X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fproject%2FJalview2XML.java;h=186f7866b2e7fdbe3652af5660ab2f7815789a67;hb=cb51e62fe2166b236ef488e0a8f35081fcd71388;hp=7b23c8d16c4415c76fd6f047f84df0e93808d888;hpb=d9a4775abc320c59c605b143c665ff0fede7783d;p=jalview.git diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java index 7b23c8d..186f786 100644 --- a/src/jalview/project/Jalview2XML.java +++ b/src/jalview/project/Jalview2XML.java @@ -28,6 +28,7 @@ import jalview.analysis.Conservation; import jalview.analysis.PCA; import jalview.analysis.scoremodels.ScoreModels; import jalview.analysis.scoremodels.SimilarityParams; +import jalview.api.AlignmentViewPanel; import jalview.api.FeatureColourI; import jalview.api.ViewStyleI; import jalview.api.analysis.ScoreModelI; @@ -38,6 +39,7 @@ 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; @@ -81,7 +83,6 @@ 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; @@ -149,9 +150,11 @@ import jalview.xml.binding.jalview.ThresholdType; import jalview.xml.binding.jalview.VAMSAS; import java.awt.Color; +import java.awt.Dimension; 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; @@ -161,7 +164,6 @@ import java.io.IOException; import java.io.InputStreamReader; import java.io.OutputStreamWriter; import java.io.PrintWriter; -import java.lang.reflect.InvocationTargetException; import java.math.BigInteger; import java.net.MalformedURLException; import java.net.URL; @@ -208,6 +210,15 @@ 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 +462,7 @@ public class Jalview2XML public boolean isResolvable() { return super.isResolvable() && mp.getTo() != null; - }; + } @Override boolean resolve() @@ -613,13 +624,14 @@ public class Jalview2XML * core method for storing state for a set of AlignFrames. * * @param frames - * - frames involving all data to be exported (including containing - * splitframes) + * - frames involving all data to be exported (including those + * contained in splitframes, though not the split frames themselves) * @param jout * - project output stream */ private void saveAllFrames(List frames, JarOutputStream jout) { + Hashtable dsses = new Hashtable<>(); /* @@ -642,21 +654,22 @@ public class Jalview2XML for (int i = frames.size() - 1; i > -1; i--) { AlignFrame af = frames.get(i); + AlignViewport vp = af.getViewport(); // skip ? if (skipList != null && skipList - .containsKey(af.getViewport().getSequenceSetId())) + .containsKey(vp.getSequenceSetId())) { continue; } String shortName = makeFilename(af, shortNames); - int apSize = af.getAlignPanels().size(); - + AlignmentI alignment = vp.getAlignment(); + List panels = af.getAlignPanels(); + int apSize = panels.size(); for (int ap = 0; ap < apSize; ap++) - { - AlignmentPanel apanel = (AlignmentPanel) af.getAlignPanels() - .get(ap); + { + AlignmentPanel apanel = (AlignmentPanel) panels.get(ap); String fileName = apSize == 1 ? shortName : ap + shortName; if (!fileName.endsWith(".xml")) { @@ -664,11 +677,17 @@ public class Jalview2XML } saveState(apanel, fileName, jout, viewIds); - - String dssid = getDatasetIdRef( - af.getViewport().getAlignment().getDataset()); + } + if (apSize > 0) + { + // BH moved next bit out of inner loop, not that it really matters. + // so we are testing to make sure we actually have an alignment, + // apparently. + String dssid = getDatasetIdRef(alignment.getDataset()); if (!dsses.containsKey(dssid)) { + // We have not already covered this data by reference from another + // frame. dsses.put(dssid, af); } } @@ -683,7 +702,6 @@ public class Jalview2XML } catch (Exception foo) { } - ; jout.close(); } catch (Exception ex) { @@ -745,9 +763,10 @@ public class Jalview2XML try { // create backupfiles object and get new temp filename destination - BackupFiles backupfiles = new BackupFiles(jarFile); - FileOutputStream fos = new FileOutputStream( - backupfiles.getTempFilePath()); + 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<>(); @@ -768,12 +787,14 @@ public class Jalview2XML } catch (Exception foo) { } - ; jout.close(); boolean success = true; - backupfiles.setWriteSuccess(success); - success = backupfiles.rollBackupsAndRenameTempFile(); + if (doBackup) + { + backupfiles.setWriteSuccess(success); + success = backupfiles.rollBackupsAndRenameTempFile(); + } return success; } catch (Exception ex) @@ -784,10 +805,22 @@ public class Jalview2XML } } + /** + * Each AlignFrame has a single data set associated with it. Note that none of + * these frames are split frames, because Desktop.getAlignFrames() collects + * top and bottom separately here. + * + * @param dsses + * @param fileName + * @param jout + */ private void writeDatasetFor(Hashtable dsses, String fileName, JarOutputStream jout) { + // Note that in saveAllFrames we have associated each specific dataset to + // ONE of its associated frames. + for (String dssids : dsses.keySet()) { AlignFrame _af = dsses.get(dssids); @@ -1068,7 +1101,7 @@ 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--) { @@ -1220,9 +1253,9 @@ 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++) { @@ -1266,9 +1299,9 @@ 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) { @@ -1659,6 +1692,7 @@ 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); @@ -1905,11 +1939,11 @@ 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) @@ -2029,6 +2063,7 @@ 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); @@ -2364,7 +2399,7 @@ 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) { @@ -2489,7 +2524,7 @@ 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())); @@ -2507,15 +2542,16 @@ 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); } @@ -2711,7 +2747,7 @@ 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; @@ -2739,13 +2775,14 @@ public class Jalview2XML { try { - SwingUtilities.invokeAndWait(new Runnable() + // BH 2019 -- can't wait + SwingUtilities.invokeLater(new Runnable() { @Override public void run() { setLoadingFinishedForNewStructureViewers(); - }; + } }); } catch (Exception x) { @@ -2755,44 +2792,52 @@ 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 @@ -2818,12 +2863,19 @@ public class Jalview2XML IdentityHashMap importedDatasets = new IdentityHashMap<>(); Map gatherToThisFrame = new HashMap<>(); final String file = jprovider.getFilename(); + + List alignFrames = new ArrayList<>(); + try { JarInputStream jin = null; JarEntry jarentry = null; int entryCount = 1; + + // Look for all the entry names ending with ".xml" + // This includes all panels and at least one frame. +// Platform.timeCheck(null, Platform.TIME_MARK); do { jin = jprovider.getJarInputStream(); @@ -2831,12 +2883,27 @@ public class Jalview2XML { jarentry = jin.getNextJarEntry(); } + String name = (jarentry == null ? null : jarentry.getName()); - if (jarentry != null && jarentry.getName().endsWith(".xml")) +// System.out.println("Jalview2XML opening " + name); + if (name != null && name.endsWith(".xml")) { - InputStreamReader in = new InputStreamReader(jin, UTF_8); - // JalviewModel object = new JalviewModel(); + // DataSet for.... is read last. + + + // The question here is what to do with the two + // .xml files in the jvp file. + // Some number of them, "...Dataset for...", will be the + // Only AlignPanels and will have Viewport. + // One or more will be the source data, with the DBRefs. + // + // JVP file writing (above) ensures tha the AlignPanels are written + // first, then all relevant datasets (which are + // Jalview.datamodel.Alignment). + // + +// Platform.timeCheck("Jalview2XML JAXB " + name, Platform.TIME_MARK); JAXBContext jc = JAXBContext .newInstance("jalview.xml.binding.jalview"); XMLStreamReader streamReader = XMLInputFactory.newInstance() @@ -2844,19 +2911,25 @@ public class Jalview2XML javax.xml.bind.Unmarshaller um = jc.createUnmarshaller(); JAXBElement jbe = um .unmarshal(streamReader, JalviewModel.class); - JalviewModel object = jbe.getValue(); + JalviewModel model = jbe.getValue(); - /* - Unmarshaller unmar = new Unmarshaller(object); - unmar.setValidation(false); - object = (JalviewModel) unmar.unmarshal(in); - */ if (true) // !skipViewport(object)) { - _af = loadFromObject(object, file, true, jprovider); - if (_af != null && object.getViewport().size() > 0) - // getJalviewModelSequence().getViewportCount() > 0) + // Q: Do we have to load from the model, even if it + // does not have a viewport, could we discover that early on? + // Q: Do we need to load this object? + _af = loadFromObject(model, file, true, jprovider); +// Platform.timeCheck("Jalview2XML.loadFromObject", + // Platform.TIME_MARK); + + if (_af != null) + { + alignFrames.add(_af); + } + if (_af != null && model.getViewport().size() > 0) { + + // That is, this is one of the AlignmentPanel models if (af == null) { // store a reference to the first view @@ -2876,6 +2949,7 @@ public class Jalview2XML af.getViewport().getAlignment().getDataset()); } } +// Platform.timeCheck("JAXB " + name, Platform.TIME_MARK); entryCount++; } else if (jarentry != null) @@ -2884,7 +2958,10 @@ public class Jalview2XML entryCount++; } } while (jarentry != null); +// Platform.timeCheck("JAXB loop exit", Platform.TIME_MARK); resolveFrefedSequences(); +// Platform.timeCheck("JAXB resolveFrefed", Platform.TIME_MARK); + } catch (IOException ex) { ex.printStackTrace(); @@ -2899,9 +2976,9 @@ public class Jalview2XML { // 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) { @@ -2918,6 +2995,13 @@ public class Jalview2XML errorMessage = "Out of memory loading jalview XML file"; System.err.println("Out of memory whilst loading jalview XML file"); e.printStackTrace(); + } finally + { + for (AlignFrame alf : alignFrames) + { + alf.alignPanel.setHoldRepaint(false); + } + } /* @@ -2929,7 +3013,7 @@ public class Jalview2XML */ for (AlignFrame fr : gatherToThisFrame.values()) { - Desktop.instance.gatherViews(fr); + Desktop.getInstance().gatherViews(fr); } restoreSplitFrames(); @@ -2937,8 +3021,7 @@ public class Jalview2XML { if (ds.getCodonFrames() != null) { - StructureSelectionManager - .getStructureSelectionManager(Desktop.instance) + Desktop.getStructureSelectionManager() .registerMappings(ds.getCodonFrames()); } } @@ -2947,9 +3030,9 @@ public class Jalview2XML reportErrors(); } - if (Desktop.instance != null) + if (Desktop.getInstance() != null) { - Desktop.instance.stopLoading(); + Desktop.getInstance().stopLoading(); } return af; @@ -3030,7 +3113,7 @@ public class Jalview2XML */ for (SplitFrame sf : gatherTo) { - Desktop.instance.gatherViews(sf); + Desktop.getInstance().gatherViews(sf); } splitFrameCandidates.clear(); @@ -3089,7 +3172,7 @@ public class Jalview2XML @Override public void run() { - JvOptionPane.showInternalMessageDialog(Desktop.desktop, + JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(), finalErrorMessage, "Error " + (saving ? "saving" : "loading") + " Jalview file", @@ -3248,7 +3331,9 @@ public class Jalview2XML } /** - * Load alignment frame from jalview XML DOM object + * Load alignment frame from jalview XML DOM object. For a DOM object that + * includes one or more Viewport elements (one with a title that does NOT + * contain "Dataset for"), create the frame. * * @param jalviewModel * DOM @@ -3263,9 +3348,13 @@ public class Jalview2XML AlignFrame loadFromObject(JalviewModel jalviewModel, String file, boolean loadTreesAndStructures, jarInputStreamProvider jprovider) { + +// Platform.timeCheck("Jalview2XML.loadFromObject0", Platform.TIME_MARK); + SequenceSet vamsasSet = jalviewModel.getVamsasModel().getSequenceSet().get(0); List vamsasSeqs = vamsasSet.getSequence(); + // JalviewModelSequence jms = object.getJalviewModelSequence(); // Viewport view = (jms.getViewportCount() > 0) ? jms.getViewport(0) @@ -3296,6 +3385,7 @@ public class Jalview2XML : view.getId() + uniqueSetSuffix); } +// Platform.timeCheck("Jalview2XML.loadFromObject1", Platform.TIME_MARK); // //////////////////////////////// // LOAD SEQUENCES @@ -3316,6 +3406,7 @@ public class Jalview2XML 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 @@ -3380,6 +3471,8 @@ public class Jalview2XML } } +// Platform.timeCheck("Jalview2XML.loadFromObject-seq", +// Platform.TIME_MARK); // / // Create the alignment object from the sequence set // /////////////////////////////// @@ -3420,6 +3513,8 @@ public class Jalview2XML recoverDatasetFor(vamsasSet, al, isdsal, uniqueSeqSetId); } +// Platform.timeCheck("Jalview2XML.loadFromObject-align", +// Platform.TIME_MARK); if (referenceseqForView != null) { al.setSeqrep(referenceseqForView); @@ -3432,6 +3527,8 @@ public class Jalview2XML al.setProperty(ssp.getKey(), ssp.getValue()); } +// Platform.timeCheck("Jalview2XML.loadFromObject-setseqprop", +// Platform.TIME_MARK); // /////////////////////////////// Hashtable pdbloaded = new Hashtable(); // TODO nothing writes to this?? @@ -3445,6 +3542,7 @@ public class Jalview2XML // now, for 2.10 projects, this is also done if the xml doc includes // dataset sequences not actually present in any particular view. // +// Platform.timeCheck("J2XML features0", Platform.TIME_RESET); for (int i = 0; i < vamsasSeqs.size(); i++) { JSeq jseq = jseqs.get(i); @@ -3499,7 +3597,9 @@ public class Jalview2XML } // adds feature to datasequence's feature set (since Jalview 2.10) +// Platform.timeCheck(null, Platform.TIME_SET); al.getSequenceAt(i).addSequenceFeature(sf); +// Platform.timeCheck(null, Platform.TIME_MARK); } } if (vamsasSeqs.get(i).getDBRef().size() > 0) @@ -3559,8 +3659,7 @@ public class Jalview2XML { entry.setProperty(prop.getName(), prop.getValue()); } - StructureSelectionManager - .getStructureSelectionManager(Desktop.instance) + Desktop.getStructureSelectionManager() .registerPDBEntry(entry); // adds PDBEntry to datasequence's set (since Jalview 2.10) if (al.getSequenceAt(i).getDatasetSequence() != null) @@ -3573,7 +3672,12 @@ public class Jalview2XML } } } + } + +// Platform.timeCheck("features done", Platform.TIME_GET); +// Platform.timeCheck("Jalview2XML.loadFromObject-endmultiview", +// Platform.TIME_MARK); } // end !multipleview // /////////////////////////////// @@ -3615,6 +3719,8 @@ public class Jalview2XML al.addCodonFrame(cf); } } +// Platform.timeCheck("Jalview2XML.loadFromObject-seqmap", +// Platform.TIME_MARK); } // //////////////////////////////// @@ -3675,6 +3781,9 @@ public class Jalview2XML } // Construct new annotation from model. List ae = annotation.getAnnotationElement(); +// System.err.println( +// "Jalview2XML processing " + ae.size() + " annotations"); + jalview.datamodel.Annotation[] anot = null; java.awt.Color firstColour = null; int anpos; @@ -3710,6 +3819,7 @@ public class Jalview2XML } } } + // create the new AlignmentAnnotation jalview.datamodel.AlignmentAnnotation jaa = null; if (annotation.isGraph()) @@ -3746,6 +3856,7 @@ public class Jalview2XML jaa._linecolour = firstColour; } // register new annotation + // Annotation graphs such as Conservation will not have id. if (annotation.getId() != null) { annotationIds.put(annotation.getId(), jaa); @@ -3834,6 +3945,8 @@ public class Jalview2XML al.addAnnotation(jaa); } } +// Platform.timeCheck("Jalview2XML.loadFromObject-annot", +// Platform.TIME_MARK); } // /////////////////////// // LOAD GROUPS @@ -3859,7 +3972,7 @@ public class Jalview2XML } else { - cs = ColourSchemeProperty.getColourScheme(al, + cs = ColourSchemeProperty.getColourScheme(null, al, jGroup.getColour()); } } @@ -3948,6 +4061,8 @@ public class Jalview2XML jGroup.getAnnotationColours(), null, al, jalviewModel, false)); } } +// Platform.timeCheck("Jalview2XML.loadFromObject-groups", +// Platform.TIME_MARK); } if (view == null) { @@ -3957,8 +4072,6 @@ public class Jalview2XML // /////////////////////////////// // LOAD VIEWPORT - AlignFrame af = null; - AlignViewport av = null; // now check to see if we really need to create a new viewport. if (multipleView && viewportsAdded.size() == 0) { @@ -3989,6 +4102,8 @@ public class Jalview2XML } } +// Platform.timeCheck("Jalview2XML.loadFromObject-viewport", +// Platform.TIME_MARK); } /** * indicate that annotation colours are applied across all groups (pre @@ -3997,8 +4112,9 @@ public class Jalview2XML boolean doGroupAnnColour = Jalview2XML.isVersionStringLaterThan("2.8.1", jalviewModel.getVersion()); + AlignFrame af = null; AlignmentPanel ap = null; - boolean isnewview = true; + AlignViewport av = null; if (viewId != null) { // Check to see if this alignment already has a view id == viewId @@ -4008,25 +4124,27 @@ public class Jalview2XML { for (int v = 0; v < views.length; v++) { - if (views[v].av.getViewId().equalsIgnoreCase(viewId)) + ap = views[v]; + av = ap.av; + if (av.getViewId().equalsIgnoreCase(viewId)) { // recover the existing alignpanel, alignframe, viewport - af = views[v].alignFrame; - av = views[v].av; - ap = views[v]; + af = ap.alignFrame; + break; // TODO: could even skip resetting view settings if we don't want to // change the local settings from other jalview processes - isnewview = false; } } } } - if (isnewview) + if (af == null) { af = loadViewport(file, jseqs, hiddenSeqs, al, jalviewModel, view, uniqueSeqSetId, viewId, autoAlan); av = af.getViewport(); + // note that this only retrieves the most recently accessed + // tab of an AlignFrame. ap = af.alignPanel; } @@ -4035,14 +4153,61 @@ public class Jalview2XML * * Not done if flag is false (when this method is used for New View) */ + final AlignFrame af0 = af; + final AlignViewport av0 = av; + final AlignmentPanel ap0 = ap; +// Platform.timeCheck("Jalview2XML.loadFromObject-beforetree", +// Platform.TIME_MARK); if (loadTreesAndStructures) { - loadTrees(jalviewModel, view, af, av, ap); - loadPCAViewers(jalviewModel, ap); - loadPDBStructures(jprovider, jseqs, af, ap); - loadRnaViewers(jprovider, jseqs, ap); + if (!jalviewModel.getTree().isEmpty()) + { + SwingUtilities.invokeLater(new Runnable() + { + @Override + public void run() + { +// Platform.timeCheck(null, Platform.TIME_MARK); + loadTrees(jalviewModel, view, af0, av0, ap0); +// Platform.timeCheck("Jalview2XML.loadTrees", Platform.TIME_MARK); + } + }); + } + if (!jalviewModel.getPcaViewer().isEmpty()) + { + SwingUtilities.invokeLater(new Runnable() + { + @Override + public void run() + { +// Platform.timeCheck(null, Platform.TIME_MARK); + loadPCAViewers(jalviewModel, ap0); +// Platform.timeCheck("Jalview2XML.loadPCA", Platform.TIME_MARK); + } + }); + } + SwingUtilities.invokeLater(new Runnable() + { + @Override + public void run() + { +// Platform.timeCheck(null, Platform.TIME_MARK); + loadPDBStructures(jprovider, jseqs, af0, ap0); +// Platform.timeCheck("Jalview2XML.loadPDB", Platform.TIME_MARK); + } + }); + SwingUtilities.invokeLater(new Runnable() + { + @Override + public void run() + { + loadRnaViewers(jprovider, jseqs, ap0); + } + }); } // and finally return. + // but do not set holdRepaint true just yet, because this could be the + // initial frame with just its dataset. return af; } @@ -4059,7 +4224,7 @@ public class Jalview2XML * @param jseqs * @param ap */ - private void loadRnaViewers(jarInputStreamProvider jprovider, + protected void loadRnaViewers(jarInputStreamProvider jprovider, List jseqs, AlignmentPanel ap) { /* @@ -4187,10 +4352,8 @@ 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" @@ -4280,7 +4443,7 @@ 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()); @@ -4599,9 +4762,9 @@ public class Jalview2XML final AlignFrame alf = af; final Rectangle rect = new Rectangle(svattrib.getX(), svattrib.getY(), svattrib.getWidth(), svattrib.getHeight()); - try - { - javax.swing.SwingUtilities.invokeAndWait(new Runnable() + // try + // { + javax.swing.SwingUtilities.invokeLater(new Runnable() { @Override public void run() @@ -4628,14 +4791,14 @@ public class Jalview2XML } } }); - } catch (InvocationTargetException ex) - { - warn("Unexpected error when opening Jmol view.", ex); - - } catch (InterruptedException e) - { - // e.printStackTrace(); - } + // } catch (InvocationTargetException ex) + // { + // warn("Unexpected error when opening Jmol view.", ex); + // + // } catch (InterruptedException e) + // { + // // e.printStackTrace(); + // } } @@ -4764,7 +4927,7 @@ public class Jalview2XML { try { - frames = Desktop.desktop.getAllFrames(); + frames = Desktop.getDesktopPane().getAllFrames(); } catch (ArrayIndexOutOfBoundsException e) { // occasional No such child exceptions are thrown here... @@ -4835,14 +4998,25 @@ public class Jalview2XML } AlignFrame loadViewport(String file, List JSEQ, - List hiddenSeqs, AlignmentI al, - JalviewModel jm, Viewport view, String uniqueSeqSetId, - String viewId, List autoAlan) + List hiddenSeqs, AlignmentI al, JalviewModel jm, + Viewport view, String uniqueSeqSetId, String viewId, + List autoAlan) { 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.alignPanel.setHoldRepaint(true); af.setFileName(file, FileFormat.Jalview); final AlignViewport viewport = af.getViewport(); @@ -4918,9 +5092,8 @@ public class Jalview2XML viewport.setColourText(safeBoolean(view.isShowColourText())); - viewport - .setConservationSelected( - safeBoolean(view.isConservationSelected())); + viewport.setConservationSelected( + safeBoolean(view.isConservationSelected())); viewport.setIncrement(safeInt(view.getConsThreshold())); viewport.setShowJVSuffix(safeBoolean(view.isShowFullId())); viewport.setRightAlignIds(safeBoolean(view.isRightAlignIds())); @@ -4951,8 +5124,18 @@ public class Jalview2XML viewport.setViewName(view.getViewName()); af.setInitialTabVisible(); } - af.setBounds(safeInt(view.getXpos()), safeInt(view.getYpos()), - safeInt(view.getWidth()), safeInt(view.getHeight())); + int x = safeInt(view.getXpos()); + int y = safeInt(view.getYpos()); + int w = safeInt(view.getWidth()); + int h = safeInt(view.getHeight()); + // // BH we cannot let the title bar go off the top + // if (Platform.isJS()) + // { + // x = Math.max(50 - w, x); + // y = Math.max(0, y); + // } + + af.setBounds(x, y, w, h); // startSeq set in af.alignPanel.updateLayout below af.alignPanel.updateLayout(); ColourSchemeI cs = null; @@ -4973,30 +5156,31 @@ 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 - .setShowSequenceFeatures( - safeBoolean(view.isShowSequenceFeatures())); + viewport.setShowSequenceFeatures( + safeBoolean(view.isShowSequenceFeatures())); viewport.setCentreColumnLabels(view.isCentreColumnLabels()); viewport.setIgnoreGapsConsensus(view.isIgnoreGapsinConsensus(), null); @@ -5017,13 +5201,13 @@ public class Jalview2XML .getFeatureRenderer(); FeaturesDisplayed fdi; viewport.setFeaturesDisplayed(fdi = new FeaturesDisplayed()); - String[] renderOrder = new String[jm.getFeatureSettings() - .getSetting().size()]; + String[] renderOrder = new String[jm.getFeatureSettings().getSetting() + .size()]; Map featureColours = new Hashtable<>(); Map featureOrder = new Hashtable<>(); - for (int fs = 0; fs < jm.getFeatureSettings() - .getSetting().size(); fs++) + for (int fs = 0; fs < jm.getFeatureSettings().getSetting() + .size(); fs++) { Setting setting = jm.getFeatureSettings().getSetting().get(fs); String featureType = setting.getType(); @@ -5035,8 +5219,8 @@ public class Jalview2XML .getMatcherSet(); if (filters != null) { - FeatureMatcherSetI filter = Jalview2XML - .parseFilter(featureType, filters); + FeatureMatcherSetI filter = Jalview2XML.parseFilter(featureType, + filters); if (!filter.isEmpty()) { fr.setFeatureFilter(featureType, filter); @@ -5067,8 +5251,8 @@ public class Jalview2XML float min = safeFloat(safeFloat(setting.getMin())); float max = setting.getMax() == null ? 1f : setting.getMax().floatValue(); - FeatureColourI gc = new FeatureColour(minColour, maxColour, - noValueColour, min, max); + FeatureColourI gc = new FeatureColour(maxColour, minColour, + maxColour, noValueColour, min, max); if (setting.getAttributeName().size() > 0) { gc.setAttributeName(setting.getAttributeName().toArray( @@ -5102,8 +5286,7 @@ public class Jalview2XML } else { - featureColours.put(featureType, - new FeatureColour(maxColour)); + featureColours.put(featureType, new FeatureColour(maxColour)); } renderOrder[fs] = featureType; if (setting.getOrder() != null) @@ -5171,8 +5354,9 @@ public class Jalview2XML String complementaryViewId = view.getComplementId(); if (complementaryViewId == null) { - Desktop.addInternalFrame(af, view.getTitle(), + Dimension dim = Platform.getDimIfEmbedded(af, safeInt(view.getWidth()), safeInt(view.getHeight())); + Desktop.addInternalFrame(af, view.getTitle(), dim.width, dim.height); // recompute any autoannotation af.alignPanel.updateAnnotation(false, true); reorderAutoannotation(af, al, autoAlan); @@ -5269,7 +5453,7 @@ public class Jalview2XML else { cs = new AnnotationColourGradient(matchedAnnotation, - ColourSchemeProperty.getColourScheme(al, + ColourSchemeProperty.getColourScheme(af.getViewport(), al, viewAnnColour.getColourScheme()), safeInt(viewAnnColour.getAboveThreshold())); } @@ -5517,8 +5701,8 @@ public class Jalview2XML SequenceI[] dsseqs = new SequenceI[dseqs.size()]; dseqs.copyInto(dsseqs); ds = new jalview.datamodel.Alignment(dsseqs); - debug("Created new dataset " + vamsasSet.getDatasetId() - + " for alignment " + System.identityHashCode(al)); +// debug("Jalview2XML Created new dataset " + vamsasSet.getDatasetId() +// + " for alignment " + System.identityHashCode(al)); addDatasetRef(vamsasSet.getDatasetId(), ds); } // set the dataset for the newly imported alignment. @@ -5835,15 +6019,16 @@ 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)); @@ -5853,9 +6038,9 @@ public class Jalview2XML frefedSequence.add(newMappingRef(dsfor, jmap)); } } - else + else if (m.getSequence() != null) { - /** + /* * local sequence definition */ Sequence ms = m.getSequence(); @@ -5931,14 +6116,7 @@ public class Jalview2XML AlignFrame af = loadFromObject(jm, null, false, null); af.getAlignPanels().clear(); af.closeMenuItem_actionPerformed(true); - - /* - * if(ap.av.getAlignment().getAlignmentAnnotation()!=null) { for(int i=0; - * i attributeName = colourModel.getAttributeName();