+ * Model ids
+ * Chains
+ * Residue positions
+ * </pre>
+ *
+ * Ordering is by order of addition (for colours), natural ordering (for
+ * models and chains)
+ *
+ * @param ssm
+ * @param files
+ * @param sequence
+ * @param sr
+ * @param viewPanel
+ * @return
+ */
+ protected Map<Object, AtomSpecModel> buildColoursMap(
+ StructureSelectionManager ssm, String[] files,
+ SequenceI[][] sequence, SequenceRenderer sr, AlignmentViewPanel viewPanel)
+ {
+ FeatureRenderer fr = viewPanel.getFeatureRenderer();
+ FeatureColourFinder finder = new FeatureColourFinder(fr);
+ AlignViewportI viewport = viewPanel.getAlignViewport();
+ HiddenColumns cs = viewport.getAlignment().getHiddenColumns();
+ AlignmentI al = viewport.getAlignment();
+ Map<Object, AtomSpecModel> colourMap = new LinkedHashMap<>();
+ Color lastColour = null;
+
+ for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
+ {
+ // todo indirect this resolution / allow override
+ 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++)
+ {
+ for (int sp, m = 0; m < mapping.length; m++)
+ {
+ final SequenceI seq = sequence[pdbfnum][s];
+ if (mapping[m].getSequence() == seq
+ && (sp = al.findIndex(seq)) > -1)
+ {
+ SequenceI asp = al.getSequenceAt(sp);
+ for (int r = 0; r < asp.getLength(); r++)
+ {
+ // no mapping to gaps in sequence
+ if (Comparison.isGap(asp.getCharAt(r)))
+ {
+ 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
+ */
+ if (!cs.isVisible(r))
+ {
+ 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
+ * gap in the mapped residue sequence
+ */
+ final boolean newColour = !colour.equals(lastColour);
+ final boolean nonContig = lastPos + 1 != pos;
+ final boolean newChain = !chain.equals(lastChain);
+ if (newColour || nonContig || newChain)
+ {
+ if (startPos != -1)
+ {
+ addAtomSpecRange(colourMap, lastColour, modelId,
+ startPos, lastPos, lastChain);
+ }
+ startPos = pos;
+ }
+ lastColour = colour;
+ lastPos = pos;
+ lastChain = chain;
+ }
+ // final colour range
+ if (lastColour != null)
+ {
+ addAtomSpecRange(colourMap, lastColour, modelId, startPos,
+ lastPos, lastChain);
+ }
+ // break;
+ }
+ }
+ }
+ }
+ return colourMap;
+ }
+
+ /**
+ * todo better refactoring (map lookup or similar to get viewer structure id)
+ *
+ * @param pdbfnum
+ * @param file
+ * @return
+ */
+ protected String getModelId(int pdbfnum, String file)
+ {
+ return String.valueOf(pdbfnum);
+ }
+
+ /**
+ * Saves chains, formatted as "pdbId:chainCode", and lookups from this to the
+ * full PDB file path
+ *
+ * @param pdb
+ * @param file
+ */
+ public void stashFoundChains(StructureFile pdb, String file)
+ {
+ for (int i = 0; i < pdb.getChains().size(); i++)
+ {
+ String chid = pdb.getId() + ":" + pdb.getChains().elementAt(i).id;
+ addChainFile(chid, file);
+ getChainNames().add(chid);
+ }
+ }
+
+ /**
+ * 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'
+ * command</li>
+ * </ul>
+ *
+ * @param map
+ * @param value
+ * @param model
+ * @param startPos
+ * @param endPos
+ * @param chain
+ */
+ public static final void addAtomSpecRange(Map<Object, AtomSpecModel> map,
+ Object value,
+ String model, int startPos, int endPos, String chain)
+ {
+ /*
+ * Get/initialize map of data for the colour
+ */
+ AtomSpecModel atomSpec = map.get(value);
+ if (atomSpec == null)
+ {
+ atomSpec = new AtomSpecModel();
+ map.put(value, atomSpec);
+ }
+
+ atomSpec.addRange(model, startPos, endPos, chain);
+ }
}