import java.util.ArrayList;
import java.util.Arrays;
import java.util.BitSet;
+import java.util.Collections;
import java.util.HashMap;
+import java.util.Iterator;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
import jalview.bin.Cache;
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.Desktop;
import jalview.gui.StructureViewer.ViewerType;
import jalview.io.DataSourceType;
import jalview.io.StructureFile;
private boolean finishedInit = false;
- /**
- * current set of model filenames loaded in the viewer
+ /*
+ * current set of model filenames loaded in the Jmol instance
+ * array index 0, 1, 2... corresponds to Jmol model numbers 1, 2, 3...
*/
protected String[] modelFileNames = null;
public String fileLoadingError;
+ private boolean showAlignmentOnly;
+
+ /*
+ * a list of chains "pdbid:chainid" to hide in the viewer
+ */
+ // TODO make private once deprecated JalviewJmolBinding.centerViewer removed
+ protected List<String> chainsToHide;
+
+ private boolean hideHiddenRegions;
+
/**
* Constructor
*
{
this.ssm = ssm;
this.sequence = seqs;
+ chainsToHide = new ArrayList<>();
chainNames = new ArrayList<>();
chainFile = new HashMap<>();
}
this.nucleotide = Comparison.isNucleotide(sequenceIs);
this.pdbEntry = pdbentry;
this.protocol = protocol;
+ chainsToHide = new ArrayList<>();
+
resolveChains();
}
/**
* 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
+ * prior to matching the viewer's contents to the list of structure files
* Jalview knows about. By default does nothing, override as required.
*/
public void refreshPdbEntries()
AlignmentViewPanel alignment);
/**
+ * Recolours mapped residues in the structure viewer to match colours in the
+ * given alignment panel, provided colourBySequence is selected. Colours
+ * should also be applied to any hidden mapped residues (so that they are
+ * shown correctly if these get unhidden).
+ *
+ * @param viewPanel
+ */
+ protected void colourBySequence(AlignmentViewPanel viewPanel)
+ {
+
+ if (!colourBySequence || !isLoadingFinished() || getSsm() == null)
+ {
+ return;
+ }
+ Map<Object, AtomSpecModel> colourMap = buildColoursMap(ssm, sequence,
+ viewPanel);
+
+ List<StructureCommandI> colourBySequenceCommands = commandGenerator
+ .colourBySequence(colourMap);
+ executeCommands(colourBySequenceCommands, false, null);
+
+ }
+
+ /**
* 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;
-
// TODO: JAL-628 colour chains distinctly across all visible models
-
executeCommand(commandGenerator.colourByChain(), false,
COLOURING_STRUCTURES);
}
* @param getReply
* @param msg
*/
- private List<String> executeCommands(List<StructureCommandI> commands,
+ protected List<String> executeCommands(
+ List<StructureCommandI> commands,
boolean getReply, String msg)
{
return executeCommands(getReply, msg,
}
/**
- * colour any structures associated with sequences in the given alignment
- * using the getFeatureRenderer() and getSequenceRenderer() renderers but only
- * if colourBySequence is enabled.
+ * Recolours the displayed structures, if they are coloured by
+ * sequence, or 'show only visible alignment' is selected. This supports
+ * updating structure colours on either change of alignment colours, or change
+ * to the visible region of the alignment.
*/
- public void colourBySequence(AlignmentViewPanel alignmentv)
+ public void updateStructureColours(AlignmentViewPanel alignmentv)
{
- if (!colourBySequence || !isLoadingFinished())
+ if (!isLoadingFinished())
+ {
+ return;
+ }
+
+ /*
+ * if structure is not coloured by sequence, but restricted to the alignment,
+ * then redraw it (but don't recolour it) in case hidden regions have changed
+ * (todo: specific messaging for change of hidden region only)
+ */
+ if (!colourBySequence)
{
+ if (isShowAlignmentOnly())
+ {
+ showStructures(alignmentv.getAlignViewport(), false);
+ }
return;
}
if (getSsm() == null)
{
return;
}
- String[] files = getStructureFiles();
-
- SequenceRenderer sr = getSequenceRenderer(alignmentv);
- Map<Object, AtomSpecModel> colourMap = buildColoursMap(ssm, files,
- sequence, sr, alignmentv);
-
- List<StructureCommandI> colourBySequenceCommands = commandGenerator
- .colourBySequence(colourMap);
- executeCommands(colourBySequenceCommands, false, null);
+ colourBySequence(alignmentv);
}
/**
}
/**
+ * Sets the flag for whether only mapped visible residues in the alignment
+ * should be visible in the structure viewer
+ *
+ * @param b
+ */
+ public void setShowAlignmentOnly(boolean b)
+ {
+ showAlignmentOnly = b;
+ }
+
+ /**
+ * Answers true if only residues mapped to the alignment should be shown in the
+ * structure viewer, else false
+ *
+ * @return
+ */
+ public boolean isShowAlignmentOnly()
+ {
+ return showAlignmentOnly;
+ }
+
+ /**
+ * Sets the flag for hiding regions of structure which are hidden in the
+ * alignment (only applies when the structure viewer is restricted to the
+ * alignment only)
+ *
+ * @param b
+ */
+ public void setHideHiddenRegions(boolean b)
+ {
+ hideHiddenRegions = b;
+ }
+
+ /**
+ * Answers true if regions hidden in the alignment should also be hidden in the
+ * structure viewer, else false (only applies when the structure viewer is
+ * restricted to the alignment only)
+ *
+ * @return
+ */
+ public boolean isHideHiddenRegions()
+ {
+ return hideHiddenRegions;
+ }
+
+ /**
+ * Shows the structures in the viewer, without changing their colouring. This is
+ * to support toggling of whether the whole structure is shown, or only residues
+ * mapped to visible regions of the alignment.
+ *
+ * @param alignViewportI
+ * @param refocus
+ * if true, refit the display to the viewer
+ */
+ public void showStructures(AlignViewportI alignViewportI, boolean refocus)
+ {
+ // override with implementation
+ }
+
+ /**
+ * Sets the list of chains to hide (as "pdbid:chain")
+ *
+ * @param chains
+ */
+ public void setChainsToHide(List<String> chains)
+ {
+ chainsToHide = chains;
+ }
+
+ /**
+ * Answers true if the specified structure and chain are selected to be shown in
+ * the viewer, else false
+ *
+ * @param pdbId
+ * @param chainId
+ * @return
+ */
+ protected boolean isShowChain(String pdbId, String chainId)
+ {
+ if (chainsToHide.isEmpty())
+ {
+ return true;
+ }
+ return !chainsToHide.contains(pdbId + ":" + chainId);
+ }
+
+ @Override
+ public abstract String[] getStructureFiles();
+
+ /**
+ * Builds a model of residues mapped from sequences to show on structure, taking
+ * into account user choices of
+ * <ul>
+ * <li>which chains are shown</li>
+ * <li>whether all structure is shown, or only that mapped to the alignment</li>
+ * <li>whether hidden regions of the alignment are hidden (excluded) or grayed
+ * out (included)</li>
+ * </ul>
+ *
+ * @param av
+ * @return
+ */
+ protected AtomSpecModel getShownResidues(AlignViewportI av)
+ {
+ AlignmentI alignment = av.getAlignment();
+ final int width = alignment.getWidth();
+
+ String[] files = getStructureFiles();
+
+ AtomSpecModel model = new AtomSpecModel();
+
+ for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
+ {
+ String fileName = files[pdbfnum];
+ final String modelId = getModelIdForFile(files[pdbfnum]);
+ StructureMapping[] mappings = getSsm().getMapping(fileName);
+
+ /*
+ * Find the first mapped sequence (if any) for this PDB entry which is in
+ * the alignment
+ */
+ final int seqCountForPdbFile = getSequence()[pdbfnum].length;
+ for (int s = 0; s < seqCountForPdbFile; s++)
+ {
+ for (StructureMapping mapping : mappings)
+ {
+ final SequenceI theSequence = getSequence()[pdbfnum][s];
+ if (mapping.getSequence() == theSequence
+ && alignment.findIndex(theSequence) > -1)
+ {
+ String chainCd = mapping.getChain();
+ if (!isShowChain(mapping.getPdbId(), chainCd))
+ {
+ // continue;
+ }
+ Iterator<int[]> visible;
+ if (isShowAlignmentOnly() && isHideHiddenRegions())
+ {
+ visible = alignment.getHiddenColumns()
+ .getVisContigsIterator(0, width, true);
+ }
+ else
+ {
+ visible = Collections.singletonList(new int[] { 0, width })
+ .iterator();
+ }
+ while (visible.hasNext())
+ {
+ int[] visibleRegion = visible.next();
+ int seqStartPos = theSequence.findPosition(visibleRegion[0]);
+ int seqEndPos = theSequence.findPosition(visibleRegion[1]);
+ List<int[]> residueRanges = mapping
+ .getPDBResNumRanges(seqStartPos, seqEndPos);
+ if (!residueRanges.isEmpty())
+ {
+ for (int[] range : residueRanges)
+ {
+ model.addRange(modelId, range[0], range[1], chainCd);
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+
+ return model;
+ }
+
+ /**
+ * Answers the structure viewer's model number for the given PDB file, or -1 if
+ * not found
+ *
+ * @param fileName
+ * @param fileIndex
+ * index of the file in the stored array of file names
+ * @return
+ */
+ public int getModelForPdbFile(String fileName, int fileIndex)
+ {
+ return fileIndex;
+ }
+
+ /**
+ * Answers a default structure model specification which is simply the string
+ * form of the model number. Override if needed to specify submodels.
+ *
+ * @param model
+ * @return
+ */
+ public String getModelSpec(int model)
+ {
+ return String.valueOf(model);
+ }
+
+ /**
* Returns the FeatureRenderer for the given alignment view, or null if
* feature display is turned off in the view.
*
{
AlignmentViewPanel ap = (avp == null) ? getViewer().getAlignmentPanel()
: avp;
+ if (ap == null)
+ {
+ return null;
+ }
return ap.getAlignViewport().isShowSequenceFeatures()
? ap.getFeatureRenderer()
: null;
}
if (!isLoadingFromArchive())
{
- colourBySequence(ap);
+ updateStructureColours(ap);
}
}
* 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)
+ 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();
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 shuts down that program.
+ *
+ * @param forceClose
+ */
+ public void closeViewer(boolean forceClose)
+ {
+ getSsm().removeStructureViewerListener(this, this.getStructureFiles());
+ releaseUIResources();
+
+ // add external viewer shutdown in overrides
+ // todo - or can maybe pull up to here
+ }
+
+ /**
+ * 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;
+ }
}
git://source.jalview.org / jalview.git / blobdiff