- @Override
- public boolean isResolvable()
- {
- return super.isResolvable() && mp.getTo() != null;
- }
-
- @Override
- boolean resolve()
- {
- SequenceI seq = getSrefDatasetSeq();
- if (seq == null)
- {
- return false;
- }
- cf.addMap(seq, mp.getTo(), mp.getMap());
- return true;
- }
- };
- return fref;
- }
-
- public void resolveFrefedSequences()
- {
- Iterator<SeqFref> nextFref = frefedSequence.iterator();
- int toresolve = frefedSequence.size();
- int unresolved = 0, failedtoresolve = 0;
- while (nextFref.hasNext())
- {
- SeqFref ref = nextFref.next();
- if (ref.isResolvable())
- {
- try
- {
- if (ref.resolve())
- {
- nextFref.remove();
- }
- else
- {
- failedtoresolve++;
- }
- } catch (Exception x)
- {
- System.err.println(
- "IMPLEMENTATION ERROR: Failed to resolve forward reference for sequence "
- + ref.getSref());
- x.printStackTrace();
- failedtoresolve++;
- }
- }
- else
- {
- unresolved++;
- }
- }
- if (unresolved > 0)
- {
- System.err.println("Jalview Project Import: There were " + unresolved
- + " forward references left unresolved on the stack.");
- }
- if (failedtoresolve > 0)
- {
- System.err.println("SERIOUS! " + failedtoresolve
- + " resolvable forward references failed to resolve.");
- }
- if (incompleteSeqs != null && incompleteSeqs.size() > 0)
- {
- System.err.println(
- "Jalview Project Import: There are " + incompleteSeqs.size()
- + " sequences which may have incomplete metadata.");
- if (incompleteSeqs.size() < 10)
- {
- for (SequenceI s : incompleteSeqs.values())
- {
- System.err.println(s.toString());
- }
- }
- else
- {
- System.err.println(
- "Too many to report. Skipping output of incomplete sequences.");
- }
- }
- }
-
- /**
- * This maintains a map of viewports, the key being the seqSetId. Important to
- * set historyItem and redoList for multiple views
- */
- Map<String, AlignViewport> viewportsAdded = new HashMap<>();
-
- Map<String, AlignmentAnnotation> annotationIds = new HashMap<>();
-
- String uniqueSetSuffix = "";
-
- /**
- * List of pdbfiles added to Jar
- */
- List<String> pdbfiles = null;
-
- // SAVES SEVERAL ALIGNMENT WINDOWS TO SAME JARFILE
- public void saveState(File statefile)
- {
- FileOutputStream fos = null;
-
- try
- {
-
- fos = new FileOutputStream(statefile);
-
- JarOutputStream jout = new JarOutputStream(fos);
- saveState(jout);
- fos.close();
-
- } catch (Exception e)
- {
- Cache.log.error("Couln't write Jalview state to " + statefile, e);
- // TODO: inform user of the problem - they need to know if their data was
- // not saved !
- if (errorMessage == null)
- {
- errorMessage = "Did't write Jalview Archive to output file '"
- + statefile + "' - See console error log for details";
- }
- else
- {
- errorMessage += "(Didn't write Jalview Archive to output file '"
- + statefile + ")";
- }
- e.printStackTrace();
- } finally
- {
- if (fos != null)
- {
- try
- {
- fos.close();
- } catch (IOException e)
- {
- // ignore
- }
- }
- }
- reportErrors();
- }
-
- /**
- * Writes a jalview project archive to the given Jar output stream.
- *
- * @param jout
- */
- public void saveState(JarOutputStream jout)
- {
- AlignFrame[] frames = Desktop.getAlignFrames();
-
- if (frames == null)
- {
- return;
- }
- saveAllFrames(Arrays.asList(frames), jout);
- }
-
- /**
- * core method for storing state for a set of AlignFrames.
- *
- * @param frames
- * - frames involving all data to be exported (including containing
- * splitframes)
- * @param jout
- * - project output stream
- */
- private void saveAllFrames(List<AlignFrame> frames, JarOutputStream jout)
- {
- Hashtable<String, AlignFrame> dsses = new Hashtable<>();
-
- /*
- * ensure cached data is clear before starting
- */
- // todo tidy up seqRefIds, seqsToIds initialisation / reset
- rnaSessions.clear();
- splitFrameCandidates.clear();
-
- 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
- {
- // create backupfiles object and get new temp filename destination
- boolean doBackup = BackupFiles.getEnabled();
- BackupFiles backupfiles = doBackup ? new BackupFiles(jarFile) : null;
- FileOutputStream fos = new FileOutputStream(
- doBackup ? backupfiles.getTempFilePath() : 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();
- boolean success = true;
-
- if (doBackup)
- {
- backupfiles.setWriteSuccess(success);
- success = backupfiles.rollBackupsAndRenameTempFile();
- }
-
- return success;
- } 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 = saveStructureViewer(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();
- String viewerType = viewFrame.getViewerType().toString();
- if (!storeDS && !viewIds.contains(viewId))
- {
- viewIds.add(viewId);
- File viewerState = viewFrame.saveSession();
- if (viewerState != null)
- {
- copyFileToJar(jout, viewerState.getPath(),
- getViewerJarEntryName(viewId), viewerType);
- }
- else
- {
- Cache.log.error(
- "Failed to save viewer state for " + viewerType);
- }
- }
- }
- }
-
- 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, 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));
- tree.setLinkToAllViews(
- tp.getTreeCanvas().isApplyToAllViews());
-
- // jms.addTree(tree);
- object.getTree().add(tree);
- }
- }
- }
- }
- }
-
- /*
- * save PCA viewers
- */
- if (!storeDS && Desktop.desktop != null)
- {
- for (JInternalFrame frame : Desktop.desktop.getAllFrames())
- {
- if (frame instanceof PCAPanel)
- {
- PCAPanel panel = (PCAPanel) frame;
- if (panel.getAlignViewport().getAlignment() == jal)
- {
- savePCA(panel, object);
- }
- }
- }
- }
-
- // 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());
- view.setShowComplementFeatures(av.isShowComplementFeatures());
- view.setShowComplementFeaturesOnTop(
- av.isShowComplementFeaturesOnTop());
- if (av.getFeaturesDisplayed() != null)
- {
- FeatureSettings fs = new FeatureSettings();
-
- FeatureRendererModel 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
- {
- fileName = fileName.replace('\\', '/');
- 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;
- }
-
- /**
- * Writes PCA viewer attributes and computed values to an XML model object and
- * adds it to the JalviewModel. Any exceptions are reported by logging.
- */
- protected void savePCA(PCAPanel panel, JalviewModel object)
- {
- try
- {
- PcaViewer viewer = new PcaViewer();
- viewer.setHeight(panel.getHeight());
- viewer.setWidth(panel.getWidth());
- viewer.setXpos(panel.getX());
- viewer.setYpos(panel.getY());
- viewer.setTitle(panel.getTitle());
- PCAModel pcaModel = panel.getPcaModel();
- viewer.setScoreModelName(pcaModel.getScoreModelName());
- viewer.setXDim(panel.getSelectedDimensionIndex(X));
- viewer.setYDim(panel.getSelectedDimensionIndex(Y));
- viewer.setZDim(panel.getSelectedDimensionIndex(Z));
- viewer.setBgColour(
- panel.getRotatableCanvas().getBackgroundColour().getRGB());
- viewer.setScaleFactor(panel.getRotatableCanvas().getScaleFactor());
- float[] spMin = panel.getRotatableCanvas().getSeqMin();
- SeqPointMin spmin = new SeqPointMin();
- spmin.setXPos(spMin[0]);
- spmin.setYPos(spMin[1]);
- spmin.setZPos(spMin[2]);
- viewer.setSeqPointMin(spmin);
- float[] spMax = panel.getRotatableCanvas().getSeqMax();
- SeqPointMax spmax = new SeqPointMax();
- spmax.setXPos(spMax[0]);
- spmax.setYPos(spMax[1]);
- spmax.setZPos(spMax[2]);
- viewer.setSeqPointMax(spmax);
- viewer.setShowLabels(panel.getRotatableCanvas().isShowLabels());
- viewer.setLinkToAllViews(
- panel.getRotatableCanvas().isApplyToAllViews());
- SimilarityParamsI sp = pcaModel.getSimilarityParameters();
- viewer.setIncludeGaps(sp.includeGaps());
- viewer.setMatchGaps(sp.matchGaps());
- viewer.setIncludeGappedColumns(sp.includeGappedColumns());
- viewer.setDenominateByShortestLength(sp.denominateByShortestLength());
-
- /*
- * sequence points on display
- */
- for (jalview.datamodel.SequencePoint spt : pcaModel
- .getSequencePoints())
- {
- SequencePoint point = new SequencePoint();
- point.setSequenceRef(seqHash(spt.getSequence()));
- point.setXPos(spt.coord.x);
- point.setYPos(spt.coord.y);
- point.setZPos(spt.coord.z);
- viewer.getSequencePoint().add(point);
- }
-
- /*
- * (end points of) axes on display
- */
- for (Point p : panel.getRotatableCanvas().getAxisEndPoints())
- {
-
- Axis axis = new Axis();
- axis.setXPos(p.x);
- axis.setYPos(p.y);
- axis.setZPos(p.z);
- viewer.getAxis().add(axis);
- }
-
- /*
- * raw PCA data (note we are not restoring PCA inputs here -
- * alignment view, score model, similarity parameters)
- */
- PcaDataType data = new PcaDataType();
- viewer.setPcaData(data);
- PCA pca = pcaModel.getPcaData();
-
- DoubleMatrix pm = new DoubleMatrix();
- saveDoubleMatrix(pca.getPairwiseScores(), pm);
- data.setPairwiseMatrix(pm);
-
- DoubleMatrix tm = new DoubleMatrix();
- saveDoubleMatrix(pca.getTridiagonal(), tm);
- data.setTridiagonalMatrix(tm);
-
- DoubleMatrix eigenMatrix = new DoubleMatrix();
- data.setEigenMatrix(eigenMatrix);
- saveDoubleMatrix(pca.getEigenmatrix(), eigenMatrix);
-
- object.getPcaViewer().add(viewer);
- } catch (Throwable t)
- {
- Cache.log.error("Error saving PCA: " + t.getMessage());
- }
- }
-
- /**
- * Stores values from a matrix into an XML element, including (if present) the
- * D or E vectors
- *
- * @param m
- * @param xmlMatrix
- * @see #loadDoubleMatrix(DoubleMatrix)
- */
- protected void saveDoubleMatrix(MatrixI m, DoubleMatrix xmlMatrix)
- {
- xmlMatrix.setRows(m.height());
- xmlMatrix.setColumns(m.width());
- for (int i = 0; i < m.height(); i++)
- {
- DoubleVector row = new DoubleVector();
- for (int j = 0; j < m.width(); j++)
- {
- row.getV().add(m.getValue(i, j));
- }
- xmlMatrix.getRow().add(row);
- }
- if (m.getD() != null)
- {
- DoubleVector dVector = new DoubleVector();
- for (double d : m.getD())
- {
- dVector.getV().add(d);
- }
- xmlMatrix.setD(dVector);
- }
- if (m.getE() != null)
- {
- DoubleVector eVector = new DoubleVector();
- for (double e : m.getE())
- {
- eVector.getV().add(e);
- }
- xmlMatrix.setE(eVector);
- }
- }
-
- /**
- * Loads XML matrix data into a new Matrix object, including the D and/or E
- * vectors (if present)
- *
- * @param mData
- * @return
- * @see Jalview2XML#saveDoubleMatrix(MatrixI, DoubleMatrix)
- */
- protected MatrixI loadDoubleMatrix(DoubleMatrix mData)
- {
- int rows = mData.getRows();
- double[][] vals = new double[rows][];
-
- for (int i = 0; i < rows; i++)
- {
- List<Double> dVector = mData.getRow().get(i).getV();
- vals[i] = new double[dVector.size()];
- int dvi = 0;
- for (Double d : dVector)
- {
- vals[i][dvi++] = d;
- }
- }
-
- MatrixI m = new Matrix(vals);
-
- if (mData.getD() != null)
- {
- List<Double> dVector = mData.getD().getV();
- double[] vec = new double[dVector.size()];
- int dvi = 0;
- for (Double d : dVector)
- {
- vec[dvi++] = d;
- }
- m.setD(vec);
- }
- if (mData.getE() != null)
- {
- List<Double> dVector = mData.getE().getV();
- double[] vec = new double[dVector.size()];
- int dvi = 0;
- for (Double d : dVector)
- {
- vec[dvi++] = d;
- }
- m.setE(vec);
- }
-
- return m;
- }
-
- /**
- * 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, "Varna");
- 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
- * @param msg
- * additional identifying info to log to the console
- */
- protected void copyFileToJar(JarOutputStream jout, String infilePath,
- String jarEntryName, String msg)
- {
- try (InputStream is = new FileInputStream(infilePath))
- {
- File file = new File(infilePath);
- if (file.exists() && jout != null)
- {
- System.out.println(
- "Writing jar entry " + jarEntryName + " (" + msg + ")");
- jout.putNextEntry(new JarEntry(jarEntryName));
- copyAll(is, jout);
- jout.closeEntry();
- // 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();
- }
- }
-
- /**
- * Copies input to output, in 4K buffers; handles any data (text or binary)
- *
- * @param in
- * @param out
- * @throws IOException
- */
- protected void copyAll(InputStream in, OutputStream out)
- throws IOException
- {
- byte[] buffer = new byte[4096];
- int bytesRead = 0;
- while ((bytesRead = in.read(buffer)) != -1)
- {
- out.write(buffer, 0, bytesRead);
- }
- }
-
- /**
- * 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 saveStructureViewer(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(Locale.ROOT)
- .startsWith(pdbId.toLowerCase(Locale.ROOT))))
- {
- /*
- * 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());
- List<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;
- }
- }
-
- /*
- * save any dbrefs; special subclass GeneLocus is flagged as 'locus'
- */
- if (dbrefs != null)
- {
- for (int d = 0, nd = dbrefs.size(); d < nd; d++)
- {
- DBRef dbref = new DBRef();
- DBRefEntry ref = dbrefs.get(d);
- dbref.setSource(ref.getSource());
- dbref.setVersion(ref.getVersion());
- dbref.setAccessionId(ref.getAccessionId());
- dbref.setCanonical(ref.isCanonical());
- if (ref instanceof GeneLocus)
- {
- dbref.setLocus(true);
- }
- if (ref.hasMap())
- {
- Mapping mp = createVamsasMapping(ref.getMap(), parentseq, jds,
- recurse);
- dbref.setMapping(mp);
- }
- 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(Locale.ROOT));
- 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 Object 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;
- }
-
- @SuppressWarnings("unused")
- private jarInputStreamProvider createjarInputStreamProvider(
- final Object ofile) throws MalformedURLException
- {
-
- // BH 2018 allow for bytes already attached to File object
- try
- {
- String file = (ofile instanceof File
- ? ((File) ofile).getCanonicalPath()
- : ofile.toString());
- byte[] bytes = Platform.isJS() ? Platform.getFileBytes((File) ofile)
- : null;
- URL url = null;
- errorMessage = null;
- uniqueSetSuffix = null;
- seqRefIds = null;
- viewportsAdded.clear();
- frefedSequence = null;
-
- if (HttpUtils.startsWithHttpOrHttps(file))
- {
- url = new URL(file);
- }
- final URL _url = url;
- return new jarInputStreamProvider()
- {
-
- @Override
- public JarInputStream getJarInputStream() throws IOException
- {
- if (bytes != null)
- {
- // System.out.println("Jalview2XML: opening byte jarInputStream for
- // bytes.length=" + bytes.length);
- return new JarInputStream(new ByteArrayInputStream(bytes));
- }
- if (_url != null)
- {
- // System.out.println("Jalview2XML: opening url jarInputStream for "
- // + _url);
- return new JarInputStream(_url.openStream());
- }
- else
- {
- // System.out.println("Jalview2XML: opening file jarInputStream for
- // " + file);
- return new JarInputStream(new FileInputStream(file));
- }
- }
-
- @Override
- public String getFilename()
- {
- return file;
- }
- };
- } catch (IOException e)
- {
- e.printStackTrace();
- return null;
- }
- }
-
- /**
- * 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"))
- {
- 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();
-
- 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);
- jin.close();
- 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)
- {
- // used to attempt to parse as V1 castor-generated xml
- }
- 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 suffixModel
- * 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 suffixModel)
- {
- String suffix = ".tmp";
- if (suffixModel == null)
- {
- suffixModel = jarEntryName;
- }
- int sfpos = suffixModel.lastIndexOf(".");
- if (sfpos > -1 && sfpos < (suffixModel.length() - 1))
- {
- suffix = "." + suffixModel.substring(sfpos + 1);
- }
-
- try (JarInputStream jin = jprovider.getJarInputStream())
- {
- 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();
- try (OutputStream os = new FileOutputStream(outFile))
- {
- copyAll(jin, os);
- }
- String t = outFile.getAbsolutePath();
- return t;
- }
- else
- {
- warn("Couldn't find entry in Jalview Jar for " + jarEntryName);
- }
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
-
- 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;
-
- // ////////////////////////////////
- // INITIALISE ALIGNMENT SEQUENCESETID AND VIEWID
- //
- //
- // 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
-
- /**
- * used to resolve correct alignment dataset for alignments with multiple
- * views
- */
- String uniqueSeqSetId = null;
- String viewId = null;
- if (view != null)
- {
- uniqueSeqSetId = view.getSequenceSetId() + uniqueSetSuffix;
- viewId = (view.getId() == null ? null
- : view.getId() + uniqueSetSuffix);
- }
-
- // ////////////////////////////////
- // 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(String.format(
- "Warning JAL-2154 regression: updating start/end for sequence %s from %d/%d to %d/%d",
- tmpSeq.getName(), tmpSeq.getStart(), tmpSeq.getEnd(),
- jseq.getStart(), jseq.getEnd()));
- }
- }
- 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, uniqueSeqSetId);
- }
-
- 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(null, 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);