X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fproject%2FJalview2XML.java;h=d5f6a5d907855ab654b858ccf21d460112fd5675;hb=daff9052085d427cd0856ee07c4057d01f5f3bf4;hp=74b6bf060b6995b16083618e075e7bc2108f398f;hpb=41d39ae9fa7cea070094d6e0230bca8c0cfba23a;p=jalview.git diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java index 74b6bf0..d5f6a5d 100644 --- a/src/jalview/project/Jalview2XML.java +++ b/src/jalview/project/Jalview2XML.java @@ -38,7 +38,10 @@ import jalview.datamodel.AlignedCodonFrame; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; +import jalview.datamodel.DBRefEntry; +import jalview.datamodel.GeneLocus; import jalview.datamodel.GraphLine; +import jalview.datamodel.HiddenMarkovModel; import jalview.datamodel.PDBEntry; import jalview.datamodel.Point; import jalview.datamodel.RnaViewerModel; @@ -58,8 +61,6 @@ import jalview.gui.AlignmentPanel; import jalview.gui.AppVarna; import jalview.gui.ChimeraViewFrame; import jalview.gui.Desktop; -import jalview.gui.FeatureRenderer; -import jalview.gui.Jalview2XML_V1; import jalview.gui.JvOptionPane; import jalview.gui.OOMWarning; import jalview.gui.PCAPanel; @@ -69,8 +70,10 @@ import jalview.gui.StructureViewer; import jalview.gui.StructureViewer.ViewerType; import jalview.gui.StructureViewerBase; import jalview.gui.TreePanel; +import jalview.io.BackupFiles; import jalview.io.DataSourceType; import jalview.io.FileFormat; +import jalview.io.HMMFile; import jalview.io.NewickFile; import jalview.math.Matrix; import jalview.math.MatrixI; @@ -92,6 +95,7 @@ import jalview.util.matcher.Condition; import jalview.viewmodel.AlignmentViewport; import jalview.viewmodel.PCAModel; import jalview.viewmodel.ViewportRanges; +import jalview.viewmodel.seqfeatures.FeatureRendererModel; import jalview.viewmodel.seqfeatures.FeatureRendererSettings; import jalview.viewmodel.seqfeatures.FeaturesDisplayed; import jalview.ws.jws2.Jws2Discoverer; @@ -212,6 +216,8 @@ public class Jalview2XML private static final String RNA_PREFIX = "rna_"; + private static final String HMMER_PREFIX = "hmmer_"; + private static final String UTF_8 = "UTF-8"; /** @@ -551,24 +557,30 @@ public class Jalview2XML 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 = "Couldn't write Jalview Archive to output file '" + errorMessage = "Did't write Jalview Archive to output file '" + statefile + "' - See console error log for details"; } else { - errorMessage += "(output file was '" + statefile + "')"; + errorMessage += "(Didn't write Jalview Archive to output file '" + + statefile + ")"; } e.printStackTrace(); } finally @@ -738,7 +750,11 @@ public class Jalview2XML { try { - FileOutputStream fos = new FileOutputStream(jarFile); + // create backupfiles object and get new temp filename destination + BackupFiles backupfiles = new BackupFiles(jarFile); + FileOutputStream fos = new FileOutputStream( + backupfiles.getTempFilePath()); + JarOutputStream jout = new JarOutputStream(fos); List frames = new ArrayList<>(); @@ -760,7 +776,12 @@ public class Jalview2XML } ; jout.close(); - return true; + boolean success = true; + + 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"; @@ -1035,6 +1056,9 @@ public class Jalview2XML jseq.getFeatures().add(features); } + /* + * save PDB entries for sequence + */ if (jdatasq.getAllPDBEntries() != null) { Enumeration en = jdatasq.getAllPDBEntries().elements(); @@ -1127,6 +1151,11 @@ public class Jalview2XML saveRnaViewers(jout, jseq, jds, viewIds, ap, storeDS); + if (jds.hasHMMProfile()) + { + saveHmmerProfile(jout, jseq, jds); + } + // jms.addJSeq(jseq); object.getJSeq().add(jseq); } @@ -1484,11 +1513,14 @@ public class Jalview2XML 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(); - FeatureRenderer fr = ap.getSeqPanel().seqCanvas + FeatureRendererModel fr = ap.getSeqPanel().seqCanvas .getFeatureRenderer(); String[] renderOrder = fr.getRenderOrder().toArray(new String[0]); @@ -1671,7 +1703,39 @@ public class Jalview2XML } return object; } + /** + * Saves the HMMER profile associated with the sequence as a file in the jar, + * in HMMER format, and saves the name of the file as a child element of the + * XML sequence element + * + * @param jout + * @param xmlSeq + * @param seq + */ + protected void saveHmmerProfile(JarOutputStream jout, JSeq xmlSeq, + SequenceI seq) + { + HiddenMarkovModel profile = seq.getHMM(); + if (profile == null) + { + warn("Want to save HMM profile for " + seq.getName() + + " but none found"); + return; + } + HMMFile hmmFile = new HMMFile(profile); + String hmmAsString = hmmFile.print(); + String jarEntryName = HMMER_PREFIX + nextCounter(); + try + { + writeJarEntry(jout, jarEntryName, hmmAsString.getBytes()); + xmlSeq.setHmmerProfile(jarEntryName); + } catch (IOException e) + { + warn("Error saving HMM profile: " + e.getMessage()); + } + } + /** * Writes PCA viewer attributes and computed values to an XML model object and * adds it to the JalviewModel. Any exceptions are reported by logging. @@ -2065,9 +2129,9 @@ public class Jalview2XML } 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()); + 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 @@ -2382,7 +2446,7 @@ public class Jalview2XML argList = parmSet.getArguments(); parmSet = null; } - AAConSettings settings = new AAConSettings( + AutoCalcSetting settings = new AAConSettings( calcIdParam.isAutoUpdate(), service, parmSet, argList); av.setCalcIdSettingsFor(calcIdParam.getCalcId(), settings, calcIdParam.isNeedsUpdate()); @@ -2490,21 +2554,29 @@ public class Jalview2XML parentseq = jds; } } + + /* + * save any dbrefs; special subclass GeneLocus is flagged as 'locus' + */ 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()) + DBRefEntry dbRefEntry = dbrefs[d]; + dbref.setSource(dbRefEntry.getSource()); + dbref.setVersion(dbRefEntry.getVersion()); + dbref.setAccessionId(dbRefEntry.getAccessionId()); + if (dbRefEntry instanceof GeneLocus) + { + dbref.setLocus(true); + } + if (dbRefEntry.hasMap()) { - Mapping mp = createVamsasMapping(dbrefs[d].getMap(), parentseq, + Mapping mp = createVamsasMapping(dbRefEntry.getMap(), parentseq, jds, recurse); dbref.setMapping(mp); } - // vamsasSeq.addDBRef(dbref); vamsasSeq.getDBRef().add(dbref); } } @@ -2882,16 +2954,7 @@ public class Jalview2XML 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; - } + // used to attempt to parse as V1 castor-generated xml } if (Desktop.instance != null) { @@ -3144,25 +3207,25 @@ public class Jalview2XML * @param prefix * a prefix for the temporary file name, must be at least three * characters long - * @param origFile + * @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 origFile) + String jarEntryName, String prefix, String suffixModel) { BufferedReader in = null; PrintWriter out = null; String suffix = ".tmp"; - if (origFile == null) + if (suffixModel == null) { - origFile = jarEntryName; + suffixModel = jarEntryName; } - int sfpos = origFile.lastIndexOf("."); - if (sfpos > -1 && sfpos < (origFile.length() - 3)) + int sfpos = suffixModel.lastIndexOf("."); + if (sfpos > -1 && sfpos < (suffixModel.length() - 1)) { - suffix = "." + origFile.substring(sfpos + 1); + suffix = "." + suffixModel.substring(sfpos + 1); } try { @@ -3567,6 +3630,18 @@ public class Jalview2XML } } } + + /* + * load any HMMER profile + */ + // TODO fix this + + String hmmJarFile = jseqs.get(i).getHmmerProfile(); + if (hmmJarFile != null && jprovider != null) + { + loadHmmerProfile(jprovider, hmmJarFile, al.getSequenceAt(i)); + } + } } // end !multipleview @@ -3853,7 +3928,7 @@ public class Jalview2XML } else { - cs = ColourSchemeProperty.getColourScheme(al, + cs = ColourSchemeProperty.getColourScheme(null, al, jGroup.getColour()); } } @@ -4041,6 +4116,31 @@ public class Jalview2XML } /** + * Loads a HMMER profile from a file stored in the project, and associates it + * with the specified sequence + * + * @param jprovider + * @param hmmJarFile + * @param seq + */ + protected void loadHmmerProfile(jarInputStreamProvider jprovider, + String hmmJarFile, SequenceI seq) + { + try + { + String hmmFile = copyJarEntry(jprovider, hmmJarFile, "hmm", null); + HMMFile parser = new HMMFile(hmmFile, DataSourceType.FILE); + HiddenMarkovModel hmmModel = parser.getHMM(); + hmmModel = new HiddenMarkovModel(hmmModel, seq); + seq.setHMM(hmmModel); + } catch (IOException e) + { + warn("Error loading HMM profile for " + seq.getName() + ": " + + e.getMessage()); + } + } + + /** * 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. @@ -4181,10 +4281,8 @@ public class Jalview2XML // TODO: verify 'associate with all views' works still tp.getTreeCanvas().setViewport(av); // af.viewport; tp.getTreeCanvas().setAssociatedPanel(ap); // af.alignPanel; - // FIXME: should we use safeBoolean here ? - tp.getTreeCanvas().setApplyToAllViews(tree.isLinkToAllViews()); - } + tp.getTreeCanvas().setApplyToAllViews(tree.isLinkToAllViews()); if (tp == null) { warn("There was a problem recovering stored Newick tree: \n" @@ -4430,7 +4528,7 @@ public class Jalview2XML */ String viewerJarEntryName = getViewerJarEntryName(data.getViewId()); chimeraSessionFile = copyJarEntry(jprovider, viewerJarEntryName, - "chimera", null); + "chimera", ".py"); Set> fileData = data.getFileData() .entrySet(); @@ -4516,7 +4614,7 @@ public class Jalview2XML String reformatedOldFilename = oldfilenam.replaceAll("/", "\\\\"); filedat = oldFiles.get(new File(reformatedOldFilename)); } - newFileLoc.append(Platform.escapeString(filedat.getFilePath())); + newFileLoc.append(Platform.escapeBackslashes(filedat.getFilePath())); pdbfilenames.add(filedat.getFilePath()); pdbids.add(filedat.getPdbId()); seqmaps.add(filedat.getSeqList().toArray(new SequenceI[0])); @@ -4967,25 +5065,27 @@ public class Jalview2XML } else { - cs = ColourSchemeProperty.getColourScheme(al, view.getBgColour()); + cs = ColourSchemeProperty.getColourScheme(af.getViewport(), al, + view.getBgColour()); } } + /* + * turn off 'alignment colour applies to all groups' + * while restoring global colour scheme + */ + viewport.setColourAppliesToAllGroups(false); viewport.setGlobalColourScheme(cs); viewport.getResidueShading().setThreshold(pidThreshold, view.isIgnoreGapsinConsensus()); viewport.getResidueShading() .setConsensus(viewport.getSequenceConsensusHash()); - viewport.setColourAppliesToAllGroups(false); - if (safeBoolean(view.isConservationSelected()) && cs != null) { viewport.getResidueShading() .setConservationInc(safeInt(view.getConsThreshold())); } - af.changeColour(cs); - viewport.setColourAppliesToAllGroups(true); viewport @@ -5003,11 +5103,14 @@ public class Jalview2XML viewport.setShowNPFeats(safeBoolean(view.isShowNPfeatureTooltip())); viewport.setShowGroupConsensus(view.isShowGroupConsensus()); viewport.setShowGroupConservation(view.isShowGroupConservation()); + viewport.setShowComplementFeatures(view.isShowComplementFeatures()); + viewport.setShowComplementFeaturesOnTop( + view.isShowComplementFeaturesOnTop()); // recover feature settings if (jm.getFeatureSettings() != null) { - FeatureRenderer fr = af.alignPanel.getSeqPanel().seqCanvas + FeatureRendererModel fr = af.alignPanel.getSeqPanel().seqCanvas .getFeatureRenderer(); FeaturesDisplayed fdi; viewport.setFeaturesDisplayed(fdi = new FeaturesDisplayed()); @@ -5061,7 +5164,8 @@ public class Jalview2XML float min = safeFloat(safeFloat(setting.getMin())); float max = setting.getMax() == null ? 1f : setting.getMax().floatValue(); - FeatureColourI gc = new FeatureColour(minColour, maxColour, + FeatureColourI gc = new FeatureColour(maxColour, minColour, + maxColour, noValueColour, min, max); if (setting.getAttributeName().size() > 0) { @@ -5106,7 +5210,7 @@ public class Jalview2XML } else { - featureOrder.put(featureType, new Float( + featureOrder.put(featureType, Float.valueOf( fs / jm.getFeatureSettings().getSetting().size())); } if (safeBoolean(setting.isDisplay())) @@ -5118,7 +5222,7 @@ public class Jalview2XML for (int gs = 0; gs < jm.getFeatureSettings().getGroup().size(); gs++) { Group grp = jm.getFeatureSettings().getGroup().get(gs); - fgtable.put(grp.getName(), new Boolean(grp.isDisplay())); + fgtable.put(grp.getName(), Boolean.valueOf(grp.isDisplay())); } // FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder, // fgtable, featureColours, jms.getFeatureSettings().hasTransparency() ? @@ -5263,7 +5367,7 @@ public class Jalview2XML else { cs = new AnnotationColourGradient(matchedAnnotation, - ColourSchemeProperty.getColourScheme(al, + ColourSchemeProperty.getColourScheme(af.getViewport(), al, viewAnnColour.getColourScheme()), safeInt(viewAnnColour.getAboveThreshold())); } @@ -5424,10 +5528,10 @@ public class Jalview2XML String id = object.getViewport().get(0).getSequenceSetId(); if (skipList.containsKey(id)) { - if (Cache.log != null && Cache.log.isDebugEnabled()) - { - Cache.log.debug("Skipping seuqence set id " + id); - } + if (Cache.log != null && Cache.log.isDebugEnabled()) + { + Cache.log.debug("Skipping seuqence set id " + id); + } return true; } return false; @@ -5791,13 +5895,29 @@ public class Jalview2XML return datasetId; } + /** + * Add any saved DBRefEntry's to the sequence. An entry flagged as 'locus' is + * constructed as a special subclass GeneLocus. + * + * @param datasetSequence + * @param sequence + */ private void addDBRefs(SequenceI datasetSequence, Sequence sequence) { for (int d = 0; d < sequence.getDBRef().size(); d++) { DBRef dr = sequence.getDBRef().get(d); - jalview.datamodel.DBRefEntry entry = new jalview.datamodel.DBRefEntry( - dr.getSource(), dr.getVersion(), dr.getAccessionId()); + DBRefEntry entry; + if (dr.isLocus()) + { + entry = new GeneLocus(dr.getSource(), dr.getVersion(), + dr.getAccessionId()); + } + else + { + entry = new DBRefEntry(dr.getSource(), dr.getVersion(), + dr.getAccessionId()); + } if (dr.getMapping() != null) { entry.setMap(addMapping(dr.getMapping())); @@ -5829,15 +5949,16 @@ public class Jalview2XML jalview.datamodel.Mapping jmap = new jalview.datamodel.Mapping(dsto, fr, fto, m.getMapFromUnit().intValue(), m.getMapToUnit().intValue()); - // if (m.getMappingChoice() != null) - // { - // MappingChoice mc = m.getMappingChoice(); + + /* + * (optional) choice of dseqFor or Sequence + */ if (m.getDseqFor() != null) { String dsfor = m.getDseqFor(); if (seqRefIds.containsKey(dsfor)) { - /** + /* * recover from hash */ jmap.setTo(seqRefIds.get(dsfor)); @@ -5847,9 +5968,9 @@ public class Jalview2XML frefedSequence.add(newMappingRef(dsfor, jmap)); } } - else + else if (m.getSequence() != null) { - /** + /* * local sequence definition */ Sequence ms = m.getSequence(); @@ -5884,7 +6005,6 @@ public class Jalview2XML jmap.setTo(djs); incompleteSeqs.put(sqid, djs); seqRefIds.put(sqid, djs); - } jalview.bin.Cache.log.debug("about to recurse on addDBRefs."); addDBRefs(djs, ms); @@ -6068,7 +6188,7 @@ public class Jalview2XML } else { - Cache.log.debug("Ignoring " + jvobj.getClass() + " (ID = " + id); + Cache.log.debug("Ignoring " + jvobj.getClass() + " (ID = " + id); } } } @@ -6542,7 +6662,7 @@ public class Jalview2XML maxcol = new Color(Integer.parseInt(colourModel.getRGB(), 16)); } catch (Exception e) { - Cache.log.warn("Couldn't parse out graduated feature color.", e); + Cache.log.warn("Couldn't parse out graduated feature color.", e); } NoValueColour noCol = colourModel.getNoValueColour(); @@ -6555,7 +6675,7 @@ public class Jalview2XML noValueColour = maxcol; } - colour = new FeatureColour(mincol, maxcol, noValueColour, + colour = new FeatureColour(maxcol, mincol, maxcol, noValueColour, safeFloat(colourModel.getMin()), safeFloat(colourModel.getMax())); final List attributeName = colourModel.getAttributeName();