- try
- {
-
- // NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
- // //////////////////////////////////////////////////
-
- List<String> shortNames = new ArrayList<>();
- List<String> viewIds = new ArrayList<>();
-
- // REVERSE ORDER
- for (int i = frames.size() - 1; i > -1; i--)
- {
- AlignFrame af = frames.get(i);
- // skip ?
- if (skipList != null && skipList
- .containsKey(af.getViewport().getSequenceSetId()))
- {
- continue;
- }
-
- String shortName = makeFilename(af, shortNames);
-
- int apSize = af.getAlignPanels().size();
-
- for (int ap = 0; ap < apSize; ap++)
- {
- AlignmentPanel apanel = (AlignmentPanel) af.getAlignPanels()
- .get(ap);
- String fileName = apSize == 1 ? shortName : ap + shortName;
- if (!fileName.endsWith(".xml"))
- {
- fileName = fileName + ".xml";
- }
-
- saveState(apanel, fileName, jout, viewIds);
-
- String dssid = getDatasetIdRef(
- af.getViewport().getAlignment().getDataset());
- if (!dsses.containsKey(dssid))
- {
- dsses.put(dssid, af);
- }
- }
- }
-
- writeDatasetFor(dsses, "" + jout.hashCode() + " " + uniqueSetSuffix,
- jout);
-
- try
- {
- jout.flush();
- } catch (Exception foo)
- {
- }
- ;
- jout.close();
- } catch (Exception ex)
- {
- // TODO: inform user of the problem - they need to know if their data was
- // not saved !
- if (errorMessage == null)
- {
- errorMessage = "Couldn't write Jalview Archive - see error output for details";
- }
- ex.printStackTrace();
- }
- }
-
- /**
- * Generates a distinct file name, based on the title of the AlignFrame, by
- * appending _n for increasing n until an unused name is generated. The new
- * name (without its extension) is added to the list.
- *
- * @param af
- * @param namesUsed
- * @return the generated name, with .xml extension
- */
- protected String makeFilename(AlignFrame af, List<String> namesUsed)
- {
- String shortName = af.getTitle();
-
- if (shortName.indexOf(File.separatorChar) > -1)
- {
- shortName = shortName
- .substring(shortName.lastIndexOf(File.separatorChar) + 1);
- }
-
- int count = 1;
-
- while (namesUsed.contains(shortName))
- {
- if (shortName.endsWith("_" + (count - 1)))
- {
- shortName = shortName.substring(0, shortName.lastIndexOf("_"));
- }
-
- shortName = shortName.concat("_" + count);
- count++;
- }
-
- namesUsed.add(shortName);
-
- if (!shortName.endsWith(".xml"))
- {
- shortName = shortName + ".xml";
- }
- return shortName;
- }
-
- // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW
- public boolean saveAlignment(AlignFrame af, String jarFile,
- String fileName)
- {
- try
- {
- FileOutputStream fos = new FileOutputStream(jarFile);
- JarOutputStream jout = new JarOutputStream(fos);
- List<AlignFrame> frames = new ArrayList<>();
-
- // resolve splitframes
- if (af.getViewport().getCodingComplement() != null)
- {
- frames = ((SplitFrame) af.getSplitViewContainer()).getAlignFrames();
- }
- else
- {
- frames.add(af);
- }
- saveAllFrames(frames, jout);
- try
- {
- jout.flush();
- } catch (Exception foo)
- {
- }
- ;
- jout.close();
- return true;
- } catch (Exception ex)
- {
- errorMessage = "Couldn't Write alignment view to Jalview Archive - see error output for details";
- ex.printStackTrace();
- return false;
- }
- }
-
- private void writeDatasetFor(Hashtable<String, AlignFrame> dsses,
- String fileName, JarOutputStream jout)
- {
-
- for (String dssids : dsses.keySet())
- {
- AlignFrame _af = dsses.get(dssids);
- String jfileName = fileName + " Dataset for " + _af.getTitle();
- if (!jfileName.endsWith(".xml"))
- {
- jfileName = jfileName + ".xml";
- }
- saveState(_af.alignPanel, jfileName, true, jout, null);
- }
- }
-
- /**
- * create a JalviewModel from an alignment view and marshall it to a
- * JarOutputStream
- *
- * @param ap
- * panel to create jalview model for
- * @param fileName
- * name of alignment panel written to output stream
- * @param jout
- * jar output stream
- * @param viewIds
- * @param out
- * jar entry name
- */
- public JalviewModel saveState(AlignmentPanel ap, String fileName,
- JarOutputStream jout, List<String> viewIds)
- {
- return saveState(ap, fileName, false, jout, viewIds);
- }
-
- /**
- * create a JalviewModel from an alignment view and marshall it to a
- * JarOutputStream
- *
- * @param ap
- * panel to create jalview model for
- * @param fileName
- * name of alignment panel written to output stream
- * @param storeDS
- * when true, only write the dataset for the alignment, not the data
- * associated with the view.
- * @param jout
- * jar output stream
- * @param out
- * jar entry name
- */
- public JalviewModel saveState(AlignmentPanel ap, String fileName,
- boolean storeDS, JarOutputStream jout, List<String> viewIds)
- {
- if (viewIds == null)
- {
- viewIds = new ArrayList<>();
- }
-
- initSeqRefs();
-
- List<UserColourScheme> userColours = new ArrayList<>();
-
- AlignViewport av = ap.av;
- ViewportRanges vpRanges = av.getRanges();
-
- final ObjectFactory objectFactory = new ObjectFactory();
- JalviewModel object = objectFactory.createJalviewModel();
- object.setVamsasModel(new VAMSAS());
-
- // object.setCreationDate(new java.util.Date(System.currentTimeMillis()));
- try
- {
- GregorianCalendar c = new GregorianCalendar();
- DatatypeFactory datatypeFactory = DatatypeFactory.newInstance();
- XMLGregorianCalendar now = datatypeFactory.newXMLGregorianCalendar(c);// gregorianCalendar);
- object.setCreationDate(now);
- } catch (DatatypeConfigurationException e)
- {
- System.err.println("error writing date: " + e.toString());
- }
- object.setVersion(
- jalview.bin.Cache.getDefault("VERSION", "Development Build"));
-
- /**
- * rjal is full height alignment, jal is actual alignment with full metadata
- * but excludes hidden sequences.
- */
- jalview.datamodel.AlignmentI rjal = av.getAlignment(), jal = rjal;
-
- if (av.hasHiddenRows())
- {
- rjal = jal.getHiddenSequences().getFullAlignment();
- }
-
- SequenceSet vamsasSet = new SequenceSet();
- Sequence vamsasSeq;
- // JalviewModelSequence jms = new JalviewModelSequence();
-
- vamsasSet.setGapChar(jal.getGapCharacter() + "");
-
- if (jal.getDataset() != null)
- {
- // dataset id is the dataset's hashcode
- vamsasSet.setDatasetId(getDatasetIdRef(jal.getDataset()));
- if (storeDS)
- {
- // switch jal and the dataset
- jal = jal.getDataset();
- rjal = jal;
- }
- }
- if (jal.getProperties() != null)
- {
- Enumeration en = jal.getProperties().keys();
- while (en.hasMoreElements())
- {
- String key = en.nextElement().toString();
- SequenceSetProperties ssp = new SequenceSetProperties();
- ssp.setKey(key);
- ssp.setValue(jal.getProperties().get(key).toString());
- // vamsasSet.addSequenceSetProperties(ssp);
- vamsasSet.getSequenceSetProperties().add(ssp);
- }
- }
-
- JSeq jseq;
- Set<String> calcIdSet = new HashSet<>();
- // record the set of vamsas sequence XML POJO we create.
- HashMap<String, Sequence> vamsasSetIds = new HashMap<>();
- // SAVE SEQUENCES
- for (final SequenceI jds : rjal.getSequences())
- {
- final SequenceI jdatasq = jds.getDatasetSequence() == null ? jds
- : jds.getDatasetSequence();
- String id = seqHash(jds);
- if (vamsasSetIds.get(id) == null)
- {
- if (seqRefIds.get(id) != null && !storeDS)
- {
- // This happens for two reasons: 1. multiple views are being
- // serialised.
- // 2. the hashCode has collided with another sequence's code. This
- // DOES
- // HAPPEN! (PF00072.15.stk does this)
- // JBPNote: Uncomment to debug writing out of files that do not read
- // back in due to ArrayOutOfBoundExceptions.
- // System.err.println("vamsasSeq backref: "+id+"");
- // System.err.println(jds.getName()+"
- // "+jds.getStart()+"-"+jds.getEnd()+" "+jds.getSequenceAsString());
- // System.err.println("Hashcode: "+seqHash(jds));
- // SequenceI rsq = (SequenceI) seqRefIds.get(id + "");
- // System.err.println(rsq.getName()+"
- // "+rsq.getStart()+"-"+rsq.getEnd()+" "+rsq.getSequenceAsString());
- // System.err.println("Hashcode: "+seqHash(rsq));
- }
- else
- {
- vamsasSeq = createVamsasSequence(id, jds);
-// vamsasSet.addSequence(vamsasSeq);
- vamsasSet.getSequence().add(vamsasSeq);
- vamsasSetIds.put(id, vamsasSeq);
- seqRefIds.put(id, jds);
- }
- }
- jseq = new JSeq();
- jseq.setStart(jds.getStart());
- jseq.setEnd(jds.getEnd());
- jseq.setColour(av.getSequenceColour(jds).getRGB());
-
- jseq.setId(id); // jseq id should be a string not a number
- if (!storeDS)
- {
- // Store any sequences this sequence represents
- if (av.hasHiddenRows())
- {
- // use rjal, contains the full height alignment
- jseq.setHidden(
- av.getAlignment().getHiddenSequences().isHidden(jds));
-
- if (av.isHiddenRepSequence(jds))
- {
- jalview.datamodel.SequenceI[] reps = av
- .getRepresentedSequences(jds).getSequencesInOrder(rjal);
-
- for (int h = 0; h < reps.length; h++)
- {
- if (reps[h] != jds)
- {
- // jseq.addHiddenSequences(rjal.findIndex(reps[h]));
- jseq.getHiddenSequences().add(rjal.findIndex(reps[h]));
- }
- }
- }
- }
- // mark sequence as reference - if it is the reference for this view
- if (jal.hasSeqrep())
- {
- jseq.setViewreference(jds == jal.getSeqrep());
- }
- }
-
- // TODO: omit sequence features from each alignment view's XML dump if we
- // are storing dataset
- List<SequenceFeature> sfs = jds.getSequenceFeatures();
- for (SequenceFeature sf : sfs)
- {
- // Features features = new Features();
- Feature features = new Feature();
-
- features.setBegin(sf.getBegin());
- features.setEnd(sf.getEnd());
- features.setDescription(sf.getDescription());
- features.setType(sf.getType());
- features.setFeatureGroup(sf.getFeatureGroup());
- features.setScore(sf.getScore());
- if (sf.links != null)
- {
- for (int l = 0; l < sf.links.size(); l++)
- {
- OtherData keyValue = new OtherData();
- keyValue.setKey("LINK_" + l);
- keyValue.setValue(sf.links.elementAt(l).toString());
- // features.addOtherData(keyValue);
- features.getOtherData().add(keyValue);
- }
- }
- if (sf.otherDetails != null)
- {
- /*
- * save feature attributes, which may be simple strings or
- * map valued (have sub-attributes)
- */
- for (Entry<String, Object> entry : sf.otherDetails.entrySet())
- {
- String key = entry.getKey();
- Object value = entry.getValue();
- if (value instanceof Map<?, ?>)
- {
- for (Entry<String, Object> subAttribute : ((Map<String, Object>) value)
- .entrySet())
- {
- OtherData otherData = new OtherData();
- otherData.setKey(key);
- otherData.setKey2(subAttribute.getKey());
- otherData.setValue(subAttribute.getValue().toString());
- // features.addOtherData(otherData);
- features.getOtherData().add(otherData);
- }
- }
- else
- {
- OtherData otherData = new OtherData();
- otherData.setKey(key);
- otherData.setValue(value.toString());
- // features.addOtherData(otherData);
- features.getOtherData().add(otherData);
- }
- }
- }
-
- // jseq.addFeatures(features);
- jseq.getFeatures().add(features);
- }
-
- if (jdatasq.getAllPDBEntries() != null)
- {
- Enumeration<PDBEntry> en = jdatasq.getAllPDBEntries().elements();
- while (en.hasMoreElements())
- {
- Pdbids pdb = new Pdbids();
- jalview.datamodel.PDBEntry entry = en.nextElement();
-
- String pdbId = entry.getId();
- pdb.setId(pdbId);
- pdb.setType(entry.getType());
-
- /*
- * Store any structure views associated with this sequence. This
- * section copes with duplicate entries in the project, so a dataset
- * only view *should* be coped with sensibly.
- */
- // This must have been loaded, is it still visible?
- JInternalFrame[] frames = Desktop.desktop.getAllFrames();
- String matchedFile = null;
- for (int f = frames.length - 1; f > -1; f--)
- {
- if (frames[f] instanceof StructureViewerBase)
- {
- StructureViewerBase viewFrame = (StructureViewerBase) frames[f];
- matchedFile = saveStructureState(ap, jds, pdb, entry, viewIds,
- matchedFile, viewFrame);
- /*
- * Only store each structure viewer's state once in the project
- * jar. First time through only (storeDS==false)
- */
- String viewId = viewFrame.getViewId();
- if (!storeDS && !viewIds.contains(viewId))
- {
- viewIds.add(viewId);
- try
- {
- String viewerState = viewFrame.getStateInfo();
- writeJarEntry(jout, getViewerJarEntryName(viewId),
- viewerState.getBytes());
- } catch (IOException e)
- {
- System.err.println(
- "Error saving viewer state: " + e.getMessage());
- }
- }
- }
- }
-
- if (matchedFile != null || entry.getFile() != null)
- {
- if (entry.getFile() != null)
- {
- // use entry's file
- matchedFile = entry.getFile();
- }
- pdb.setFile(matchedFile); // entry.getFile());
- if (pdbfiles == null)
- {
- pdbfiles = new ArrayList<>();
- }
-
- if (!pdbfiles.contains(pdbId))
- {
- pdbfiles.add(pdbId);
- copyFileToJar(jout, matchedFile, pdbId);
- }
- }
-
- Enumeration<String> props = entry.getProperties();
- if (props.hasMoreElements())
- {
- // PdbentryItem item = new PdbentryItem();
- while (props.hasMoreElements())
- {
- Property prop = new Property();
- String key = props.nextElement();
- prop.setName(key);
- prop.setValue(entry.getProperty(key).toString());
- // item.addProperty(prop);
- pdb.getProperty().add(prop);
- }
- // pdb.addPdbentryItem(item);
- }
-
- // jseq.addPdbids(pdb);
- jseq.getPdbids().add(pdb);
- }
- }
-
- saveRnaViewers(jout, jseq, jds, viewIds, ap, storeDS);
-
- // jms.addJSeq(jseq);
- object.getJSeq().add(jseq);
- }
-
- if (!storeDS && av.hasHiddenRows())
- {
- jal = av.getAlignment();
- }
- // SAVE MAPPINGS
- // FOR DATASET
- if (storeDS && jal.getCodonFrames() != null)
- {
- List<AlignedCodonFrame> jac = jal.getCodonFrames();
- for (AlignedCodonFrame acf : jac)
- {
- AlcodonFrame alc = new AlcodonFrame();
- if (acf.getProtMappings() != null
- && acf.getProtMappings().length > 0)
- {
- boolean hasMap = false;
- SequenceI[] dnas = acf.getdnaSeqs();
- jalview.datamodel.Mapping[] pmaps = acf.getProtMappings();
- for (int m = 0; m < pmaps.length; m++)
- {
- AlcodMap alcmap = new AlcodMap();
- alcmap.setDnasq(seqHash(dnas[m]));
- alcmap.setMapping(
- createVamsasMapping(pmaps[m], dnas[m], null, false));
- // alc.addAlcodMap(alcmap);
- alc.getAlcodMap().add(alcmap);
- hasMap = true;
- }
- if (hasMap)
- {
- // vamsasSet.addAlcodonFrame(alc);
- vamsasSet.getAlcodonFrame().add(alc);
- }
- }
- // TODO: delete this ? dead code from 2.8.3->2.9 ?
- // {
- // AlcodonFrame alc = new AlcodonFrame();
- // vamsasSet.addAlcodonFrame(alc);
- // for (int p = 0; p < acf.aaWidth; p++)
- // {
- // Alcodon cmap = new Alcodon();
- // if (acf.codons[p] != null)
- // {
- // // Null codons indicate a gapped column in the translated peptide
- // // alignment.
- // cmap.setPos1(acf.codons[p][0]);
- // cmap.setPos2(acf.codons[p][1]);
- // cmap.setPos3(acf.codons[p][2]);
- // }
- // alc.addAlcodon(cmap);
- // }
- // if (acf.getProtMappings() != null
- // && acf.getProtMappings().length > 0)
- // {
- // SequenceI[] dnas = acf.getdnaSeqs();
- // jalview.datamodel.Mapping[] pmaps = acf.getProtMappings();
- // for (int m = 0; m < pmaps.length; m++)
- // {
- // AlcodMap alcmap = new AlcodMap();
- // alcmap.setDnasq(seqHash(dnas[m]));
- // alcmap.setMapping(createVamsasMapping(pmaps[m], dnas[m], null,
- // false));
- // alc.addAlcodMap(alcmap);
- // }
- // }
- }
- }
-
- // SAVE TREES
- // /////////////////////////////////
- if (!storeDS && av.getCurrentTree() != null)
- {
- // FIND ANY ASSOCIATED TREES
- // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
- if (Desktop.desktop != null)
- {
- JInternalFrame[] frames = Desktop.desktop.getAllFrames();
-
- for (int t = 0; t < frames.length; t++)
- {
- if (frames[t] instanceof TreePanel)
- {
- TreePanel tp = (TreePanel) frames[t];
-
- if (tp.getTreeCanvas().getViewport().getAlignment() == jal)
- {
- JalviewModel.Tree tree = new JalviewModel.Tree();
- tree.setTitle(tp.getTitle());
- tree.setCurrentTree((av.getCurrentTree() == tp.getTree()));
- tree.setNewick(tp.getTree().print());
- tree.setThreshold(tp.getTreeCanvas().getThreshold());
-
- tree.setFitToWindow(tp.fitToWindow.getState());
- tree.setFontName(tp.getTreeFont().getName());
- tree.setFontSize(tp.getTreeFont().getSize());
- tree.setFontStyle(tp.getTreeFont().getStyle());
- tree.setMarkUnlinked(tp.placeholdersMenu.getState());
-
- tree.setShowBootstrap(tp.bootstrapMenu.getState());
- tree.setShowDistances(tp.distanceMenu.getState());
-
- tree.setHeight(tp.getHeight());
- tree.setWidth(tp.getWidth());
- tree.setXpos(tp.getX());
- tree.setYpos(tp.getY());
- tree.setId(makeHashCode(tp, null));
- // jms.addTree(tree);
- object.getTree().add(tree);
- }
- }
- }
- }
- }
-
- // SAVE ANNOTATIONS
- /**
- * store forward refs from an annotationRow to any groups
- */
- IdentityHashMap<SequenceGroup, String> groupRefs = new IdentityHashMap<>();
- if (storeDS)
- {
- for (SequenceI sq : jal.getSequences())
- {
- // Store annotation on dataset sequences only
- AlignmentAnnotation[] aa = sq.getAnnotation();
- if (aa != null && aa.length > 0)
- {
- storeAlignmentAnnotation(aa, groupRefs, av, calcIdSet, storeDS,
- vamsasSet);
- }
- }
- }
- else
- {
- if (jal.getAlignmentAnnotation() != null)
- {
- // Store the annotation shown on the alignment.
- AlignmentAnnotation[] aa = jal.getAlignmentAnnotation();
- storeAlignmentAnnotation(aa, groupRefs, av, calcIdSet, storeDS,
- vamsasSet);
- }
- }
- // SAVE GROUPS
- if (jal.getGroups() != null)
- {
- JGroup[] groups = new JGroup[jal.getGroups().size()];
- int i = -1;
- for (jalview.datamodel.SequenceGroup sg : jal.getGroups())
- {
- JGroup jGroup = new JGroup();
- groups[++i] = jGroup;
-
- jGroup.setStart(sg.getStartRes());
- jGroup.setEnd(sg.getEndRes());
- jGroup.setName(sg.getName());
- if (groupRefs.containsKey(sg))
- {
- // group has references so set its ID field
- jGroup.setId(groupRefs.get(sg));
- }
- ColourSchemeI colourScheme = sg.getColourScheme();
- if (colourScheme != null)
- {
- ResidueShaderI groupColourScheme = sg.getGroupColourScheme();
- if (groupColourScheme.conservationApplied())
- {
- jGroup.setConsThreshold(groupColourScheme.getConservationInc());
-
- if (colourScheme instanceof jalview.schemes.UserColourScheme)
- {
- jGroup.setColour(
- setUserColourScheme(colourScheme, userColours,
- object));
- }
- else
- {
- jGroup.setColour(colourScheme.getSchemeName());
- }
- }
- else if (colourScheme instanceof jalview.schemes.AnnotationColourGradient)
- {
- jGroup.setColour("AnnotationColourGradient");
- jGroup.setAnnotationColours(constructAnnotationColours(
- (jalview.schemes.AnnotationColourGradient) colourScheme,
- userColours, object));
- }
- else if (colourScheme instanceof jalview.schemes.UserColourScheme)
- {
- jGroup.setColour(
- setUserColourScheme(colourScheme, userColours, object));
- }
- else
- {
- jGroup.setColour(colourScheme.getSchemeName());
- }
-
- jGroup.setPidThreshold(groupColourScheme.getThreshold());
- }
-
- jGroup.setOutlineColour(sg.getOutlineColour().getRGB());
- jGroup.setDisplayBoxes(sg.getDisplayBoxes());
- jGroup.setDisplayText(sg.getDisplayText());
- jGroup.setColourText(sg.getColourText());
- jGroup.setTextCol1(sg.textColour.getRGB());
- jGroup.setTextCol2(sg.textColour2.getRGB());
- jGroup.setTextColThreshold(sg.thresholdTextColour);
- jGroup.setShowUnconserved(sg.getShowNonconserved());
- jGroup.setIgnoreGapsinConsensus(sg.getIgnoreGapsConsensus());
- jGroup.setShowConsensusHistogram(sg.isShowConsensusHistogram());
- jGroup.setShowSequenceLogo(sg.isShowSequenceLogo());
- jGroup.setNormaliseSequenceLogo(sg.isNormaliseSequenceLogo());
- for (SequenceI seq : sg.getSequences())
- {
- // jGroup.addSeq(seqHash(seq));
- jGroup.getSeq().add(seqHash(seq));
- }
- }
-
- //jms.setJGroup(groups);
- Object group;
- for (JGroup grp : groups)
- {
- object.getJGroup().add(grp);
- }
- }
- if (!storeDS)
- {
- // /////////SAVE VIEWPORT
- Viewport view = new Viewport();
- view.setTitle(ap.alignFrame.getTitle());
- view.setSequenceSetId(
- makeHashCode(av.getSequenceSetId(), av.getSequenceSetId()));
- view.setId(av.getViewId());
- if (av.getCodingComplement() != null)
- {
- view.setComplementId(av.getCodingComplement().getViewId());
- }
- view.setViewName(av.getViewName());
- view.setGatheredViews(av.isGatherViewsHere());
-
- Rectangle size = ap.av.getExplodedGeometry();
- Rectangle position = size;
- if (size == null)
- {
- size = ap.alignFrame.getBounds();
- if (av.getCodingComplement() != null)
- {
- position = ((SplitFrame) ap.alignFrame.getSplitViewContainer())
- .getBounds();
- }
- else
- {
- position = size;
- }
- }
- view.setXpos(position.x);
- view.setYpos(position.y);
-
- view.setWidth(size.width);
- view.setHeight(size.height);
-
- view.setStartRes(vpRanges.getStartRes());
- view.setStartSeq(vpRanges.getStartSeq());
-
- if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
- {
- view.setBgColour(setUserColourScheme(av.getGlobalColourScheme(),
- userColours, object));
- }
- else if (av
- .getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient)
- {
- AnnotationColourScheme ac = constructAnnotationColours(
- (jalview.schemes.AnnotationColourGradient) av
- .getGlobalColourScheme(),
- userColours, object);
-
- view.setAnnotationColours(ac);
- view.setBgColour("AnnotationColourGradient");
- }
- else
- {
- view.setBgColour(ColourSchemeProperty
- .getColourName(av.getGlobalColourScheme()));
- }
-
- ResidueShaderI vcs = av.getResidueShading();
- ColourSchemeI cs = av.getGlobalColourScheme();
-
- if (cs != null)
- {
- if (vcs.conservationApplied())
- {
- view.setConsThreshold(vcs.getConservationInc());
- if (cs instanceof jalview.schemes.UserColourScheme)
- {
- view.setBgColour(setUserColourScheme(cs, userColours, object));
- }
- }
- view.setPidThreshold(vcs.getThreshold());
- }
-
- view.setConservationSelected(av.getConservationSelected());
- view.setPidSelected(av.getAbovePIDThreshold());
- final Font font = av.getFont();
- view.setFontName(font.getName());
- view.setFontSize(font.getSize());
- view.setFontStyle(font.getStyle());
- view.setScaleProteinAsCdna(av.getViewStyle().isScaleProteinAsCdna());
- view.setRenderGaps(av.isRenderGaps());
- view.setShowAnnotation(av.isShowAnnotation());
- view.setShowBoxes(av.getShowBoxes());
- view.setShowColourText(av.getColourText());
- view.setShowFullId(av.getShowJVSuffix());
- view.setRightAlignIds(av.isRightAlignIds());
- view.setShowSequenceFeatures(av.isShowSequenceFeatures());
- view.setShowText(av.getShowText());
- view.setShowUnconserved(av.getShowUnconserved());
- view.setWrapAlignment(av.getWrapAlignment());
- view.setTextCol1(av.getTextColour().getRGB());
- view.setTextCol2(av.getTextColour2().getRGB());
- view.setTextColThreshold(av.getThresholdTextColour());
- view.setShowConsensusHistogram(av.isShowConsensusHistogram());
- view.setShowSequenceLogo(av.isShowSequenceLogo());
- view.setNormaliseSequenceLogo(av.isNormaliseSequenceLogo());
- view.setShowGroupConsensus(av.isShowGroupConsensus());
- view.setShowGroupConservation(av.isShowGroupConservation());
- view.setShowNPfeatureTooltip(av.isShowNPFeats());
- view.setShowDbRefTooltip(av.isShowDBRefs());
- view.setFollowHighlight(av.isFollowHighlight());
- view.setFollowSelection(av.followSelection);
- view.setIgnoreGapsinConsensus(av.isIgnoreGapsConsensus());
- if (av.getFeaturesDisplayed() != null)
- {
- FeatureSettings fs = new FeatureSettings();
-
- FeatureRenderer fr = ap.getSeqPanel().seqCanvas
- .getFeatureRenderer();
- String[] renderOrder = fr.getRenderOrder().toArray(new String[0]);
-
- Vector<String> settingsAdded = new Vector<>();
- if (renderOrder != null)
- {
- for (String featureType : renderOrder)
- {
- FeatureSettings.Setting setting = new FeatureSettings.Setting();
- setting.setType(featureType);
-
- /*
- * save any filter for the feature type
- */
- FeatureMatcherSetI filter = fr.getFeatureFilter(featureType);
- if (filter != null) {
- Iterator<FeatureMatcherI> filters = filter.getMatchers().iterator();
- FeatureMatcherI firstFilter = filters.next();
- setting.setMatcherSet(Jalview2XML.marshalFilter(
- firstFilter, filters, filter.isAnded()));
- }
-
- /*
- * save colour scheme for the feature type
- */
- FeatureColourI fcol = fr.getFeatureStyle(featureType);
- if (!fcol.isSimpleColour())
- {
- setting.setColour(fcol.getMaxColour().getRGB());
- setting.setMincolour(fcol.getMinColour().getRGB());
- setting.setMin(fcol.getMin());
- setting.setMax(fcol.getMax());
- setting.setColourByLabel(fcol.isColourByLabel());
- if (fcol.isColourByAttribute())
- {
- String[] attName = fcol.getAttributeName();
- setting.getAttributeName().add(attName[0]);
- if (attName.length > 1)
- {
- setting.getAttributeName().add(attName[1]);
- }
- }
- setting.setAutoScale(fcol.isAutoScaled());
- setting.setThreshold(fcol.getThreshold());
- Color noColour = fcol.getNoColour();
- if (noColour == null)
- {
- setting.setNoValueColour(NoValueColour.NONE);
- }
- else if (noColour.equals(fcol.getMaxColour()))
- {
- setting.setNoValueColour(NoValueColour.MAX);
- }
- else
- {
- setting.setNoValueColour(NoValueColour.MIN);
- }
- // -1 = No threshold, 0 = Below, 1 = Above
- setting.setThreshstate(fcol.isAboveThreshold() ? 1
- : (fcol.isBelowThreshold() ? 0 : -1));
- }
- else
- {
- setting.setColour(fcol.getColour().getRGB());
- }
-
- setting.setDisplay(
- av.getFeaturesDisplayed().isVisible(featureType));
- float rorder = fr
- .getOrder(featureType);
- if (rorder > -1)
- {
- setting.setOrder(rorder);
- }
- /// fs.addSetting(setting);
- fs.getSetting().add(setting);
- settingsAdded.addElement(featureType);
- }
- }
-
- // is groups actually supposed to be a map here ?
- Iterator<String> en = fr.getFeatureGroups().iterator();
- Vector<String> groupsAdded = new Vector<>();
- while (en.hasNext())
- {
- String grp = en.next();
- if (groupsAdded.contains(grp))
- {
- continue;
- }
- Group g = new Group();
- g.setName(grp);
- g.setDisplay(((Boolean) fr.checkGroupVisibility(grp, false))
- .booleanValue());
- // fs.addGroup(g);
- fs.getGroup().add(g);
- groupsAdded.addElement(grp);
- }
- // jms.setFeatureSettings(fs);
- object.setFeatureSettings(fs);
- }
-
- if (av.hasHiddenColumns())
- {
- jalview.datamodel.HiddenColumns hidden = av.getAlignment()
- .getHiddenColumns();
- if (hidden == null)
- {
- warn("REPORT BUG: avoided null columnselection bug (DMAM reported). Please contact Jim about this.");
- }
- else
- {
- Iterator<int[]> hiddenRegions = hidden.iterator();
- while (hiddenRegions.hasNext())
- {
- int[] region = hiddenRegions.next();
- HiddenColumns hc = new HiddenColumns();
- hc.setStart(region[0]);
- hc.setEnd(region[1]);
- // view.addHiddenColumns(hc);
- view.getHiddenColumns().add(hc);
- }
- }
- }
- if (calcIdSet.size() > 0)
- {
- for (String calcId : calcIdSet)
- {
- if (calcId.trim().length() > 0)
- {
- CalcIdParam cidp = createCalcIdParam(calcId, av);
- // Some calcIds have no parameters.
- if (cidp != null)
- {
- // view.addCalcIdParam(cidp);
- view.getCalcIdParam().add(cidp);
- }
- }
- }
- }
-
- // jms.addViewport(view);
- object.getViewport().add(view);
- }
- // object.setJalviewModelSequence(jms);
- // object.getVamsasModel().addSequenceSet(vamsasSet);
- object.getVamsasModel().getSequenceSet().add(vamsasSet);
-
- if (jout != null && fileName != null)
- {
- // We may not want to write the object to disk,
- // eg we can copy the alignViewport to a new view object
- // using save and then load
- try
- {
- System.out.println("Writing jar entry " + fileName);
- JarEntry entry = new JarEntry(fileName);
- jout.putNextEntry(entry);
- PrintWriter pout = new PrintWriter(
- new OutputStreamWriter(jout, UTF_8));
- JAXBContext jaxbContext = JAXBContext
- .newInstance(JalviewModel.class);
- Marshaller jaxbMarshaller = jaxbContext.createMarshaller();
-
- // output pretty printed
- // jaxbMarshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, true);
- jaxbMarshaller.marshal(
- new ObjectFactory().createJalviewModel(object), pout);
-
- // jaxbMarshaller.marshal(object, pout);
- // marshaller.marshal(object);
- pout.flush();
- jout.closeEntry();
- } catch (Exception ex)
- {
- // TODO: raise error in GUI if marshalling failed.
- System.err.println("Error writing Jalview project");
- ex.printStackTrace();
- }
- }
- return object;
- }
-
- /**
- * Save any Varna viewers linked to this sequence. Writes an rnaViewer element
- * for each viewer, with
- * <ul>
- * <li>viewer geometry (position, size, split pane divider location)</li>
- * <li>index of the selected structure in the viewer (currently shows gapped
- * or ungapped)</li>
- * <li>the id of the annotation holding RNA secondary structure</li>
- * <li>(currently only one SS is shown per viewer, may be more in future)</li>
- * </ul>
- * Varna viewer state is also written out (in native Varna XML) to separate
- * project jar entries. A separate entry is written for each RNA structure
- * displayed, with the naming convention
- * <ul>
- * <li>rna_viewId_sequenceId_annotationId_[gapped|trimmed]</li>
- * </ul>
- *
- * @param jout
- * @param jseq
- * @param jds
- * @param viewIds
- * @param ap
- * @param storeDataset
- */
- protected void saveRnaViewers(JarOutputStream jout, JSeq jseq,
- final SequenceI jds, List<String> viewIds, AlignmentPanel ap,
- boolean storeDataset)
- {
- if (Desktop.desktop == null)
- {
- return;
- }
- JInternalFrame[] frames = Desktop.desktop.getAllFrames();
- for (int f = frames.length - 1; f > -1; f--)
- {
- if (frames[f] instanceof AppVarna)
- {
- AppVarna varna = (AppVarna) frames[f];
- /*
- * link the sequence to every viewer that is showing it and is linked to
- * its alignment panel
- */
- if (varna.isListeningFor(jds) && ap == varna.getAlignmentPanel())
- {
- String viewId = varna.getViewId();
- RnaViewer rna = new RnaViewer();
- rna.setViewId(viewId);
- rna.setTitle(varna.getTitle());
- rna.setXpos(varna.getX());
- rna.setYpos(varna.getY());
- rna.setWidth(varna.getWidth());
- rna.setHeight(varna.getHeight());
- rna.setDividerLocation(varna.getDividerLocation());
- rna.setSelectedRna(varna.getSelectedIndex());
- // jseq.addRnaViewer(rna);
- jseq.getRnaViewer().add(rna);
-
- /*
- * Store each Varna panel's state once in the project per sequence.
- * First time through only (storeDataset==false)
- */
- // boolean storeSessions = false;
- // String sequenceViewId = viewId + seqsToIds.get(jds);
- // if (!storeDataset && !viewIds.contains(sequenceViewId))
- // {
- // viewIds.add(sequenceViewId);
- // storeSessions = true;
- // }
- for (RnaModel model : varna.getModels())
- {
- if (model.seq == jds)
- {
- /*
- * VARNA saves each view (sequence or alignment secondary
- * structure, gapped or trimmed) as a separate XML file
- */
- String jarEntryName = rnaSessions.get(model);
- if (jarEntryName == null)
- {
-
- String varnaStateFile = varna.getStateInfo(model.rna);
- jarEntryName = RNA_PREFIX + viewId + "_" + nextCounter();
- copyFileToJar(jout, varnaStateFile, jarEntryName);
- rnaSessions.put(model, jarEntryName);
- }
- SecondaryStructure ss = new SecondaryStructure();
- String annotationId = varna.getAnnotation(jds).annotationId;
- ss.setAnnotationId(annotationId);
- ss.setViewerState(jarEntryName);
- ss.setGapped(model.gapped);
- ss.setTitle(model.title);
- // rna.addSecondaryStructure(ss);
- rna.getSecondaryStructure().add(ss);
- }
- }
- }
- }
- }
- }
-
- /**
- * Copy the contents of a file to a new entry added to the output jar
- *
- * @param jout
- * @param infilePath
- * @param jarEntryName
- */
- protected void copyFileToJar(JarOutputStream jout, String infilePath,
- String jarEntryName)
- {
- DataInputStream dis = null;
- try
- {
- File file = new File(infilePath);
- if (file.exists() && jout != null)
- {
- dis = new DataInputStream(new FileInputStream(file));
- byte[] data = new byte[(int) file.length()];
- dis.readFully(data);
- writeJarEntry(jout, jarEntryName, data);
- }
- } catch (Exception ex)
- {
- ex.printStackTrace();
- } finally
- {
- if (dis != null)
- {
- try
- {
- dis.close();
- } catch (IOException e)
- {
- // ignore
- }
- }
- }
- }
-
- /**
- * Write the data to a new entry of given name in the output jar file
- *
- * @param jout
- * @param jarEntryName
- * @param data
- * @throws IOException
- */
- protected void writeJarEntry(JarOutputStream jout, String jarEntryName,
- byte[] data) throws IOException
- {
- if (jout != null)
- {
- System.out.println("Writing jar entry " + jarEntryName);
- jout.putNextEntry(new JarEntry(jarEntryName));
- DataOutputStream dout = new DataOutputStream(jout);
- dout.write(data, 0, data.length);
- dout.flush();
- jout.closeEntry();
- }
- }
-
- /**
- * Save the state of a structure viewer
- *
- * @param ap
- * @param jds
- * @param pdb
- * the archive XML element under which to save the state
- * @param entry
- * @param viewIds
- * @param matchedFile
- * @param viewFrame
- * @return
- */
- protected String saveStructureState(AlignmentPanel ap, SequenceI jds,
- Pdbids pdb, PDBEntry entry, List<String> viewIds,
- String matchedFile, StructureViewerBase viewFrame)
- {
- final AAStructureBindingModel bindingModel = viewFrame.getBinding();
-
- /*
- * Look for any bindings for this viewer to the PDB file of interest
- * (including part matches excluding chain id)
- */
- for (int peid = 0; peid < bindingModel.getPdbCount(); peid++)
- {
- final PDBEntry pdbentry = bindingModel.getPdbEntry(peid);
- final String pdbId = pdbentry.getId();
- if (!pdbId.equals(entry.getId())
- && !(entry.getId().length() > 4 && entry.getId().toLowerCase()
- .startsWith(pdbId.toLowerCase())))
- {
- /*
- * not interested in a binding to a different PDB entry here
- */
- continue;
- }
- if (matchedFile == null)
- {
- matchedFile = pdbentry.getFile();
- }
- else if (!matchedFile.equals(pdbentry.getFile()))
- {
- Cache.log.warn(
- "Probably lost some PDB-Sequence mappings for this structure file (which apparently has same PDB Entry code): "
- + pdbentry.getFile());
- }
- // record the
- // file so we
- // can get at it if the ID
- // match is ambiguous (e.g.
- // 1QIP==1qipA)
-
- for (int smap = 0; smap < viewFrame.getBinding()
- .getSequence()[peid].length; smap++)
- {
- // if (jal.findIndex(jmol.jmb.sequence[peid][smap]) > -1)
- if (jds == viewFrame.getBinding().getSequence()[peid][smap])
- {
- StructureState state = new StructureState();
- state.setVisible(true);
- state.setXpos(viewFrame.getX());
- state.setYpos(viewFrame.getY());
- state.setWidth(viewFrame.getWidth());
- state.setHeight(viewFrame.getHeight());
- final String viewId = viewFrame.getViewId();
- state.setViewId(viewId);
- state.setAlignwithAlignPanel(viewFrame.isUsedforaligment(ap));
- state.setColourwithAlignPanel(viewFrame.isUsedforcolourby(ap));
- state.setColourByJmol(viewFrame.isColouredByViewer());
- state.setType(viewFrame.getViewerType().toString());
- // pdb.addStructureState(state);
- pdb.getStructureState().add(state);
- }
- }
- }
- return matchedFile;
- }
-
- /**
- * Populates the AnnotationColourScheme xml for save. This captures the
- * settings of the options in the 'Colour by Annotation' dialog.
- *
- * @param acg
- * @param userColours
- * @param jm
- * @return
- */
- private AnnotationColourScheme constructAnnotationColours(
- AnnotationColourGradient acg, List<UserColourScheme> userColours,
- JalviewModel jm)
- {
- AnnotationColourScheme ac = new AnnotationColourScheme();
- ac.setAboveThreshold(acg.getAboveThreshold());
- ac.setThreshold(acg.getAnnotationThreshold());
- // 2.10.2 save annotationId (unique) not annotation label
- ac.setAnnotation(acg.getAnnotation().annotationId);
- if (acg.getBaseColour() instanceof UserColourScheme)
- {
- ac.setColourScheme(
- setUserColourScheme(acg.getBaseColour(), userColours, jm));
- }
- else
- {
- ac.setColourScheme(
- ColourSchemeProperty.getColourName(acg.getBaseColour()));
- }
-
- ac.setMaxColour(acg.getMaxColour().getRGB());
- ac.setMinColour(acg.getMinColour().getRGB());
- ac.setPerSequence(acg.isSeqAssociated());
- ac.setPredefinedColours(acg.isPredefinedColours());
- return ac;
- }
-
- private void storeAlignmentAnnotation(AlignmentAnnotation[] aa,
- IdentityHashMap<SequenceGroup, String> groupRefs,
- AlignmentViewport av, Set<String> calcIdSet, boolean storeDS,
- SequenceSet vamsasSet)
- {
-
- for (int i = 0; i < aa.length; i++)
- {
- Annotation an = new Annotation();
-
- AlignmentAnnotation annotation = aa[i];
- if (annotation.annotationId != null)
- {
- annotationIds.put(annotation.annotationId, annotation);
- }
-
- an.setId(annotation.annotationId);
-
- an.setVisible(annotation.visible);
-
- an.setDescription(annotation.description);
-
- if (annotation.sequenceRef != null)
- {
- // 2.9 JAL-1781 xref on sequence id rather than name
- an.setSequenceRef(seqsToIds.get(annotation.sequenceRef));
- }
- if (annotation.groupRef != null)
- {
- String groupIdr = groupRefs.get(annotation.groupRef);
- if (groupIdr == null)
- {
- // make a locally unique String
- groupRefs.put(annotation.groupRef,
- groupIdr = ("" + System.currentTimeMillis()
- + annotation.groupRef.getName()
- + groupRefs.size()));
- }
- an.setGroupRef(groupIdr.toString());
- }
-
- // store all visualization attributes for annotation
- an.setGraphHeight(annotation.graphHeight);
- an.setCentreColLabels(annotation.centreColLabels);
- an.setScaleColLabels(annotation.scaleColLabel);
- an.setShowAllColLabels(annotation.showAllColLabels);
- an.setBelowAlignment(annotation.belowAlignment);
-
- if (annotation.graph > 0)
- {
- an.setGraph(true);
- an.setGraphType(annotation.graph);
- an.setGraphGroup(annotation.graphGroup);
- if (annotation.getThreshold() != null)
- {
- ThresholdLine line = new ThresholdLine();
- line.setLabel(annotation.getThreshold().label);
- line.setValue(annotation.getThreshold().value);
- line.setColour(annotation.getThreshold().colour.getRGB());
- an.setThresholdLine(line);
- }
- }
- else
- {
- an.setGraph(false);
- }
-
- an.setLabel(annotation.label);
-
- if (annotation == av.getAlignmentQualityAnnot()
- || annotation == av.getAlignmentConservationAnnotation()
- || annotation == av.getAlignmentConsensusAnnotation()
- || annotation.autoCalculated)
- {
- // new way of indicating autocalculated annotation -
- an.setAutoCalculated(annotation.autoCalculated);
- }
- if (annotation.hasScore())
- {
- an.setScore(annotation.getScore());
- }
-
- if (annotation.getCalcId() != null)
- {
- calcIdSet.add(annotation.getCalcId());
- an.setCalcId(annotation.getCalcId());
- }
- if (annotation.hasProperties())
- {
- for (String pr : annotation.getProperties())
- {
- jalview.xml.binding.jalview.Annotation.Property prop = new jalview.xml.binding.jalview.Annotation.Property();
- prop.setName(pr);
- prop.setValue(annotation.getProperty(pr));
- // an.addProperty(prop);
- an.getProperty().add(prop);
- }
- }
-
- AnnotationElement ae;
- if (annotation.annotations != null)
- {
- an.setScoreOnly(false);
- for (int a = 0; a < annotation.annotations.length; a++)
- {
- if ((annotation == null) || (annotation.annotations[a] == null))
- {
- continue;
- }
-
- ae = new AnnotationElement();
- if (annotation.annotations[a].description != null)
- {
- ae.setDescription(annotation.annotations[a].description);
- }
- if (annotation.annotations[a].displayCharacter != null)
- {
- ae.setDisplayCharacter(
- annotation.annotations[a].displayCharacter);
- }
-
- if (!Float.isNaN(annotation.annotations[a].value))
- {
- ae.setValue(annotation.annotations[a].value);
- }
-
- ae.setPosition(a);
- if (annotation.annotations[a].secondaryStructure > ' ')
- {
- ae.setSecondaryStructure(
- annotation.annotations[a].secondaryStructure + "");
- }
-
- if (annotation.annotations[a].colour != null
- && annotation.annotations[a].colour != java.awt.Color.black)
- {
- ae.setColour(annotation.annotations[a].colour.getRGB());
- }
-
- // an.addAnnotationElement(ae);
- an.getAnnotationElement().add(ae);
- if (annotation.autoCalculated)
- {
- // only write one non-null entry into the annotation row -
- // sufficient to get the visualization attributes necessary to
- // display data
- continue;
- }
- }
- }
- else
- {
- an.setScoreOnly(true);
- }
- if (!storeDS || (storeDS && !annotation.autoCalculated))
- {
- // skip autocalculated annotation - these are only provided for
- // alignments
- // vamsasSet.addAnnotation(an);
- vamsasSet.getAnnotation().add(an);
- }
- }
-
- }
-
- private CalcIdParam createCalcIdParam(String calcId, AlignViewport av)
- {
- AutoCalcSetting settings = av.getCalcIdSettingsFor(calcId);
- if (settings != null)
- {
- CalcIdParam vCalcIdParam = new CalcIdParam();
- vCalcIdParam.setCalcId(calcId);
- // vCalcIdParam.addServiceURL(settings.getServiceURI());
- vCalcIdParam.getServiceURL().add(settings.getServiceURI());
- // generic URI allowing a third party to resolve another instance of the
- // service used for this calculation
- for (String url : settings.getServiceURLs())
- {
- // vCalcIdParam.addServiceURL(urls);
- vCalcIdParam.getServiceURL().add(url);
- }
- vCalcIdParam.setVersion("1.0");
- if (settings.getPreset() != null)
- {
- WsParamSetI setting = settings.getPreset();
- vCalcIdParam.setName(setting.getName());
- vCalcIdParam.setDescription(setting.getDescription());
- }
- else
- {
- vCalcIdParam.setName("");
- vCalcIdParam.setDescription("Last used parameters");
- }
- // need to be able to recover 1) settings 2) user-defined presets or
- // recreate settings from preset 3) predefined settings provided by
- // service - or settings that can be transferred (or discarded)
- vCalcIdParam.setParameters(
- settings.getWsParamFile().replace("\n", "|\\n|"));
- vCalcIdParam.setAutoUpdate(settings.isAutoUpdate());
- // todo - decide if updateImmediately is needed for any projects.
-
- return vCalcIdParam;
- }
- return null;
- }
-
- private boolean recoverCalcIdParam(CalcIdParam calcIdParam,
- AlignViewport av)
- {
- if (calcIdParam.getVersion().equals("1.0"))
- {
- final String[] calcIds = calcIdParam.getServiceURL().toArray(new String[0]);
- Jws2Instance service = Jws2Discoverer.getDiscoverer()
- .getPreferredServiceFor(calcIds);
- if (service != null)
- {
- WsParamSetI parmSet = null;
- try
- {
- parmSet = service.getParamStore().parseServiceParameterFile(
- calcIdParam.getName(), calcIdParam.getDescription(),
- calcIds,
- calcIdParam.getParameters().replace("|\\n|", "\n"));
- } catch (IOException x)
- {
- warn("Couldn't parse parameter data for "
- + calcIdParam.getCalcId(), x);
- return false;
- }
- List<ArgumentI> argList = null;
- if (calcIdParam.getName().length() > 0)
- {
- parmSet = service.getParamStore()
- .getPreset(calcIdParam.getName());
- if (parmSet != null)
- {
- // TODO : check we have a good match with settings in AACon -
- // otherwise we'll need to create a new preset
- }
- }
- else
- {
- argList = parmSet.getArguments();
- parmSet = null;
- }
- AAConSettings settings = new AAConSettings(
- calcIdParam.isAutoUpdate(), service, parmSet, argList);
- av.setCalcIdSettingsFor(calcIdParam.getCalcId(), settings,
- calcIdParam.isNeedsUpdate());
- return true;
- }
- else
- {
- warn("Cannot resolve a service for the parameters used in this project. Try configuring a JABAWS server.");
- return false;
- }
- }
- throw new Error(MessageManager.formatMessage(
- "error.unsupported_version_calcIdparam", new Object[]
- { calcIdParam.toString() }));
- }
-
- /**
- * External mapping between jalview objects and objects yielding a valid and
- * unique object ID string. This is null for normal Jalview project IO, but
- * non-null when a jalview project is being read or written as part of a
- * vamsas session.
- */
- IdentityHashMap jv2vobj = null;
-
- /**
- * Construct a unique ID for jvobj using either existing bindings or if none
- * exist, the result of the hashcode call for the object.
- *
- * @param jvobj
- * jalview data object
- * @return unique ID for referring to jvobj
- */
- private String makeHashCode(Object jvobj, String altCode)
- {
- if (jv2vobj != null)
- {
- Object id = jv2vobj.get(jvobj);
- if (id != null)
- {
- return id.toString();
- }
- // check string ID mappings
- if (jvids2vobj != null && jvobj instanceof String)
- {
- id = jvids2vobj.get(jvobj);
- }
- if (id != null)
- {
- return id.toString();
- }
- // give up and warn that something has gone wrong
- warn("Cannot find ID for object in external mapping : " + jvobj);
- }
- return altCode;
- }
-
- /**
- * return local jalview object mapped to ID, if it exists
- *
- * @param idcode
- * (may be null)
- * @return null or object bound to idcode
- */
- private Object retrieveExistingObj(String idcode)
- {
- if (idcode != null && vobj2jv != null)
- {
- return vobj2jv.get(idcode);
- }
- return null;
- }
-
- /**
- * binding from ID strings from external mapping table to jalview data model
- * objects.
- */
- private Hashtable vobj2jv;
-
- private Sequence createVamsasSequence(String id, SequenceI jds)
- {
- return createVamsasSequence(true, id, jds, null);
- }
-
- private Sequence createVamsasSequence(boolean recurse, String id,
- SequenceI jds, SequenceI parentseq)
- {
- Sequence vamsasSeq = new Sequence();
- vamsasSeq.setId(id);
- vamsasSeq.setName(jds.getName());
- vamsasSeq.setSequence(jds.getSequenceAsString());
- vamsasSeq.setDescription(jds.getDescription());
- jalview.datamodel.DBRefEntry[] dbrefs = null;
- if (jds.getDatasetSequence() != null)
- {
- vamsasSeq.setDsseqid(seqHash(jds.getDatasetSequence()));
- }
- else
- {
- // seqId==dsseqid so we can tell which sequences really are
- // dataset sequences only
- vamsasSeq.setDsseqid(id);
- dbrefs = jds.getDBRefs();
- if (parentseq == null)
- {
- parentseq = jds;
- }
- }
- if (dbrefs != null)
- {
- for (int d = 0; d < dbrefs.length; d++)
- {
- DBRef dbref = new DBRef();
- dbref.setSource(dbrefs[d].getSource());
- dbref.setVersion(dbrefs[d].getVersion());
- dbref.setAccessionId(dbrefs[d].getAccessionId());
- if (dbrefs[d].hasMap())
- {
- Mapping mp = createVamsasMapping(dbrefs[d].getMap(), parentseq,
- jds, recurse);
- dbref.setMapping(mp);
- }
- // vamsasSeq.addDBRef(dbref);
- vamsasSeq.getDBRef().add(dbref);
- }
- }
- return vamsasSeq;
- }
-
- private Mapping createVamsasMapping(jalview.datamodel.Mapping jmp,
- SequenceI parentseq, SequenceI jds, boolean recurse)
- {
- Mapping mp = null;
- if (jmp.getMap() != null)
- {
- mp = new Mapping();
-
- jalview.util.MapList mlst = jmp.getMap();
- List<int[]> r = mlst.getFromRanges();
- for (int[] range : r)
- {
- MapListFrom mfrom = new MapListFrom();
- mfrom.setStart(range[0]);
- mfrom.setEnd(range[1]);
- // mp.addMapListFrom(mfrom);
- mp.getMapListFrom().add(mfrom);
- }
- r = mlst.getToRanges();
- for (int[] range : r)
- {
- MapListTo mto = new MapListTo();
- mto.setStart(range[0]);
- mto.setEnd(range[1]);
- // mp.addMapListTo(mto);
- mp.getMapListTo().add(mto);
- }
- mp.setMapFromUnit(BigInteger.valueOf(mlst.getFromRatio()));
- mp.setMapToUnit(BigInteger.valueOf(mlst.getToRatio()));
- if (jmp.getTo() != null)
- {
- // MappingChoice mpc = new MappingChoice();
-
- // check/create ID for the sequence referenced by getTo()
-
- String jmpid = "";
- SequenceI ps = null;
- if (parentseq != jmp.getTo()
- && parentseq.getDatasetSequence() != jmp.getTo())
- {
- // chaining dbref rather than a handshaking one
- jmpid = seqHash(ps = jmp.getTo());
- }
- else
- {
- jmpid = seqHash(ps = parentseq);
- }
- // mpc.setDseqFor(jmpid);
- mp.setDseqFor(jmpid);
- if (!seqRefIds.containsKey(jmpid))
- {
- jalview.bin.Cache.log.debug("creatign new DseqFor ID");
- seqRefIds.put(jmpid, ps);
- }
- else
- {
- jalview.bin.Cache.log.debug("reusing DseqFor ID");
- }
-
- // mp.setMappingChoice(mpc);
- }
- }
- return mp;
- }
-
- String setUserColourScheme(jalview.schemes.ColourSchemeI cs,
- List<UserColourScheme> userColours, JalviewModel jm)
- {
- String id = null;
- jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;
- boolean newucs = false;
- if (!userColours.contains(ucs))
- {
- userColours.add(ucs);
- newucs = true;
- }
- id = "ucs" + userColours.indexOf(ucs);
- if (newucs)
- {
- // actually create the scheme's entry in the XML model
- java.awt.Color[] colours = ucs.getColours();
- UserColours uc = new UserColours();
- // UserColourScheme jbucs = new UserColourScheme();
- JalviewUserColours jbucs = new JalviewUserColours();
-
- for (int i = 0; i < colours.length; i++)
- {
- Colour col = new Colour();
- col.setName(ResidueProperties.aa[i]);
- col.setRGB(jalview.util.Format.getHexString(colours[i]));
- // jbucs.addColour(col);
- jbucs.getColour().add(col);
- }
- if (ucs.getLowerCaseColours() != null)
- {
- colours = ucs.getLowerCaseColours();
- for (int i = 0; i < colours.length; i++)
- {
- Colour col = new Colour();
- col.setName(ResidueProperties.aa[i].toLowerCase());
- col.setRGB(jalview.util.Format.getHexString(colours[i]));
- // jbucs.addColour(col);
- jbucs.getColour().add(col);
- }
- }
-
- uc.setId(id);
- uc.setUserColourScheme(jbucs);
- // jm.addUserColours(uc);
- jm.getUserColours().add(uc);
- }
-
- return id;
- }
-
- jalview.schemes.UserColourScheme getUserColourScheme(
- JalviewModel jm, String id)
- {
- List<UserColours> uc = jm.getUserColours();
- UserColours colours = null;
-/*
- for (int i = 0; i < uc.length; i++)
- {
- if (uc[i].getId().equals(id))
- {
- colours = uc[i];
- break;
- }
- }
-*/
- for (UserColours c : uc)
- {
- if (c.getId().equals(id))
- {
- colours = c;
- break;
- }
- }
-
- java.awt.Color[] newColours = new java.awt.Color[24];
-
- for (int i = 0; i < 24; i++)
- {
- newColours[i] = new java.awt.Color(Integer.parseInt(
- // colours.getUserColourScheme().getColour(i).getRGB(), 16));
- colours.getUserColourScheme().getColour().get(i).getRGB(),
- 16));
- }
-
- jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
- newColours);
-
- if (colours.getUserColourScheme().getColour().size()/*Count()*/ > 24)
- {
- newColours = new java.awt.Color[23];
- for (int i = 0; i < 23; i++)
- {
- newColours[i] = new java.awt.Color(Integer.parseInt(
- colours.getUserColourScheme().getColour().get(i + 24)
- .getRGB(),
- 16));
- }
- ucs.setLowerCaseColours(newColours);
- }
-
- return ucs;
- }
-
- /**
- * contains last error message (if any) encountered by XML loader.
- */
- String errorMessage = null;
-
- /**
- * flag to control whether the Jalview2XML_V1 parser should be deferred to if
- * exceptions are raised during project XML parsing
- */
- public boolean attemptversion1parse = false;
-
- /**
- * Load a jalview project archive from a jar file
- *
- * @param file
- * - HTTP URL or filename
- */
- public AlignFrame loadJalviewAlign(final String file)
- {
-
- jalview.gui.AlignFrame af = null;
-
- try
- {
- // create list to store references for any new Jmol viewers created
- newStructureViewers = new Vector<>();
- // UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
- // Workaround is to make sure caller implements the JarInputStreamProvider
- // interface
- // so we can re-open the jar input stream for each entry.
-
- jarInputStreamProvider jprovider = createjarInputStreamProvider(file);
- af = loadJalviewAlign(jprovider);
- if (af != null)
- {
- af.setMenusForViewport();
- }
- } catch (MalformedURLException e)
- {
- errorMessage = "Invalid URL format for '" + file + "'";
- reportErrors();
- } finally
- {
- try
- {
- SwingUtilities.invokeAndWait(new Runnable()
- {
- @Override
- public void run()
- {
- setLoadingFinishedForNewStructureViewers();
- };
- });
- } catch (Exception x)
- {
- System.err.println("Error loading alignment: " + x.getMessage());
- }
- }
- return af;
- }
-
- private jarInputStreamProvider createjarInputStreamProvider(
- final String file) throws MalformedURLException
- {
- URL url = null;
- errorMessage = null;
- uniqueSetSuffix = null;
- seqRefIds = null;
- viewportsAdded.clear();
- frefedSequence = null;
-
- if (file.startsWith("http://"))
- {
- url = new URL(file);
- }
- final URL _url = url;
- return new jarInputStreamProvider()
- {
-
- @Override
- public JarInputStream getJarInputStream() throws IOException
- {
- if (_url != null)
- {
- return new JarInputStream(_url.openStream());
- }
- else
- {
- return new JarInputStream(new FileInputStream(file));
- }
- }
-
- @Override
- public String getFilename()
- {
- return file;
- }
- };
- }
-
- /**
- * Recover jalview session from a jalview project archive. Caller may
- * initialise uniqueSetSuffix, seqRefIds, viewportsAdded and frefedSequence
- * themselves. Any null fields will be initialised with default values,
- * non-null fields are left alone.
- *
- * @param jprovider
- * @return
- */
- public AlignFrame loadJalviewAlign(final jarInputStreamProvider jprovider)
- {
- errorMessage = null;
- if (uniqueSetSuffix == null)
- {
- uniqueSetSuffix = System.currentTimeMillis() % 100000 + "";
- }
- if (seqRefIds == null)
- {
- initSeqRefs();
- }
- AlignFrame af = null, _af = null;
- IdentityHashMap<AlignmentI, AlignmentI> importedDatasets = new IdentityHashMap<>();
- Map<String, AlignFrame> gatherToThisFrame = new HashMap<>();
- final String file = jprovider.getFilename();
- try
- {
- JarInputStream jin = null;
- JarEntry jarentry = null;
- int entryCount = 1;
-
- do
- {
- jin = jprovider.getJarInputStream();
- for (int i = 0; i < entryCount; i++)
- {
- jarentry = jin.getNextJarEntry();
- }
-
- if (jarentry != null && jarentry.getName().endsWith(".xml"))
- {
- InputStreamReader in = new InputStreamReader(jin, UTF_8);
- // JalviewModel object = new JalviewModel();
-
- JAXBContext jc = JAXBContext
- .newInstance("jalview.xml.binding.jalview");
- XMLStreamReader streamReader = XMLInputFactory.newInstance()
- .createXMLStreamReader(jin);
- javax.xml.bind.Unmarshaller um = jc.createUnmarshaller();
- JAXBElement<JalviewModel> jbe = um
- .unmarshal(streamReader, JalviewModel.class);
- JalviewModel object = jbe.getValue();
-
- /*
- Unmarshaller unmar = new Unmarshaller(object);
- unmar.setValidation(false);
- object = (JalviewModel) unmar.unmarshal(in);
- */
- if (true) // !skipViewport(object))
- {
- _af = loadFromObject(object, file, true, jprovider);
- if (_af != null && object.getViewport().size() > 0)
- // getJalviewModelSequence().getViewportCount() > 0)
- {
- if (af == null)
- {
- // store a reference to the first view
- af = _af;
- }
- if (_af.getViewport().isGatherViewsHere())
- {
- // if this is a gathered view, keep its reference since
- // after gathering views, only this frame will remain
- af = _af;
- gatherToThisFrame.put(_af.getViewport().getSequenceSetId(),
- _af);
- }
- // Save dataset to register mappings once all resolved
- importedDatasets.put(
- af.getViewport().getAlignment().getDataset(),
- af.getViewport().getAlignment().getDataset());
- }
- }
- entryCount++;
- }
- else if (jarentry != null)
- {
- // Some other file here.
- entryCount++;
- }
- } while (jarentry != null);
- resolveFrefedSequences();
- } catch (IOException ex)
- {
- ex.printStackTrace();
- errorMessage = "Couldn't locate Jalview XML file : " + file;
- System.err.println(
- "Exception whilst loading jalview XML file : " + ex + "\n");
- } catch (Exception ex)
- {
- System.err.println("Parsing as Jalview Version 2 file failed.");
- ex.printStackTrace(System.err);
- if (attemptversion1parse)
- {
- // Is Version 1 Jar file?
- try
- {
- af = new Jalview2XML_V1(raiseGUI).LoadJalviewAlign(jprovider);
- } catch (Exception ex2)
- {
- System.err.println("Exception whilst loading as jalviewXMLV1:");
- ex2.printStackTrace();
- af = null;
- }
- }
- if (Desktop.instance != null)
- {
- Desktop.instance.stopLoading();
- }
- if (af != null)
- {
- System.out.println("Successfully loaded archive file");
- return af;
- }
- ex.printStackTrace();
-
- System.err.println(
- "Exception whilst loading jalview XML file : " + ex + "\n");
- } catch (OutOfMemoryError e)
- {
- // Don't use the OOM Window here
- errorMessage = "Out of memory loading jalview XML file";
- System.err.println("Out of memory whilst loading jalview XML file");
- e.printStackTrace();
- }
-
- /*
- * Regather multiple views (with the same sequence set id) to the frame (if
- * any) that is flagged as the one to gather to, i.e. convert them to tabbed
- * views instead of separate frames. Note this doesn't restore a state where
- * some expanded views in turn have tabbed views - the last "first tab" read
- * in will play the role of gatherer for all.
- */
- for (AlignFrame fr : gatherToThisFrame.values())
- {
- Desktop.instance.gatherViews(fr);
- }
-
- restoreSplitFrames();
- for (AlignmentI ds : importedDatasets.keySet())
- {
- if (ds.getCodonFrames() != null)
- {
- StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance)
- .registerMappings(ds.getCodonFrames());
- }
- }
- if (errorMessage != null)
- {
- reportErrors();
- }
-
- if (Desktop.instance != null)
- {
- Desktop.instance.stopLoading();
- }
-
- return af;
- }
-
- /**
- * Try to reconstruct and display SplitFrame windows, where each contains
- * complementary dna and protein alignments. Done by pairing up AlignFrame
- * objects (created earlier) which have complementary viewport ids associated.
- */
- protected void restoreSplitFrames()
- {
- List<SplitFrame> gatherTo = new ArrayList<>();
- List<AlignFrame> addedToSplitFrames = new ArrayList<>();
- Map<String, AlignFrame> dna = new HashMap<>();
-
- /*
- * Identify the DNA alignments
- */
- for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
- .entrySet())
- {
- AlignFrame af = candidate.getValue();
- if (af.getViewport().getAlignment().isNucleotide())
- {
- dna.put(candidate.getKey().getId(), af);
- }
- }
-
- /*
- * Try to match up the protein complements
- */
- for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
- .entrySet())
- {
- AlignFrame af = candidate.getValue();
- if (!af.getViewport().getAlignment().isNucleotide())
- {
- String complementId = candidate.getKey().getComplementId();
- // only non-null complements should be in the Map
- if (complementId != null && dna.containsKey(complementId))
- {
- final AlignFrame dnaFrame = dna.get(complementId);
- SplitFrame sf = createSplitFrame(dnaFrame, af);
- addedToSplitFrames.add(dnaFrame);
- addedToSplitFrames.add(af);
- dnaFrame.setMenusForViewport();
- af.setMenusForViewport();
- if (af.getViewport().isGatherViewsHere())
- {
- gatherTo.add(sf);
- }
- }
- }
- }
-
- /*
- * Open any that we failed to pair up (which shouldn't happen!) as
- * standalone AlignFrame's.
- */
- for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
- .entrySet())
- {
- AlignFrame af = candidate.getValue();
- if (!addedToSplitFrames.contains(af))
- {
- Viewport view = candidate.getKey();
- Desktop.addInternalFrame(af, view.getTitle(),
- safeInt(view.getWidth()), safeInt(view.getHeight()));
- af.setMenusForViewport();
- System.err.println("Failed to restore view " + view.getTitle()
- + " to split frame");
- }
- }
-
- /*
- * Gather back into tabbed views as flagged.
- */
- for (SplitFrame sf : gatherTo)
- {
- Desktop.instance.gatherViews(sf);
- }
-
- splitFrameCandidates.clear();
- }
-
- /**
- * Construct and display one SplitFrame holding DNA and protein alignments.
- *
- * @param dnaFrame
- * @param proteinFrame
- * @return
- */
- protected SplitFrame createSplitFrame(AlignFrame dnaFrame,
- AlignFrame proteinFrame)
- {
- SplitFrame splitFrame = new SplitFrame(dnaFrame, proteinFrame);
- String title = MessageManager.getString("label.linked_view_title");
- int width = (int) dnaFrame.getBounds().getWidth();
- int height = (int) (dnaFrame.getBounds().getHeight()
- + proteinFrame.getBounds().getHeight() + 50);
-
- /*
- * SplitFrame location is saved to both enclosed frames
- */
- splitFrame.setLocation(dnaFrame.getX(), dnaFrame.getY());
- Desktop.addInternalFrame(splitFrame, title, width, height);
-
- /*
- * And compute cDNA consensus (couldn't do earlier with consensus as
- * mappings were not yet present)
- */
- proteinFrame.getViewport().alignmentChanged(proteinFrame.alignPanel);
-
- return splitFrame;
- }
-
- /**
- * check errorMessage for a valid error message and raise an error box in the
- * GUI or write the current errorMessage to stderr and then clear the error
- * state.
- */
- protected void reportErrors()
- {
- reportErrors(false);
- }
-
- protected void reportErrors(final boolean saving)
- {
- if (errorMessage != null)
- {
- final String finalErrorMessage = errorMessage;
- if (raiseGUI)
- {
- javax.swing.SwingUtilities.invokeLater(new Runnable()
- {
- @Override
- public void run()
- {
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
- finalErrorMessage,
- "Error " + (saving ? "saving" : "loading")
- + " Jalview file",
- JvOptionPane.WARNING_MESSAGE);
- }
- });
- }
- else
- {
- System.err.println("Problem loading Jalview file: " + errorMessage);
- }
- }
- errorMessage = null;
- }
-
- Map<String, String> alreadyLoadedPDB = new HashMap<>();
-
- /**
- * when set, local views will be updated from view stored in JalviewXML
- * Currently (28th Sep 2008) things will go horribly wrong in vamsas document
- * sync if this is set to true.
- */
- private final boolean updateLocalViews = false;
-
- /**
- * Returns the path to a temporary file holding the PDB file for the given PDB
- * id. The first time of asking, searches for a file of that name in the
- * Jalview project jar, and copies it to a new temporary file. Any repeat
- * requests just return the path to the file previously created.
- *
- * @param jprovider
- * @param pdbId
- * @return
- */
- String loadPDBFile(jarInputStreamProvider jprovider, String pdbId,
- String origFile)
- {
- if (alreadyLoadedPDB.containsKey(pdbId))
- {
- return alreadyLoadedPDB.get(pdbId).toString();
- }
-
- String tempFile = copyJarEntry(jprovider, pdbId, "jalview_pdb",
- origFile);
- if (tempFile != null)
- {
- alreadyLoadedPDB.put(pdbId, tempFile);
- }
- return tempFile;
- }
-
- /**
- * Copies the jar entry of given name to a new temporary file and returns the
- * path to the file, or null if the entry is not found.
- *
- * @param jprovider
- * @param jarEntryName
- * @param prefix
- * a prefix for the temporary file name, must be at least three
- * characters long
- * @param origFile
- * null or original file - so new file can be given the same suffix
- * as the old one
- * @return
- */
- protected String copyJarEntry(jarInputStreamProvider jprovider,
- String jarEntryName, String prefix, String origFile)
- {
- BufferedReader in = null;
- PrintWriter out = null;
- String suffix = ".tmp";
- if (origFile == null)
- {
- origFile = jarEntryName;
- }
- int sfpos = origFile.lastIndexOf(".");
- if (sfpos > -1 && sfpos < (origFile.length() - 3))
- {
- suffix = "." + origFile.substring(sfpos + 1);
- }
- try
- {
- JarInputStream jin = jprovider.getJarInputStream();
- /*
- * if (jprovider.startsWith("http://")) { jin = new JarInputStream(new
- * URL(jprovider).openStream()); } else { jin = new JarInputStream(new
- * FileInputStream(jprovider)); }
- */
-
- JarEntry entry = null;
- do
- {
- entry = jin.getNextJarEntry();
- } while (entry != null && !entry.getName().equals(jarEntryName));
- if (entry != null)
- {
- in = new BufferedReader(new InputStreamReader(jin, UTF_8));
- File outFile = File.createTempFile(prefix, suffix);
- outFile.deleteOnExit();
- out = new PrintWriter(new FileOutputStream(outFile));
- String data;
-
- while ((data = in.readLine()) != null)
- {
- out.println(data);
- }
- out.flush();
- String t = outFile.getAbsolutePath();
- return t;
- }
- else
- {
- warn("Couldn't find entry in Jalview Jar for " + jarEntryName);
- }
- } catch (Exception ex)
- {
- ex.printStackTrace();
- } finally
- {
- if (in != null)
- {
- try
- {
- in.close();
- } catch (IOException e)
- {
- // ignore
- }
- }
- if (out != null)
- {
- out.close();
- }
- }
-
- return null;
- }
-
- private class JvAnnotRow
- {
- public JvAnnotRow(int i, AlignmentAnnotation jaa)
- {
- order = i;
- template = jaa;
- }
-
- /**
- * persisted version of annotation row from which to take vis properties
- */
- public jalview.datamodel.AlignmentAnnotation template;
-
- /**
- * original position of the annotation row in the alignment
- */
- public int order;
- }
-
- /**
- * Load alignment frame from jalview XML DOM object
- *
- * @param jalviewModel
- * DOM
- * @param file
- * filename source string
- * @param loadTreesAndStructures
- * when false only create Viewport
- * @param jprovider
- * data source provider
- * @return alignment frame created from view stored in DOM
- */
- AlignFrame loadFromObject(JalviewModel jalviewModel, String file,
- boolean loadTreesAndStructures, jarInputStreamProvider jprovider)
- {
- SequenceSet vamsasSet = jalviewModel.getVamsasModel().getSequenceSet().get(0);
- List<Sequence> vamsasSeqs = vamsasSet.getSequence();
-
- // JalviewModelSequence jms = object.getJalviewModelSequence();
-
- // Viewport view = (jms.getViewportCount() > 0) ? jms.getViewport(0)
- // : null;
- Viewport view = (jalviewModel.getViewport().size() > 0)
- ? jalviewModel.getViewport().get(0)
- : null;
-
- // ////////////////////////////////
- // LOAD SEQUENCES
-
- List<SequenceI> hiddenSeqs = null;
-
- List<SequenceI> tmpseqs = new ArrayList<>();
-
- boolean multipleView = false;
- SequenceI referenceseqForView = null;
- // JSeq[] jseqs = object.getJalviewModelSequence().getJSeq();
- List<JSeq> jseqs = jalviewModel.getJSeq();
- int vi = 0; // counter in vamsasSeq array
- for (int i = 0; i < jseqs.size(); i++)
- {
- JSeq jseq = jseqs.get(i);
- String seqId = jseq.getId();
-
- SequenceI tmpSeq = seqRefIds.get(seqId);
- if (tmpSeq != null)
- {
- if (!incompleteSeqs.containsKey(seqId))
- {
- // may not need this check, but keep it for at least 2.9,1 release
- if (tmpSeq.getStart() != jseq.getStart()
- || tmpSeq.getEnd() != jseq.getEnd())
- {
- System.err.println(
- "Warning JAL-2154 regression: updating start/end for sequence "
- + tmpSeq.toString() + " to " + jseq);
- }
- }
- else
- {
- incompleteSeqs.remove(seqId);
- }
- if (vamsasSeqs.size() > vi
- && vamsasSeqs.get(vi).getId().equals(seqId))
- {
- // most likely we are reading a dataset XML document so
- // update from vamsasSeq section of XML for this sequence
- tmpSeq.setName(vamsasSeqs.get(vi).getName());
- tmpSeq.setDescription(vamsasSeqs.get(vi).getDescription());
- tmpSeq.setSequence(vamsasSeqs.get(vi).getSequence());
- vi++;
- }
- else
- {
- // reading multiple views, so vamsasSeq set is a subset of JSeq
- multipleView = true;
- }
- tmpSeq.setStart(jseq.getStart());
- tmpSeq.setEnd(jseq.getEnd());
- tmpseqs.add(tmpSeq);
- }
- else
- {
- Sequence vamsasSeq = vamsasSeqs.get(vi);
- tmpSeq = new jalview.datamodel.Sequence(vamsasSeq.getName(),
- vamsasSeq.getSequence());
- tmpSeq.setDescription(vamsasSeq.getDescription());
- tmpSeq.setStart(jseq.getStart());
- tmpSeq.setEnd(jseq.getEnd());
- tmpSeq.setVamsasId(uniqueSetSuffix + seqId);
- seqRefIds.put(vamsasSeq.getId(), tmpSeq);
- tmpseqs.add(tmpSeq);
- vi++;
- }
-
- if (safeBoolean(jseq.isViewreference()))
- {
- referenceseqForView = tmpseqs.get(tmpseqs.size() - 1);
- }
-
- if (jseq.isHidden() != null && jseq.isHidden().booleanValue())
- {
- if (hiddenSeqs == null)
- {
- hiddenSeqs = new ArrayList<>();
- }
-
- hiddenSeqs.add(tmpSeq);
- }
- }
-
- // /
- // Create the alignment object from the sequence set
- // ///////////////////////////////
- SequenceI[] orderedSeqs = tmpseqs
- .toArray(new SequenceI[tmpseqs.size()]);
-
- AlignmentI al = null;
- // so we must create or recover the dataset alignment before going further
- // ///////////////////////////////
- if (vamsasSet.getDatasetId() == null || vamsasSet.getDatasetId() == "")
- {
- // older jalview projects do not have a dataset - so creat alignment and
- // dataset
- al = new Alignment(orderedSeqs);
- al.setDataset(null);
- }
- else
- {
- boolean isdsal = jalviewModel.getViewport().isEmpty();
- if (isdsal)
- {
- // we are importing a dataset record, so
- // recover reference to an alignment already materialsed as dataset
- al = getDatasetFor(vamsasSet.getDatasetId());
- }
- if (al == null)
- {
- // materialse the alignment
- al = new Alignment(orderedSeqs);
- }
- if (isdsal)
- {
- addDatasetRef(vamsasSet.getDatasetId(), al);
- }
-
- // finally, verify all data in vamsasSet is actually present in al
- // passing on flag indicating if it is actually a stored dataset
- recoverDatasetFor(vamsasSet, al, isdsal);
- }
-
- if (referenceseqForView != null)
- {
- al.setSeqrep(referenceseqForView);
- }
- // / Add the alignment properties
- for (int i = 0; i < vamsasSet.getSequenceSetProperties().size(); i++)
- {
- SequenceSetProperties ssp = vamsasSet.getSequenceSetProperties()
- .get(i);
- al.setProperty(ssp.getKey(), ssp.getValue());
- }
-
- // ///////////////////////////////
-
- Hashtable pdbloaded = new Hashtable(); // TODO nothing writes to this??
- if (!multipleView)
- {
- // load sequence features, database references and any associated PDB
- // structures for the alignment
- //
- // prior to 2.10, this part would only be executed the first time a
- // sequence was encountered, but not afterwards.
- // now, for 2.10 projects, this is also done if the xml doc includes
- // dataset sequences not actually present in any particular view.
- //
- for (int i = 0; i < vamsasSeqs.size(); i++)
- {
- JSeq jseq = jseqs.get(i);
- if (jseq.getFeatures().size() > 0)
- {
- List<Feature> features = jseq.getFeatures();
- for (int f = 0; f < features.size(); f++)
- {
- Feature feat = features.get(f);
- SequenceFeature sf = new SequenceFeature(feat.getType(),
- feat.getDescription(), feat.getBegin(), feat.getEnd(),
- safeFloat(feat.getScore()), feat.getFeatureGroup());
- sf.setStatus(feat.getStatus());
-
- /*
- * load any feature attributes - include map-valued attributes
- */
- Map<String, Map<String, String>> mapAttributes = new HashMap<>();
- for (int od = 0; od < feat.getOtherData().size(); od++)
- {
- OtherData keyValue = feat.getOtherData().get(od);
- String attributeName = keyValue.getKey();
- String attributeValue = keyValue.getValue();
- if (attributeName.startsWith("LINK"))
- {
- sf.addLink(attributeValue);
- }
- else
- {
- String subAttribute = keyValue.getKey2();
- if (subAttribute == null)
- {
- // simple string-valued attribute
- sf.setValue(attributeName, attributeValue);
- }
- else
- {
- // attribute 'key' has sub-attribute 'key2'
- if (!mapAttributes.containsKey(attributeName))
- {
- mapAttributes.put(attributeName, new HashMap<>());
- }
- mapAttributes.get(attributeName).put(subAttribute,
- attributeValue);
- }
- }
- }
- for (Entry<String, Map<String, String>> mapAttribute : mapAttributes
- .entrySet())
- {
- sf.setValue(mapAttribute.getKey(), mapAttribute.getValue());
- }
-
- // adds feature to datasequence's feature set (since Jalview 2.10)
- al.getSequenceAt(i).addSequenceFeature(sf);
- }
- }
- if (vamsasSeqs.get(i).getDBRef().size() > 0)
- {
- // adds dbrefs to datasequence's set (since Jalview 2.10)
- addDBRefs(
- al.getSequenceAt(i).getDatasetSequence() == null
- ? al.getSequenceAt(i)
- : al.getSequenceAt(i).getDatasetSequence(),
- vamsasSeqs.get(i));
- }
- if (jseq.getPdbids().size() > 0)
- {
- List<Pdbids> ids = jseq.getPdbids();
- for (int p = 0; p < ids.size(); p++)
- {
- Pdbids pdbid = ids.get(p);
- jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
- entry.setId(pdbid.getId());
- if (pdbid.getType() != null)
- {
- if (PDBEntry.Type.getType(pdbid.getType()) != null)
- {
- entry.setType(PDBEntry.Type.getType(pdbid.getType()));
- }
- else
- {
- entry.setType(PDBEntry.Type.FILE);
- }
- }
- // jprovider is null when executing 'New View'
- if (pdbid.getFile() != null && jprovider != null)
- {
- if (!pdbloaded.containsKey(pdbid.getFile()))
- {
- entry.setFile(loadPDBFile(jprovider, pdbid.getId(),
- pdbid.getFile()));
- }
- else
- {
- entry.setFile(pdbloaded.get(pdbid.getId()).toString());
- }
- }
- /*
- if (pdbid.getPdbentryItem() != null)
- {
- for (PdbentryItem item : pdbid.getPdbentryItem())
- {
- for (Property pr : item.getProperty())
- {
- entry.setProperty(pr.getName(), pr.getValue());
- }
- }
- }
- */
- for (Property prop : pdbid.getProperty())
- {
- entry.setProperty(prop.getName(), prop.getValue());
- }
- StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance)
- .registerPDBEntry(entry);
- // adds PDBEntry to datasequence's set (since Jalview 2.10)
- if (al.getSequenceAt(i).getDatasetSequence() != null)
- {
- al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
- }
- else
- {
- al.getSequenceAt(i).addPDBId(entry);
- }
- }
- }
- }
- } // end !multipleview
-
- // ///////////////////////////////
- // LOAD SEQUENCE MAPPINGS
-
- if (vamsasSet.getAlcodonFrame().size() > 0)
- {
- // TODO Potentially this should only be done once for all views of an
- // alignment
- List<AlcodonFrame> alc = vamsasSet.getAlcodonFrame();
- for (int i = 0; i < alc.size(); i++)
- {
- AlignedCodonFrame cf = new AlignedCodonFrame();
- if (alc.get(i).getAlcodMap().size() > 0)
- {
- List<AlcodMap> maps = alc.get(i).getAlcodMap();
- for (int m = 0; m < maps.size(); m++)
- {
- AlcodMap map = maps.get(m);
- SequenceI dnaseq = seqRefIds.get(map.getDnasq());
- // Load Mapping
- jalview.datamodel.Mapping mapping = null;
- // attach to dna sequence reference.
- if (map.getMapping() != null)
- {
- mapping = addMapping(map.getMapping());
- if (dnaseq != null && mapping.getTo() != null)
- {
- cf.addMap(dnaseq, mapping.getTo(), mapping.getMap());
- }
- else
- {
- // defer to later
- frefedSequence.add(
- newAlcodMapRef(map.getDnasq(), cf, mapping));
- }
- }
- }
- al.addCodonFrame(cf);
- }
- }
- }
-
- // ////////////////////////////////
- // LOAD ANNOTATIONS
- List<JvAnnotRow> autoAlan = new ArrayList<>();
-
- /*
- * store any annotations which forward reference a group's ID
- */
- Map<String, List<AlignmentAnnotation>> groupAnnotRefs = new Hashtable<>();
-
- if (vamsasSet.getAnnotation().size()/*Count()*/ > 0)
- {
- List<Annotation> an = vamsasSet.getAnnotation();
-
- for (int i = 0; i < an.size(); i++)
- {
- Annotation annotation = an.get(i);
-
- /**
- * test if annotation is automatically calculated for this view only
- */
- boolean autoForView = false;
- if (annotation.getLabel().equals("Quality")
- || annotation.getLabel().equals("Conservation")
- || annotation.getLabel().equals("Consensus"))
- {
- // Kludge for pre 2.5 projects which lacked the autocalculated flag
- autoForView = true;
- // JAXB has no has() test; schema defaults value to false
- // if (!annotation.hasAutoCalculated())
- // {
- // annotation.setAutoCalculated(true);
- // }
- }
- if (autoForView || annotation.isAutoCalculated())
- {
- // remove ID - we don't recover annotation from other views for
- // view-specific annotation
- annotation.setId(null);
- }
-
- // set visibility for other annotation in this view
- String annotationId = annotation.getId();
- if (annotationId != null && annotationIds.containsKey(annotationId))
- {
- AlignmentAnnotation jda = annotationIds.get(annotationId);
- // in principle Visible should always be true for annotation displayed
- // in multiple views
- if (annotation.isVisible() != null)
- {
- jda.visible = annotation.isVisible();
- }
-
- al.addAnnotation(jda);
-
- continue;
- }
- // Construct new annotation from model.
- List<AnnotationElement> ae = annotation.getAnnotationElement();
- jalview.datamodel.Annotation[] anot = null;
- java.awt.Color firstColour = null;
- int anpos;
- if (!annotation.isScoreOnly())
- {
- anot = new jalview.datamodel.Annotation[al.getWidth()];
- for (int aa = 0; aa < ae.size() && aa < anot.length; aa++)
- {
- AnnotationElement annElement = ae.get(aa);
- anpos = annElement.getPosition();
-
- if (anpos >= anot.length)
- {
- continue;
- }
-
- float value = safeFloat(annElement.getValue());
- anot[anpos] = new jalview.datamodel.Annotation(
- annElement.getDisplayCharacter(),
- annElement.getDescription(),
- (annElement.getSecondaryStructure() == null
- || annElement.getSecondaryStructure()
- .length() == 0)
- ? ' '
- : annElement
- .getSecondaryStructure()
- .charAt(0),
- value);
- anot[anpos].colour = new Color(safeInt(annElement.getColour()));
- if (firstColour == null)
- {
- firstColour = anot[anpos].colour;
- }
- }
- }
- jalview.datamodel.AlignmentAnnotation jaa = null;
-
- if (annotation.isGraph())
- {
- float llim = 0, hlim = 0;
- // if (autoForView || an[i].isAutoCalculated()) {
- // hlim=11f;
- // }
- jaa = new jalview.datamodel.AlignmentAnnotation(
- annotation.getLabel(), annotation.getDescription(), anot,
- llim, hlim, safeInt(annotation.getGraphType()));
-
- jaa.graphGroup = safeInt(annotation.getGraphGroup());
- jaa._linecolour = firstColour;
- if (annotation.getThresholdLine() != null)
- {
- jaa.setThreshold(new jalview.datamodel.GraphLine(
- safeFloat(annotation.getThresholdLine().getValue()),
- annotation.getThresholdLine().getLabel(),
- new java.awt.Color(safeInt(
- annotation.getThresholdLine().getColour()))));
- }
- if (autoForView || annotation.isAutoCalculated())
- {
- // Hardwire the symbol display line to ensure that labels for
- // histograms are displayed
- jaa.hasText = true;
- }
- }
- else
- {
- jaa = new jalview.datamodel.AlignmentAnnotation(
- annotation.getLabel(), annotation.getDescription(), anot);
- jaa._linecolour = firstColour;
- }
- // register new annotation
- if (annotation.getId() != null)
- {
- annotationIds.put(annotation.getId(), jaa);
- jaa.annotationId = annotation.getId();
- }
- // recover sequence association
- String sequenceRef = annotation.getSequenceRef();
- if (sequenceRef != null)
- {
- // from 2.9 sequenceRef is to sequence id (JAL-1781)
- SequenceI sequence = seqRefIds.get(sequenceRef);
- if (sequence == null)
- {
- // in pre-2.9 projects sequence ref is to sequence name
- sequence = al.findName(sequenceRef);
- }
- if (sequence != null)
- {
- jaa.createSequenceMapping(sequence, 1, true);
- sequence.addAlignmentAnnotation(jaa);
- }
- }
- // and make a note of any group association
- if (annotation.getGroupRef() != null
- && annotation.getGroupRef().length() > 0)
- {
- List<jalview.datamodel.AlignmentAnnotation> aal = groupAnnotRefs
- .get(annotation.getGroupRef());
- if (aal == null)
- {
- aal = new ArrayList<>();
- groupAnnotRefs.put(annotation.getGroupRef(), aal);
- }
- aal.add(jaa);
- }
-
- if (annotation.getScore() != null)
- {
- jaa.setScore(annotation.getScore().doubleValue());
- }
- if (annotation.isVisible() != null)
- {
- jaa.visible = annotation.isVisible().booleanValue();
- }
-
- if (annotation.isCentreColLabels() != null)
- {
- jaa.centreColLabels = annotation.isCentreColLabels()
- .booleanValue();
- }
-
- if (annotation.isScaleColLabels() != null)
- {
- jaa.scaleColLabel = annotation.isScaleColLabels().booleanValue();
- }
- if (annotation.isAutoCalculated())
- {
- // newer files have an 'autoCalculated' flag and store calculation
- // state in viewport properties
- jaa.autoCalculated = true; // means annotation will be marked for
- // update at end of load.
- }
- if (annotation.getGraphHeight() != null)
- {
- jaa.graphHeight = annotation.getGraphHeight().intValue();
- }
- jaa.belowAlignment = annotation.isBelowAlignment();
- jaa.setCalcId(annotation.getCalcId());
- if (annotation.getProperty().size() > 0)
- {
- for (Annotation.Property prop : annotation
- .getProperty())
- {
- jaa.setProperty(prop.getName(), prop.getValue());
- }
- }
- if (jaa.autoCalculated)
- {
- autoAlan.add(new JvAnnotRow(i, jaa));
- }
- else
- // if (!autoForView)
- {
- // add autocalculated group annotation and any user created annotation
- // for the view
- al.addAnnotation(jaa);
- }
- }
- }
- // ///////////////////////
- // LOAD GROUPS
- // Create alignment markup and styles for this view
- if (jalviewModel.getJGroup().size() > 0)
- {
- List<JGroup> groups = jalviewModel.getJGroup();
- boolean addAnnotSchemeGroup = false;
- for (int i = 0; i < groups.size(); i++)
- {
- JGroup jGroup = groups.get(i);
- ColourSchemeI cs = null;
- if (jGroup.getColour() != null)
- {
- if (jGroup.getColour().startsWith("ucs"))
- {
- cs = getUserColourScheme(jalviewModel, jGroup.getColour());
- }
- else if (jGroup.getColour().equals("AnnotationColourGradient")
- && jGroup.getAnnotationColours() != null)
- {
- addAnnotSchemeGroup = true;
- }
- else
- {
- cs = ColourSchemeProperty.getColourScheme(al,
- jGroup.getColour());
- }
- }
- int pidThreshold = safeInt(jGroup.getPidThreshold());
-
- Vector<SequenceI> seqs = new Vector<>();
-
- for (int s = 0; s < jGroup.getSeq().size(); s++)
- {
- String seqId = jGroup.getSeq().get(s);
- SequenceI ts = seqRefIds.get(seqId);
-
- if (ts != null)
- {
- seqs.addElement(ts);
- }
- }
-
- if (seqs.size() < 1)
- {
- continue;
- }
-
- SequenceGroup sg = new SequenceGroup(seqs, jGroup.getName(), cs,
- safeBoolean(jGroup.isDisplayBoxes()),
- safeBoolean(jGroup.isDisplayText()),
- safeBoolean(jGroup.isColourText()),
- safeInt(jGroup.getStart()), safeInt(jGroup.getEnd()));
- sg.getGroupColourScheme().setThreshold(pidThreshold, true);
- sg.getGroupColourScheme()
- .setConservationInc(safeInt(jGroup.getConsThreshold()));
- sg.setOutlineColour(new Color(safeInt(jGroup.getOutlineColour())));
-
- sg.textColour = new Color(safeInt(jGroup.getTextCol1()));
- sg.textColour2 = new Color(safeInt(jGroup.getTextCol2()));
- sg.setShowNonconserved(safeBoolean(jGroup.isShowUnconserved()));
- sg.thresholdTextColour = safeInt(jGroup.getTextColThreshold());
- // attributes with a default in the schema are never null
- sg.setShowConsensusHistogram(jGroup.isShowConsensusHistogram());
- sg.setshowSequenceLogo(jGroup.isShowSequenceLogo());
- sg.setNormaliseSequenceLogo(jGroup.isNormaliseSequenceLogo());
- sg.setIgnoreGapsConsensus(jGroup.isIgnoreGapsinConsensus());
- if (jGroup.getConsThreshold() != null
- && jGroup.getConsThreshold().intValue() != 0)
- {
- Conservation c = new Conservation("All", sg.getSequences(null), 0,
- sg.getWidth() - 1);
- c.calculate();
- c.verdict(false, 25);
- sg.cs.setConservation(c);
- }
-
- if (jGroup.getId() != null && groupAnnotRefs.size() > 0)
- {
- // re-instate unique group/annotation row reference
- List<AlignmentAnnotation> jaal = groupAnnotRefs
- .get(jGroup.getId());
- if (jaal != null)
- {
- for (AlignmentAnnotation jaa : jaal)
- {
- jaa.groupRef = sg;
- if (jaa.autoCalculated)
- {
- // match up and try to set group autocalc alignment row for this
- // annotation
- if (jaa.label.startsWith("Consensus for "))
- {
- sg.setConsensus(jaa);
- }
- // match up and try to set group autocalc alignment row for this
- // annotation
- if (jaa.label.startsWith("Conservation for "))
- {
- sg.setConservationRow(jaa);
- }
- }
- }
- }
- }
- al.addGroup(sg);
- if (addAnnotSchemeGroup)
- {
- // reconstruct the annotation colourscheme
- sg.setColourScheme(constructAnnotationColour(
- jGroup.getAnnotationColours(), null, al, jalviewModel, false));
- }
- }
- }
- if (view == null)
- {
- // only dataset in this model, so just return.
- return null;
- }
- // ///////////////////////////////
- // LOAD VIEWPORT
-
- // If we just load in the same jar file again, the sequenceSetId
- // will be the same, and we end up with multiple references
- // to the same sequenceSet. We must modify this id on load
- // so that each load of the file gives a unique id
- String uniqueSeqSetId = view.getSequenceSetId() + uniqueSetSuffix;
- String viewId = (view.getId() == null ? null
- : view.getId() + uniqueSetSuffix);
- AlignFrame af = null;
- AlignViewport av = null;
- // now check to see if we really need to create a new viewport.
- if (multipleView && viewportsAdded.size() == 0)
- {
- // We recovered an alignment for which a viewport already exists.
- // TODO: fix up any settings necessary for overlaying stored state onto
- // state recovered from another document. (may not be necessary).
- // we may need a binding from a viewport in memory to one recovered from
- // XML.
- // and then recover its containing af to allow the settings to be applied.
- // TODO: fix for vamsas demo
- System.err.println(
- "About to recover a viewport for existing alignment: Sequence set ID is "
- + uniqueSeqSetId);
- Object seqsetobj = retrieveExistingObj(uniqueSeqSetId);
- if (seqsetobj != null)
- {
- if (seqsetobj instanceof String)
- {
- uniqueSeqSetId = (String) seqsetobj;
- System.err.println(
- "Recovered extant sequence set ID mapping for ID : New Sequence set ID is "
- + uniqueSeqSetId);
- }
- else
- {
- System.err.println(
- "Warning : Collision between sequence set ID string and existing jalview object mapping.");
- }
-
- }
- }
- /**
- * indicate that annotation colours are applied across all groups (pre
- * Jalview 2.8.1 behaviour)
- */
- boolean doGroupAnnColour = Jalview2XML.isVersionStringLaterThan("2.8.1",
- jalviewModel.getVersion());
-
- AlignmentPanel ap = null;
- boolean isnewview = true;
- if (viewId != null)
- {
- // Check to see if this alignment already has a view id == viewId
- jalview.gui.AlignmentPanel views[] = Desktop
- .getAlignmentPanels(uniqueSeqSetId);
- if (views != null && views.length > 0)
- {
- for (int v = 0; v < views.length; v++)
- {
- if (views[v].av.getViewId().equalsIgnoreCase(viewId))
- {
- // recover the existing alignpanel, alignframe, viewport
- af = views[v].alignFrame;
- av = views[v].av;
- ap = views[v];
- // TODO: could even skip resetting view settings if we don't want to
- // change the local settings from other jalview processes
- isnewview = false;
- }
- }
- }
- }
-
- if (isnewview)
- {
- af = loadViewport(file, jseqs, hiddenSeqs, al, jalviewModel, view,
- uniqueSeqSetId, viewId, autoAlan);
- av = af.getViewport();
- ap = af.alignPanel;
- }
-
- /*
- * Load any trees, PDB structures and viewers
- *
- * Not done if flag is false (when this method is used for New View)
- */
- if (loadTreesAndStructures)
- {
- loadTrees(jalviewModel, view, af, av, ap);
- loadPDBStructures(jprovider, jseqs, af, ap);
- loadRnaViewers(jprovider, jseqs, ap);
- }
- // and finally return.
- return af;
- }
-
- /**
- * Instantiate and link any saved RNA (Varna) viewers. The state of the Varna
- * panel is restored from separate jar entries, two (gapped and trimmed) per
- * sequence and secondary structure.
- *
- * Currently each viewer shows just one sequence and structure (gapped and
- * trimmed), however this method is designed to support multiple sequences or
- * structures in viewers if wanted in future.
- *
- * @param jprovider
- * @param jseqs
- * @param ap
- */
- private void loadRnaViewers(jarInputStreamProvider jprovider,
- List<JSeq> jseqs, AlignmentPanel ap)
- {
- /*
- * scan the sequences for references to viewers; create each one the first
- * time it is referenced, add Rna models to existing viewers
- */
- for (JSeq jseq : jseqs)
- {
- for (int i = 0; i < jseq.getRnaViewer().size(); i++)
- {
- RnaViewer viewer = jseq.getRnaViewer().get(i);
- AppVarna appVarna = findOrCreateVarnaViewer(viewer, uniqueSetSuffix,
- ap);
-
- for (int j = 0; j < viewer.getSecondaryStructure().size(); j++)
- {
- SecondaryStructure ss = viewer.getSecondaryStructure().get(j);
- SequenceI seq = seqRefIds.get(jseq.getId());
- AlignmentAnnotation ann = this.annotationIds
- .get(ss.getAnnotationId());
-
- /*
- * add the structure to the Varna display (with session state copied
- * from the jar to a temporary file)
- */
- boolean gapped = safeBoolean(ss.isGapped());
- String rnaTitle = ss.getTitle();
- String sessionState = ss.getViewerState();
- String tempStateFile = copyJarEntry(jprovider, sessionState,
- "varna", null);
- RnaModel rna = new RnaModel(rnaTitle, ann, seq, null, gapped);
- appVarna.addModelSession(rna, rnaTitle, tempStateFile);
- }
- appVarna.setInitialSelection(safeInt(viewer.getSelectedRna()));
- }
- }
- }
-
- /**
- * Locate and return an already instantiated matching AppVarna, or create one
- * if not found
- *
- * @param viewer
- * @param viewIdSuffix
- * @param ap
- * @return
- */
- protected AppVarna findOrCreateVarnaViewer(RnaViewer viewer,
- String viewIdSuffix, AlignmentPanel ap)
- {
- /*
- * on each load a suffix is appended to the saved viewId, to avoid conflicts
- * if load is repeated
- */
- String postLoadId = viewer.getViewId() + viewIdSuffix;
- for (JInternalFrame frame : getAllFrames())
- {
- if (frame instanceof AppVarna)
- {
- AppVarna varna = (AppVarna) frame;
- if (postLoadId.equals(varna.getViewId()))
- {
- // this viewer is already instantiated
- // could in future here add ap as another 'parent' of the
- // AppVarna window; currently just 1-to-many
- return varna;
- }
- }
- }
-
- /*
- * viewer not found - make it
- */
- RnaViewerModel model = new RnaViewerModel(postLoadId, viewer.getTitle(),
- safeInt(viewer.getXpos()), safeInt(viewer.getYpos()),
- safeInt(viewer.getWidth()), safeInt(viewer.getHeight()),
- safeInt(viewer.getDividerLocation()));
- AppVarna varna = new AppVarna(model, ap);
-
- return varna;
- }
-
- /**
- * Load any saved trees
- *
- * @param jm
- * @param view
- * @param af
- * @param av
- * @param ap
- */
- protected void loadTrees(JalviewModel jm, Viewport view,
- AlignFrame af, AlignViewport av, AlignmentPanel ap)
- {
- // TODO result of automated refactoring - are all these parameters needed?
- try
- {
- for (int t = 0; t < jm.getTree().size(); t++)
- {
-
- Tree tree = jm.getTree().get(t);
-
- TreePanel tp = (TreePanel) retrieveExistingObj(tree.getId());
- if (tp == null)
- {
- tp = af.showNewickTree(new NewickFile(tree.getNewick()),
- tree.getTitle(), safeInt(tree.getWidth()),
- safeInt(tree.getHeight()), safeInt(tree.getXpos()),
- safeInt(tree.getYpos()));
- if (tree.getId() != null)
- {
- // perhaps bind the tree id to something ?
- }
- }
- else
- {
- // update local tree attributes ?
- // TODO: should check if tp has been manipulated by user - if so its
- // settings shouldn't be modified
- tp.setTitle(tree.getTitle());
- tp.setBounds(new Rectangle(safeInt(tree.getXpos()),
- safeInt(tree.getYpos()), safeInt(tree.getWidth()),
- safeInt(tree.getHeight())));
- tp.setViewport(av); // af.viewport;
- // TODO: verify 'associate with all views' works still
- tp.getTreeCanvas().setViewport(av); // af.viewport;
- tp.getTreeCanvas().setAssociatedPanel(ap); // af.alignPanel;
-
- }
- if (tp == null)
- {
- warn("There was a problem recovering stored Newick tree: \n"
- + tree.getNewick());
- continue;
- }
-
- tp.fitToWindow.setState(safeBoolean(tree.isFitToWindow()));
- tp.fitToWindow_actionPerformed(null);
-
- if (tree.getFontName() != null)
- {
- tp.setTreeFont(
- new Font(tree.getFontName(), safeInt(tree.getFontStyle()),
- safeInt(tree.getFontSize())));
- }
- else
- {
- tp.setTreeFont(
- new Font(view.getFontName(), safeInt(view.getFontStyle()),
- safeInt(view.getFontSize())));
- }
-
- tp.showPlaceholders(safeBoolean(tree.isMarkUnlinked()));
- tp.showBootstrap(safeBoolean(tree.isShowBootstrap()));
- tp.showDistances(safeBoolean(tree.isShowDistances()));
-
- tp.getTreeCanvas().setThreshold(safeFloat(tree.getThreshold()));
-
- if (safeBoolean(tree.isCurrentTree()))
- {
- af.getViewport().setCurrentTree(tp.getTree());
- }
- }
-
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
-
- /**
- * Load and link any saved structure viewers.
- *
- * @param jprovider
- * @param jseqs
- * @param af
- * @param ap
- */
- protected void loadPDBStructures(jarInputStreamProvider jprovider,
- List<JSeq> jseqs, AlignFrame af, AlignmentPanel ap)
- {
- /*
- * Run through all PDB ids on the alignment, and collect mappings between
- * distinct view ids and all sequences referring to that view.
- */
- Map<String, StructureViewerModel> structureViewers = new LinkedHashMap<>();
-
- for (int i = 0; i < jseqs.size(); i++)
- {
- JSeq jseq = jseqs.get(i);
- if (jseq.getPdbids().size() > 0)
- {
- List<Pdbids> ids = jseq.getPdbids();
- for (int p = 0; p < ids.size(); p++)
- {
- Pdbids pdbid = ids.get(p);
- final int structureStateCount = pdbid.getStructureState().size();
- for (int s = 0; s < structureStateCount; s++)
- {
- // check to see if we haven't already created this structure view
- final StructureState structureState = pdbid
- .getStructureState().get(s);
- String sviewid = (structureState.getViewId() == null) ? null
- : structureState.getViewId() + uniqueSetSuffix;
- jalview.datamodel.PDBEntry jpdb = new jalview.datamodel.PDBEntry();
- // Originally : pdbid.getFile()
- // : TODO: verify external PDB file recovery still works in normal
- // jalview project load
- jpdb.setFile(
- loadPDBFile(jprovider, pdbid.getId(), pdbid.getFile()));
- jpdb.setId(pdbid.getId());
-
- int x = safeInt(structureState.getXpos());
- int y = safeInt(structureState.getYpos());
- int width = safeInt(structureState.getWidth());
- int height = safeInt(structureState.getHeight());
-
- // Probably don't need to do this anymore...
- // Desktop.desktop.getComponentAt(x, y);
- // TODO: NOW: check that this recovers the PDB file correctly.
- String pdbFile = loadPDBFile(jprovider, pdbid.getId(),
- pdbid.getFile());
- jalview.datamodel.SequenceI seq = seqRefIds
- .get(jseq.getId() + "");
- if (sviewid == null)
- {
- sviewid = "_jalview_pre2_4_" + x + "," + y + "," + width + ","
- + height;
- }
- if (!structureViewers.containsKey(sviewid))
- {
- structureViewers.put(sviewid,
- new StructureViewerModel(x, y, width, height, false,
- false, true, structureState.getViewId(),
- structureState.getType()));
- // Legacy pre-2.7 conversion JAL-823 :
- // do not assume any view has to be linked for colour by
- // sequence
- }
-
- // assemble String[] { pdb files }, String[] { id for each
- // file }, orig_fileloc, SequenceI[][] {{ seqs_file 1 }, {
- // seqs_file 2}, boolean[] {
- // linkAlignPanel,superposeWithAlignpanel}} from hash
- StructureViewerModel jmoldat = structureViewers.get(sviewid);
- jmoldat.setAlignWithPanel(jmoldat.isAlignWithPanel()
- || structureState.isAlignwithAlignPanel());
-
- /*
- * Default colour by linked panel to false if not specified (e.g.
- * for pre-2.7 projects)
- */
- boolean colourWithAlignPanel = jmoldat.isColourWithAlignPanel();
- colourWithAlignPanel |= structureState.isColourwithAlignPanel();
- jmoldat.setColourWithAlignPanel(colourWithAlignPanel);
-
- /*
- * Default colour by viewer to true if not specified (e.g. for
- * pre-2.7 projects)
- */
- boolean colourByViewer = jmoldat.isColourByViewer();
- colourByViewer &= structureState.isColourByJmol();
- jmoldat.setColourByViewer(colourByViewer);
-
- if (jmoldat.getStateData().length() < structureState
- .getValue()/*Content()*/.length())
- {
- jmoldat.setStateData(structureState.getValue());// Content());
- }
- if (pdbid.getFile() != null)
- {
- File mapkey = new File(pdbid.getFile());
- StructureData seqstrmaps = jmoldat.getFileData().get(mapkey);
- if (seqstrmaps == null)
- {
- jmoldat.getFileData().put(mapkey,
- seqstrmaps = jmoldat.new StructureData(pdbFile,
- pdbid.getId()));
- }
- if (!seqstrmaps.getSeqList().contains(seq))
- {
- seqstrmaps.getSeqList().add(seq);
- // TODO and chains?
- }
- }
- else
- {
- errorMessage = ("The Jmol views in this project were imported\nfrom an older version of Jalview.\nPlease review the sequence colour associations\nin the Colour by section of the Jmol View menu.\n\nIn the case of problems, see note at\nhttp://issues.jalview.org/browse/JAL-747");
- warn(errorMessage);
- }
- }
- }
- }
- }
- // Instantiate the associated structure views
- for (Entry<String, StructureViewerModel> entry : structureViewers
- .entrySet())
- {
- try
- {
- createOrLinkStructureViewer(entry, af, ap, jprovider);
- } catch (Exception e)
- {
- System.err.println(
- "Error loading structure viewer: " + e.getMessage());
- // failed - try the next one
- }
- }
- }
-
- /**
- *
- * @param viewerData
- * @param af
- * @param ap
- * @param jprovider
- */
- protected void createOrLinkStructureViewer(
- Entry<String, StructureViewerModel> viewerData, AlignFrame af,
- AlignmentPanel ap, jarInputStreamProvider jprovider)
- {
- final StructureViewerModel stateData = viewerData.getValue();
-
- /*
- * Search for any viewer windows already open from other alignment views
- * that exactly match the stored structure state
- */
- StructureViewerBase comp = findMatchingViewer(viewerData);
-
- if (comp != null)
- {
- linkStructureViewer(ap, comp, stateData);
- return;
- }
-
- /*
- * From 2.9: stateData.type contains JMOL or CHIMERA, data is in jar entry
- * "viewer_"+stateData.viewId
- */
- if (ViewerType.CHIMERA.toString().equals(stateData.getType()))
- {
- createChimeraViewer(viewerData, af, jprovider);
- }
- else
- {
- /*
- * else Jmol (if pre-2.9, stateData contains JMOL state string)
- */
- createJmolViewer(viewerData, af, jprovider);
- }
- }
-
- /**
- * Create a new Chimera viewer.
- *
- * @param data
- * @param af
- * @param jprovider
- */
- protected void createChimeraViewer(
- Entry<String, StructureViewerModel> viewerData, AlignFrame af,
- jarInputStreamProvider jprovider)
- {
- StructureViewerModel data = viewerData.getValue();
- String chimeraSessionFile = data.getStateData();
-
- /*
- * Copy Chimera session from jar entry "viewer_"+viewId to a temporary file