X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fproject%2FJalview2XML.java;h=9d9faa1a855f6ffa828f8f674f583dc869d023e0;hb=cb597de858c70703321daa67adef5089957e9f55;hp=74b6bf060b6995b16083618e075e7bc2108f398f;hpb=41d39ae9fa7cea070094d6e0230bca8c0cfba23a;p=jalview.git diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java index 74b6bf0..9d9faa1 100644 --- a/src/jalview/project/Jalview2XML.java +++ b/src/jalview/project/Jalview2XML.java @@ -38,6 +38,7 @@ import jalview.datamodel.AlignedCodonFrame; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; +import jalview.datamodel.DBRefEntry; import jalview.datamodel.GraphLine; import jalview.datamodel.PDBEntry; import jalview.datamodel.Point; @@ -59,7 +60,6 @@ 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; @@ -69,6 +69,7 @@ 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.NewickFile; @@ -81,7 +82,6 @@ import jalview.schemes.ColourSchemeProperty; import jalview.schemes.FeatureColour; import jalview.schemes.ResidueProperties; import jalview.schemes.UserColourScheme; -import jalview.structure.StructureSelectionManager; import jalview.structures.models.AAStructureBindingModel; import jalview.util.Format; import jalview.util.MessageManager; @@ -152,6 +152,7 @@ import java.awt.Color; import java.awt.Font; import java.awt.Rectangle; import java.io.BufferedReader; +import java.io.ByteArrayInputStream; import java.io.DataInputStream; import java.io.DataOutputStream; import java.io.File; @@ -208,6 +209,15 @@ import javax.xml.stream.XMLStreamReader; */ public class Jalview2XML { + + // BH 2018 we add the .jvp binary extension to J2S so that + // it will declare that binary when we do the file save from the browser + + static + { + Platform.addJ2SBinaryType(".jvp?"); + } + private static final String VIEWER_PREFIX = "viewer_"; private static final String RNA_PREFIX = "rna_"; @@ -451,7 +461,7 @@ public class Jalview2XML public boolean isResolvable() { return super.isResolvable() && mp.getTo() != null; - }; + } @Override boolean resolve() @@ -551,24 +561,30 @@ 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 @@ -677,7 +693,6 @@ public class Jalview2XML } catch (Exception foo) { } - ; jout.close(); } catch (Exception ex) { @@ -738,7 +753,12 @@ public class Jalview2XML { try { - FileOutputStream fos = new FileOutputStream(jarFile); + // 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 frames = new ArrayList<>(); @@ -758,9 +778,16 @@ public class Jalview2XML } catch (Exception foo) { } - ; jout.close(); - return true; + 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"; @@ -1053,7 +1080,7 @@ public class Jalview2XML * only view *should* be coped with sensibly. */ // This must have been loaded, is it still visible? - JInternalFrame[] frames = Desktop.desktop.getAllFrames(); + JInternalFrame[] frames = Desktop.getDesktopPane().getAllFrames(); String matchedFile = null; for (int f = frames.length - 1; f > -1; f--) { @@ -1205,9 +1232,9 @@ public class Jalview2XML { // FIND ANY ASSOCIATED TREES // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT - if (Desktop.desktop != null) + if (Desktop.getDesktopPane() != null) { - JInternalFrame[] frames = Desktop.desktop.getAllFrames(); + JInternalFrame[] frames = Desktop.getDesktopPane().getAllFrames(); for (int t = 0; t < frames.length; t++) { @@ -1251,9 +1278,9 @@ public class Jalview2XML /* * save PCA viewers */ - if (!storeDS && Desktop.desktop != null) + if (!storeDS && Desktop.getDesktopPane() != null) { - for (JInternalFrame frame : Desktop.desktop.getAllFrames()) + for (JInternalFrame frame : Desktop.getDesktopPane().getAllFrames()) { if (frame instanceof PCAPanel) { @@ -1644,6 +1671,7 @@ public class Jalview2XML // using save and then load try { + fileName = fileName.replace('\\', '/'); System.out.println("Writing jar entry " + fileName); JarEntry entry = new JarEntry(fileName); jout.putNextEntry(entry); @@ -1890,11 +1918,11 @@ public class Jalview2XML final SequenceI jds, List viewIds, AlignmentPanel ap, boolean storeDataset) { - if (Desktop.desktop == null) + if (Desktop.getDesktopPane() == null) { return; } - JInternalFrame[] frames = Desktop.desktop.getAllFrames(); + JInternalFrame[] frames = Desktop.getDesktopPane().getAllFrames(); for (int f = frames.length - 1; f > -1; f--) { if (frames[f] instanceof AppVarna) @@ -2014,6 +2042,7 @@ public class Jalview2XML { if (jout != null) { + jarEntryName = jarEntryName.replace('\\','/'); System.out.println("Writing jar entry " + jarEntryName); jout.putNextEntry(new JarEntry(jarEntryName)); DataOutputStream dout = new DataOutputStream(jout); @@ -2349,7 +2378,7 @@ public class Jalview2XML if (calcIdParam.getVersion().equals("1.0")) { final String[] calcIds = calcIdParam.getServiceURL().toArray(new String[0]); - Jws2Instance service = Jws2Discoverer.getDiscoverer() + Jws2Instance service = Jws2Discoverer.getInstance() .getPreferredServiceFor(calcIds); if (service != null) { @@ -2474,7 +2503,7 @@ public class Jalview2XML vamsasSeq.setName(jds.getName()); vamsasSeq.setSequence(jds.getSequenceAsString()); vamsasSeq.setDescription(jds.getDescription()); - jalview.datamodel.DBRefEntry[] dbrefs = null; + List dbrefs = null; if (jds.getDatasetSequence() != null) { vamsasSeq.setDsseqid(seqHash(jds.getDatasetSequence())); @@ -2492,15 +2521,16 @@ public class Jalview2XML } if (dbrefs != null) { - for (int d = 0; d < dbrefs.length; d++) + for (int d = 0, nd = dbrefs.size(); d < nd; 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 ref = dbrefs.get(d); + dbref.setSource(ref.getSource()); + dbref.setVersion(ref.getVersion()); + dbref.setAccessionId(ref.getAccessionId()); + if (ref.hasMap()) { - Mapping mp = createVamsasMapping(dbrefs[d].getMap(), parentseq, + Mapping mp = createVamsasMapping(ref.getMap(), parentseq, jds, recurse); dbref.setMapping(mp); } @@ -2696,7 +2726,7 @@ public class Jalview2XML * @param file * - HTTP URL or filename */ - public AlignFrame loadJalviewAlign(final String file) + public AlignFrame loadJalviewAlign(final Object file) { jalview.gui.AlignFrame af = null; @@ -2730,7 +2760,7 @@ public class Jalview2XML public void run() { setLoadingFinishedForNewStructureViewers(); - }; + } }); } catch (Exception x) { @@ -2740,44 +2770,52 @@ public class Jalview2XML return af; } - private jarInputStreamProvider createjarInputStreamProvider( - final String file) throws MalformedURLException - { - URL url = null; - errorMessage = null; - uniqueSetSuffix = null; - seqRefIds = null; - viewportsAdded.clear(); - frefedSequence = null; - - if (file.startsWith("http://")) - { - url = new URL(file); - } - final URL _url = url; - return new jarInputStreamProvider() - { - - @Override - public JarInputStream getJarInputStream() throws IOException - { - if (_url != null) - { - return new JarInputStream(_url.openStream()); - } - else - { - return new JarInputStream(new FileInputStream(file)); - } - } - - @Override - public String getFilename() - { - return file; - } - }; - } + @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 (file.startsWith("http://")) { + 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 @@ -2819,9 +2857,6 @@ public class Jalview2XML if (jarentry != null && jarentry.getName().endsWith(".xml")) { - InputStreamReader in = new InputStreamReader(jin, UTF_8); - // JalviewModel object = new JalviewModel(); - JAXBContext jc = JAXBContext .newInstance("jalview.xml.binding.jalview"); XMLStreamReader streamReader = XMLInputFactory.newInstance() @@ -2831,11 +2866,6 @@ public class Jalview2XML .unmarshal(streamReader, JalviewModel.class); JalviewModel object = jbe.getValue(); - /* - Unmarshaller unmar = new Unmarshaller(object); - unmar.setValidation(false); - object = (JalviewModel) unmar.unmarshal(in); - */ if (true) // !skipViewport(object)) { _af = loadFromObject(object, file, true, jprovider); @@ -2882,20 +2912,11 @@ 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) + if (Desktop.getInstance() != null) { - Desktop.instance.stopLoading(); + Desktop.getInstance().stopLoading(); } if (af != null) { @@ -2923,7 +2944,7 @@ public class Jalview2XML */ for (AlignFrame fr : gatherToThisFrame.values()) { - Desktop.instance.gatherViews(fr); + Desktop.getInstance().gatherViews(fr); } restoreSplitFrames(); @@ -2931,8 +2952,7 @@ public class Jalview2XML { if (ds.getCodonFrames() != null) { - StructureSelectionManager - .getStructureSelectionManager(Desktop.instance) + Desktop.getInstance().getStructureSelectionManager() .registerMappings(ds.getCodonFrames()); } } @@ -2941,9 +2961,9 @@ public class Jalview2XML reportErrors(); } - if (Desktop.instance != null) + if (Desktop.getInstance() != null) { - Desktop.instance.stopLoading(); + Desktop.getInstance().stopLoading(); } return af; @@ -3024,7 +3044,7 @@ public class Jalview2XML */ for (SplitFrame sf : gatherTo) { - Desktop.instance.gatherViews(sf); + Desktop.getInstance().gatherViews(sf); } splitFrameCandidates.clear(); @@ -3083,7 +3103,7 @@ public class Jalview2XML @Override public void run() { - JvOptionPane.showInternalMessageDialog(Desktop.desktop, + JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(), finalErrorMessage, "Error " + (saving ? "saving" : "loading") + " Jalview file", @@ -3553,8 +3573,7 @@ public class Jalview2XML { entry.setProperty(prop.getName(), prop.getValue()); } - StructureSelectionManager - .getStructureSelectionManager(Desktop.instance) + Desktop.getInstance().getStructureSelectionManager() .registerPDBEntry(entry); // adds PDBEntry to datasequence's set (since Jalview 2.10) if (al.getSequenceAt(i).getDatasetSequence() != null) @@ -3853,7 +3872,7 @@ public class Jalview2XML } else { - cs = ColourSchemeProperty.getColourScheme(al, + cs = ColourSchemeProperty.getColourScheme(null, al, jGroup.getColour()); } } @@ -4181,10 +4200,8 @@ 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" @@ -4274,7 +4291,7 @@ public class Jalview2XML int height = safeInt(structureState.getHeight()); // Probably don't need to do this anymore... - // Desktop.desktop.getComponentAt(x, y); + // Desktop.getDesktop().getComponentAt(x, y); // TODO: NOW: check that this recovers the PDB file correctly. String pdbFile = loadPDBFile(jprovider, pdbid.getId(), pdbid.getFile()); @@ -4758,7 +4775,7 @@ public class Jalview2XML { try { - frames = Desktop.desktop.getAllFrames(); + frames = Desktop.getDesktopPane().getAllFrames(); } catch (ArrayIndexOutOfBoundsException e) { // occasional No such child exceptions are thrown here... @@ -4835,7 +4852,18 @@ public class Jalview2XML { AlignFrame af = null; af = new AlignFrame(al, safeInt(view.getWidth()), - safeInt(view.getHeight()), uniqueSeqSetId, viewId); + safeInt(view.getHeight()), uniqueSeqSetId, viewId) +// { +// +// @Override +// protected void processKeyEvent(java.awt.event.KeyEvent e) { +// System.out.println("Jalview2XML AF " + e); +// super.processKeyEvent(e); +// +// } +// +// } + ; af.setFileName(file, FileFormat.Jalview); @@ -4967,25 +4995,27 @@ 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 @@ -5061,7 +5091,8 @@ 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) { @@ -5263,7 +5294,7 @@ public class Jalview2XML else { cs = new AnnotationColourGradient(matchedAnnotation, - ColourSchemeProperty.getColourScheme(al, + ColourSchemeProperty.getColourScheme(af.getViewport(), al, viewAnnColour.getColourScheme()), safeInt(viewAnnColour.getAboveThreshold())); } @@ -5829,15 +5860,16 @@ 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 +5879,9 @@ public class Jalview2XML frefedSequence.add(newMappingRef(dsfor, jmap)); } } - else + else if (m.getSequence() != null) { - /** + /* * local sequence definition */ Sequence ms = m.getSequence(); @@ -6555,7 +6587,7 @@ 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();