*/
package jalview.structures.models;
+import java.util.Locale;
+
+import java.awt.Color;
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.BitSet;
+import java.util.HashMap;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+
+import javax.swing.SwingUtilities;
+
+import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
+import jalview.api.FeatureRenderer;
import jalview.api.SequenceRenderer;
import jalview.api.StructureSelectionManagerProvider;
import jalview.api.structures.JalviewStructureDisplayI;
+import jalview.bin.Console;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.MappedFeatures;
import jalview.datamodel.PDBEntry;
+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.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 jalview.structure.StructureMappingcommandSet;
import jalview.structure.StructureSelectionManager;
import jalview.util.Comparison;
import jalview.util.MessageManager;
-import java.awt.Color;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.BitSet;
-import java.util.List;
-
/**
*
- * 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.
*
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 = "";
+
+ /**
+ * is the mapped sequence not protein ?
+ */
+ 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");
+
+ /*
+ * the Jalview panel through which the user interacts
+ * with the structure viewer
+ */
+ private JalviewStructureDisplayI viewer;
+
+ /*
+ * helper that generates command syntax
+ */
+ private StructureCommandsI commandGenerator;
private StructureSelectionManager ssm;
/*
+ * modelled chains, formatted as "pdbid:chainCode"
+ */
+ private List<String> chainNames;
+
+ /*
+ * lookup of pdb file name by key "pdbid:chainCode"
+ */
+ private Map<String, String> chainFile;
+
+ /*
* distinct PDB entries (pdb files) associated
* with sequences
*/
protected boolean colourBySequence = true;
+ /**
+ * true if all sequences appear to be nucleotide
+ */
private boolean nucleotide;
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;
- }
+ protected Thread externalViewerMonitor;
/**
* Constructor
{
this.ssm = ssm;
this.sequence = seqs;
+ chainNames = new ArrayList<>();
+ chainFile = new HashMap<>();
}
/**
PDBEntry[] pdbentry, SequenceI[][] sequenceIs,
DataSourceType protocol)
{
- this.ssm = ssm;
- this.sequence = sequenceIs;
+ this(ssm, sequenceIs);
this.nucleotide = Comparison.isNucleotide(sequenceIs);
this.pdbEntry = pdbentry;
this.protocol = protocol;
String chain = (chains != null && chains[pe] != null)
? chains[pe][se]
: null;
- SequenceI sq = asq.getDatasetSequence();
+ SequenceI sq = (asq.getDatasetSequence() == null) ? asq
+ : asq.getDatasetSequence();
if (sq.getAllPDBEntries() != null)
{
for (PDBEntry pdbentry : sq.getAllPDBEntries())
chains = newchains;
return chainmaps > 0;
}
+
public StructureSelectionManager getSsm()
{
return 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;
{ Integer.valueOf(pe).toString() }));
}
final String nullChain = "TheNullChain";
- List<SequenceI> s = new ArrayList<SequenceI>();
- List<String> c = new ArrayList<String>();
+ List<SequenceI> s = new ArrayList<>();
+ List<String> c = new ArrayList<>();
if (getChains() == null)
{
setChains(new String[getPdbCount()][]);
public synchronized PDBEntry[] addSequenceAndChain(PDBEntry[] pdbe,
SequenceI[][] seq, String[][] chns)
{
- List<PDBEntry> v = new ArrayList<PDBEntry>();
- List<int[]> rtn = new ArrayList<int[]>();
+ List<PDBEntry> v = new ArrayList<>();
+ List<int[]> rtn = new ArrayList<>();
for (int i = 0; i < getPdbCount(); i++)
{
v.add(getPdbEntry(i));
}
}
}
+
@Override
public abstract void highlightAtoms(List<AtomSpec> atoms);
* @return
*/
protected int findSuperposableResidues(AlignmentI alignment,
- BitSet matched, SuperposeData[] structures)
+ BitSet matched,
+ AAStructureBindingModel.SuperposeData[] structures)
{
int refStructure = -1;
String[] files = getStructureFiles();
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
* for the same structure)
*/
s = seqCountForPdbFile;
- break;
+ break; // fixme break out of two loops here!
}
}
}
}
/**
- * Returns a list of chains mapped in this viewer.
+ * Returns a list of chains mapped in this viewer, formatted as
+ * "pdbid:chainCode"
*
* @return
*/
- public abstract List<String> getChainNames();
+ public List<String> getChainNames()
+ {
+ return chainNames;
+ }
/**
* Returns the Jalview panel hosting the structure viewer (if any)
*/
public JalviewStructureDisplayI getViewer()
{
- return null;
+ return viewer;
}
- public abstract void setJalviewColourScheme(ColourSchemeI cs);
+ public void setViewer(JalviewStructureDisplayI v)
+ {
+ viewer = v;
+ }
/**
* 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.
- *
- * @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
+ * an error or warning message for the alignment command(s).
+ *
+ * @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);
+
+ boolean isNucleotide = structures[refStructure].isRna;
+ /*
+ * 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,isNucleotide);
+ List<String> replies = executeCommands(commands, true, null);
+ for (String reply : replies)
+ {
+ // return this error (Chimera only) to the user
+ if (reply.toLowerCase(Locale.ROOT).contains("unequal numbers of atoms"))
+ {
+ error += "; " + reply;
+ }
+ }
+ }
+ }
+ }
+
+ return error;
+ }
- public abstract void setBackgroundColour(Color col);
+ 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);
+ }
- protected abstract StructureMappingcommandSet[] getColourBySequenceCommands(
- String[] files, SequenceRenderer sr, AlignmentViewPanel avp);
+ return model;
+ }
/**
* returns the current sequenceRenderer that should be used to colour the
public abstract SequenceRenderer getSequenceRenderer(
AlignmentViewPanel alignment);
- protected abstract void colourBySequence(
- StructureMappingcommandSet[] colourBySequenceCommands);
+ /**
+ * Sends a command to the structure viewer to colour each chain with a
+ * distinct colour (to the extent supported by the viewer)
+ */
+ public void colourByChain()
+ {
+ colourBySequence = false;
- public abstract void colourByChain();
+ // TODO: JAL-628 colour chains distinctly across all visible models
- public abstract void colourByCharge();
+ executeCommand(false, COLOURING_STRUCTURES,
+ commandGenerator.colourByChain());
+ }
/**
- * colour any structures associated with sequences in the given alignment
- * using the getFeatureRenderer() and getSequenceRenderer() renderers but only
- * if colourBySequence is enabled.
+ * Sends a command to the structure viewer to colour each chain with a
+ * distinct colour (to the extent supported by the viewer)
*/
- public void colourBySequence(AlignmentViewPanel alignmentv)
+ public void colourByCharge()
+ {
+ colourBySequence = false;
+
+ executeCommands(commandGenerator.colourByCharge(), false,
+ COLOURING_STRUCTURES);
+ }
+
+ /**
+ * Sends a command to the structure to apply a colour scheme (defined in
+ * Jalview but not necessarily applied to the alignment), which defines a
+ * colour per residue letter. More complex schemes (e.g. that depend on
+ * consensus) cannot be used here and are ignored.
+ *
+ * @param cs
+ */
+ public void colourByJalviewColourScheme(ColourSchemeI cs)
{
- if (!colourBySequence || !isLoadingFinished())
+ colourBySequence = false;
+
+ if (cs == null || !cs.isSimple())
{
return;
}
- if (getSsm() == null)
+
+ /*
+ * build a map of {Residue3LetterCode, Color}
+ */
+ Map<String, Color> colours = new HashMap<>();
+ List<String> residues = ResidueProperties.getResidues(isNucleotide(),
+ false);
+ for (String resName : residues)
+ {
+ char res = resName.length() == 3
+ ? ResidueProperties.getSingleCharacterCode(resName)
+ : resName.charAt(0);
+ Color colour = cs.findColour(res, 0, null, null, 0f);
+ colours.put(resName, colour);
+ }
+
+ /*
+ * pass to the command constructor, and send the command
+ */
+ List<StructureCommandI> cmd = commandGenerator
+ .colourByResidues(colours);
+ executeCommands(cmd, false, COLOURING_STRUCTURES);
+ }
+
+ public void setBackgroundColour(Color col)
+ {
+ StructureCommandI cmd = commandGenerator.setBackgroundColour(col);
+ executeCommand(false, null, cmd);
+ }
+
+ /**
+ * 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)
+ {
+ 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)
+ {
+ /*
+ * execute and wait for reply
+ */
+ List<String> response = new ArrayList<>();
+ try
+ {
+ for (StructureCommandI cmd : cmds)
+ {
+ List<String> replies = executeCommand(cmd, true);
+ if (replies != null)
+ {
+ response.addAll(replies);
+ }
+ }
+ return response;
+ } finally
+ {
+ if (msg != null)
+ {
+ theViewer.stopProgressBar(null, handle);
+ }
+ }
+ }
+
+ /*
+ * fire and forget
+ */
+ String threadName = msg == null ? "StructureCommand" : msg;
+ new Thread(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ try
+ {
+ for (StructureCommandI cmd : cmds)
+ {
+ executeCommand(cmd, false);
+ }
+ } finally
+ {
+ if (msg != null)
+ {
+ SwingUtilities.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ theViewer.stopProgressBar(null, handle);
+ }
+ });
+ }
+ }
+ }
+ }, threadName).start();
+ return null;
+ }
+
+ /**
+ * Colours any structures associated with sequences in the given alignment as
+ * coloured in the alignment view, provided colourBySequence is enabled
+ */
+ public void colourBySequence(AlignmentViewPanel alignmentv)
+ {
+ if (!colourBySequence || !isLoadingFinished() || getSsm() == null)
{
return;
}
- String[] files = getStructureFiles();
+ Map<Object, AtomSpecModel> colourMap = buildColoursMap(ssm, sequence,
+ alignmentv);
+
+ List<StructureCommandI> colourBySequenceCommands = commandGenerator
+ .colourBySequence(colourMap);
+ executeCommands(colourBySequenceCommands, false, COLOURING_STRUCTURES);
+ }
+
+ /**
+ * Centre the display in the structure viewer
+ */
+ public void focusView()
+ {
+ executeCommand(false, null, commandGenerator.focusView());
+ }
- SequenceRenderer sr = getSequenceRenderer(alignmentv);
+ /**
+ * Generates and executes a command to show only specified chains in the
+ * structure viewer. The list of chains to show should contain entries
+ * formatted as "pdbid:chaincode".
+ *
+ * @param toShow
+ */
+ public void showChains(List<String> toShow)
+ {
+ // todo or reformat toShow list entries as modelNo:pdbId:chainCode ?
- StructureMappingcommandSet[] colourBySequenceCommands = getColourBySequenceCommands(
- files, sr, alignmentv);
- colourBySequence(colourBySequenceCommands);
+ /*
+ * Reformat the pdbid:chainCode values as modelNo:chainCode
+ * since this is what is needed to construct the viewer command
+ * todo: find a less messy way to do this
+ */
+ List<String> showThese = new ArrayList<>();
+ for (String chainId : toShow)
+ {
+ String[] tokens = chainId.split("\\:");
+ if (tokens.length == 2)
+ {
+ String pdbFile = getFileForChain(chainId);
+ String model = getModelIdForFile(pdbFile);
+ showThese.add(model + ":" + tokens[1]);
+ }
+ }
+ executeCommands(commandGenerator.showChains(showThese), false, null);
}
+ /**
+ * 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 String getModelIdForFile(String chainId);
+
public boolean hasFileLoadingError()
{
return fileLoadingError != null && fileLoadingError.length() > 0;
}
- public abstract jalview.api.FeatureRenderer getFeatureRenderer(
- AlignmentViewPanel alignment);
+ /**
+ * Returns the FeatureRenderer for the given alignment view
+ *
+ * @param avp
+ * @return
+ */
+ public FeatureRenderer getFeatureRenderer(AlignmentViewPanel avp)
+ {
+ AlignmentViewPanel ap = (avp == null) ? getViewer().getAlignmentPanel()
+ : avp;
+ if (ap == null)
+ {
+ return null;
+ }
+ return ap.getFeatureRenderer();
+ }
+
+ protected void setStructureCommands(StructureCommandsI cmd)
+ {
+ commandGenerator = cmd;
+ }
+
+ /**
+ * Records association of one chain id (formatted as "pdbid:chainCode") with
+ * the corresponding PDB file name
+ *
+ * @param chainId
+ * @param fileName
+ */
+ public void addChainFile(String chainId, String fileName)
+ {
+ chainFile.put(chainId, fileName);
+ }
+
+ /**
+ * Returns the PDB filename for the given chain id (formatted as
+ * "pdbid:chainCode"), or null if not found
+ *
+ * @param chainId
+ * @return
+ */
+ protected String getFileForChain(String chainId)
+ {
+ 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();
+
+ /**
+ * 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 sequence
+ * @param viewPanel
+ * @return
+ */
+ protected Map<Object, AtomSpecModel> buildColoursMap(
+ StructureSelectionManager ssm, SequenceI[][] sequence,
+ AlignmentViewPanel viewPanel)
+ {
+ String[] files = getStructureFiles();
+ SequenceRenderer sr = getSequenceRenderer(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++)
+ {
+ 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);
+ }
+
+ /**
+ * Returns the file extension (including '.' separator) to use for a saved
+ * viewer session file. Default is to return null (not supported), override as
+ * required.
+ *
+ * @return
+ */
+ public String getSessionFileExtension()
+ {
+ return null;
+ }
+
+ /**
+ * If supported, saves the state of the structure viewer to a temporary file
+ * and returns the file. Returns null and logs an error on any failure.
+ *
+ * @return
+ */
+ public File saveSession()
+ {
+ String prefix = getViewerType().toString();
+ String suffix = getSessionFileExtension();
+ File f = null;
+ try
+ {
+ f = File.createTempFile(prefix, suffix);
+ saveSession(f);
+ } catch (IOException e)
+ {
+ Console.error(String.format("Error saving %s session: %s", prefix,
+ e.toString()));
+ }
+
+ return f;
+ }
+
+ /**
+ * Saves the structure viewer session to the given file
+ *
+ * @param f
+ */
+ protected void saveSession(File f)
+ {
+ StructureCommandI cmd = commandGenerator.saveSession(f.getPath());
+ if (cmd != null)
+ {
+ executeCommand(cmd, false);
+ }
+ }
+
+ /**
+ * Returns true if the viewer is an external structure viewer for which the
+ * process is still alive, else false (for Jmol, or an external viewer which
+ * the user has independently closed)
+ *
+ * @return
+ */
+ public boolean isViewerRunning()
+ {
+ return false;
+ }
+
+ /**
+ * Closes Jalview's structure viewer panel and releases associated resources.
+ * If it is managing an external viewer program, and {@code forceClose} is
+ * true, also asks that program to close.
+ *
+ * @param forceClose
+ */
+ public void closeViewer(boolean forceClose)
+ {
+ getSsm().removeStructureViewerListener(this, this.getStructureFiles());
+ releaseUIResources();
+
+ /*
+ * end the thread that closes this panel if the external viewer closes
+ */
+ if (externalViewerMonitor != null)
+ {
+ externalViewerMonitor.interrupt();
+ externalViewerMonitor = null;
+ }
+
+ stopListening();
+
+ if (forceClose)
+ {
+ StructureCommandI cmd = getCommandGenerator().closeViewer();
+ if (cmd != null)
+ {
+ executeCommand(cmd, false);
+ }
+ }
+ }
+
+ /**
+ * Returns the URL of a help page for the structure viewer, or null if none is
+ * known
+ *
+ * @return
+ */
+ public String getHelpURL()
+ {
+ return null;
+ }
+
+ /**
+ * <pre>
+ * Helper method to build a map of
+ * { featureType, { feature value, AtomSpecModel } }
+ * </pre>
+ *
+ * @param viewPanel
+ * @return
+ */
+ protected Map<String, Map<Object, AtomSpecModel>> buildFeaturesMap(
+ AlignmentViewPanel viewPanel)
+ {
+ Map<String, Map<Object, AtomSpecModel>> theMap = new LinkedHashMap<>();
+ String[] files = getStructureFiles();
+ if (files == null)
+ {
+ return theMap;
+ }
+
+ FeatureRenderer fr = viewPanel.getFeatureRenderer();
+ if (fr == null)
+ {
+ 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
+ */
+ boolean showLinkedFeatures = viewport.isShowComplementFeatures();
+ List<String> complementFeatures = new ArrayList<>();
+ FeatureRenderer complementRenderer = null;
+ if (showLinkedFeatures)
+ {
+ AlignViewportI comp = fr.getViewport().getCodingComplement();
+ if (comp != null)
+ {
+ complementRenderer = Desktop.getAlignFrameFor(comp)
+ .getFeatureRenderer();
+ complementFeatures = complementRenderer.getDisplayedFeatureTypes();
+ }
+ }
+ if (visibleFeatures.isEmpty() && complementFeatures.isEmpty())
+ {
+ return theMap;
+ }
+
+ AlignmentI alignment = viewPanel.getAlignment();
+ SequenceI[][] seqs = getSequence();
+
+ for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
+ {
+ 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++)
+ {
+ final SequenceI seq = seqs[pdbfnum][seqNo];
+ int sp = alignment.findIndex(seq);
+ StructureMapping structureMapping = mapping[m];
+ if (structureMapping.getSequence() == seq && sp > -1)
+ {
+ /*
+ * found a sequence with a mapping to a structure;
+ * now scan its features
+ */
+ if (!visibleFeatures.isEmpty())
+ {
+ scanSequenceFeatures(visibleFeatures, structureMapping, seq,
+ theMap, modelId);
+ }
+ if (showLinkedFeatures)
+ {
+ scanComplementFeatures(complementRenderer, structureMapping,
+ seq, theMap, modelId);
+ }
+ }
+ }
+ }
+ }
+ return theMap;
+ }
+
+ /**
+ * Ask the structure viewer to open a session file. Returns true if
+ * successful, else false (or not supported).
+ *
+ * @param filepath
+ * @return
+ */
+ public boolean openSession(String filepath)
+ {
+ StructureCommandI cmd = getCommandGenerator().openSession(filepath);
+ if (cmd == null)
+ {
+ return false;
+ }
+ executeCommand(cmd, true);
+ // todo: test for failure - how?
+ return true;
+ }
+
+ /**
+ * 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
+ * @param seq
+ * @param theMap
+ * @param modelNumber
+ */
+ protected static void scanComplementFeatures(
+ FeatureRenderer complementRenderer,
+ StructureMapping structureMapping, SequenceI seq,
+ Map<String, Map<Object, AtomSpecModel>> theMap,
+ String modelNumber)
+ {
+ /*
+ * for each sequence residue mapped to a structure position...
+ */
+ for (int seqPos : structureMapping.getMapping().keySet())
+ {
+ /*
+ * find visible complementary features at mapped position(s)
+ */
+ MappedFeatures mf = complementRenderer
+ .findComplementFeaturesAtResidue(seq, seqPos);
+ if (mf != null)
+ {
+ for (SequenceFeature sf : mf.features)
+ {
+ String type = sf.getType();
+
+ /*
+ * Don't copy features which originated from Chimera
+ */
+ if (JalviewChimeraBinding.CHIMERA_FEATURE_GROUP
+ .equals(sf.getFeatureGroup()))
+ {
+ 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();
+ if (value == null || value.length() == 0)
+ {
+ value = type;
+ }
+ float score = sf.getScore();
+ if (score != 0f && !Float.isNaN(score))
+ {
+ value = Float.toString(score);
+ }
+ Map<Object, AtomSpecModel> featureValues = theMap.get(type);
+ if (featureValues == null)
+ {
+ featureValues = new HashMap<>();
+ theMap.put(type, featureValues);
+ }
+ for (int[] range : mappedRanges)
+ {
+ addAtomSpecRange(featureValues, value, modelNumber, range[0],
+ range[1], structureMapping.getChain());
+ }
+ }
+ }
+ }
+ }
+ }
+
+ /**
+ * Inspect features on the sequence; for each feature that is visible,
+ * determine its mapped ranges in the structure (if any) according to the
+ * given mapping, and add them to the map.
+ *
+ * @param visibleFeatures
+ * @param mapping
+ * @param seq
+ * @param theMap
+ * @param modelId
+ */
+ protected static void scanSequenceFeatures(List<String> visibleFeatures,
+ StructureMapping mapping, SequenceI seq,
+ Map<String, Map<Object, AtomSpecModel>> theMap, String modelId)
+ {
+ List<SequenceFeature> sfs = seq.getFeatures().getPositionalFeatures(
+ visibleFeatures.toArray(new String[visibleFeatures.size()]));
+ for (SequenceFeature sf : sfs)
+ {
+ String type = sf.getType();
+
+ /*
+ * Don't copy features which originated from Chimera
+ */
+ if (JalviewChimeraBinding.CHIMERA_FEATURE_GROUP
+ .equals(sf.getFeatureGroup()))
+ {
+ continue;
+ }
+
+ List<int[]> mappedRanges = mapping.getPDBResNumRanges(sf.getBegin(),
+ sf.getEnd());
+
+ if (!mappedRanges.isEmpty())
+ {
+ String value = sf.getDescription();
+ if (value == null || value.length() == 0)
+ {
+ value = type;
+ }
+ float score = sf.getScore();
+ if (score != 0f && !Float.isNaN(score))
+ {
+ value = Float.toString(score);
+ }
+ Map<Object, AtomSpecModel> featureValues = theMap.get(type);
+ if (featureValues == null)
+ {
+ featureValues = new HashMap<>();
+ theMap.put(type, featureValues);
+ }
+ for (int[] range : mappedRanges)
+ {
+ addAtomSpecRange(featureValues, value, modelId, range[0],
+ range[1], mapping.getChain());
+ }
+ }
+ }
+ }
+
+ /**
+ * Returns the number of structure files in the structure viewer and mapped to
+ * Jalview. This may be zero if the files are still in the process of loading
+ * in the viewer.
+ *
+ * @return
+ */
+ public int getMappedStructureCount()
+ {
+ String[] files = getStructureFiles();
+ return files == null ? 0 : files.length;
+ }
+
+ /**
+ * Starts a thread that waits for the external viewer program process to
+ * finish, so that we can then close the associated resources. This avoids
+ * leaving orphaned viewer panels in Jalview if the user closes the external
+ * viewer.
+ *
+ * @param p
+ */
+ protected void startExternalViewerMonitor(Process p)
+ {
+ externalViewerMonitor = new Thread(new Runnable()
+ {
+
+ @Override
+ public void run()
+ {
+ try
+ {
+ p.waitFor();
+ JalviewStructureDisplayI display = getViewer();
+ if (display != null)
+ {
+ display.closeViewer(false);
+ }
+ } catch (InterruptedException e)
+ {
+ // exit thread if Chimera Viewer is closed in Jalview
+ }
+ }
+ });
+ 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