X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fproject%2FJalview2XML.java;h=2c93ee52d0f156c7de70fca6871c48163084067b;hb=14bfc6fb57f123b815f08dbf5b35544abd33b3af;hp=1aac037354855b018297ffa25e1b92476c959a4c;hpb=87256ba36fb105a1115067ffe2563412e9281d2d;p=jalview.git diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java index 1aac037..2c93ee5 100644 --- a/src/jalview/project/Jalview2XML.java +++ b/src/jalview/project/Jalview2XML.java @@ -28,12 +28,14 @@ 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; import jalview.api.analysis.SimilarityParamsI; import jalview.api.structures.JalviewStructureDisplayI; import jalview.bin.Cache; +import jalview.bin.Jalview; import jalview.datamodel.AlignedCodonFrame; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentAnnotation; @@ -82,7 +84,6 @@ 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; @@ -150,6 +151,7 @@ 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; @@ -160,10 +162,10 @@ import java.io.File; import java.io.FileInputStream; import java.io.FileOutputStream; import java.io.IOException; +import java.io.InputStream; 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; @@ -188,7 +190,6 @@ import java.util.jar.JarInputStream; import java.util.jar.JarOutputStream; import javax.swing.JInternalFrame; -import javax.swing.SwingUtilities; import javax.xml.bind.JAXBContext; import javax.xml.bind.JAXBElement; import javax.xml.bind.Marshaller; @@ -266,6 +267,25 @@ public class Jalview2XML private Map rnaSessions = new HashMap<>(); /** + * 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; + + /* + * JalviewJS only -- to allow read file bytes to be saved in the + * created AlignFrame, allowing File | Reload of a project file to work + * + * BH 2019 JAL-3436 + */ + private File jarFile; + + /** * A helper method for safely using the value of an optional attribute that * may be null if not present in the XML. Answers the boolean value, or false * if null. @@ -425,7 +445,7 @@ public class Jalview2XML * @param _jmap * @return */ - public SeqFref newMappingRef(final String sref, + protected SeqFref newMappingRef(final String sref, final jalview.datamodel.Mapping _jmap) { SeqFref fref = new SeqFref(sref, "Mapping") @@ -447,7 +467,7 @@ public class Jalview2XML return fref; } - public SeqFref newAlcodMapRef(final String sref, + protected SeqFref newAlcodMapRef(final String sref, final AlignedCodonFrame _cf, final jalview.datamodel.Mapping _jmap) { @@ -479,7 +499,7 @@ public class Jalview2XML return fref; } - public void resolveFrefedSequences() + protected void resolveFrefedSequences() { Iterator nextFref = frefedSequence.iterator(); int toresolve = frefedSequence.size(); @@ -624,13 +644,14 @@ 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<>(); /* @@ -653,21 +674,22 @@ 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")) { @@ -675,11 +697,17 @@ 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); } } @@ -797,10 +825,22 @@ 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); @@ -827,7 +867,7 @@ public class Jalview2XML * @param out * jar entry name */ - public JalviewModel saveState(AlignmentPanel ap, String fileName, + protected JalviewModel saveState(AlignmentPanel ap, String fileName, JarOutputStream jout, List viewIds) { return saveState(ap, fileName, false, jout, viewIds); @@ -849,7 +889,7 @@ public class Jalview2XML * @param out * jar entry name */ - public JalviewModel saveState(AlignmentPanel ap, String fileName, + protected JalviewModel saveState(AlignmentPanel ap, String fileName, boolean storeDS, JarOutputStream jout, List viewIds) { if (viewIds == null) @@ -2379,7 +2419,7 @@ 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) { @@ -2711,17 +2751,6 @@ public class Jalview2XML } /** - * 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 @@ -2755,7 +2784,9 @@ public class Jalview2XML { try { - SwingUtilities.invokeAndWait(new Runnable() + + // BH 2019 -- can't wait + Jalview.execRunnable(new Runnable() { @Override public void run() @@ -2768,55 +2799,55 @@ public class Jalview2XML System.err.println("Error loading alignment: " + x.getMessage()); } } + this.jarFile = null; 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()); + private jarInputStreamProvider createjarInputStreamProvider( + final Object ofile) throws MalformedURLException + { + 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; - } - } + if (bytes != null) + { + this.jarFile = (File) ofile; + } + errorMessage = null; + uniqueSetSuffix = null; + seqRefIds = null; + viewportsAdded.clear(); + frefedSequence = null; + + URL url = file.startsWith("http://") ? new URL(file) : null; + return new jarInputStreamProvider() + { + @Override + public JarInputStream getJarInputStream() throws IOException + { + InputStream is = bytes != null ? new ByteArrayInputStream(bytes) + : (url != null ? url.openStream() + : new FileInputStream(file)); + return new JarInputStream(is); + } + + @Override + public String getFilename() + { + return file; + } + }; + } catch (IOException e) + { + e.printStackTrace(); + return null; + } + } /** * Recover jalview session from a jalview project archive. Caller may @@ -2842,12 +2873,19 @@ 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(); @@ -2855,9 +2893,27 @@ 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")) { + + // 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() @@ -2865,14 +2921,25 @@ 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(); 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 @@ -2892,6 +2959,7 @@ public class Jalview2XML af.getViewport().getAlignment().getDataset()); } } +// Platform.timeCheck("JAXB " + name, Platform.TIME_MARK); entryCount++; } else if (jarentry != null) @@ -2900,7 +2968,10 @@ 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(); @@ -2934,6 +3005,13 @@ 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); + } + } /* @@ -2953,8 +3031,7 @@ public class Jalview2XML { if (ds.getCodonFrames() != null) { - StructureSelectionManager - .getStructureSelectionManager(Desktop.getInstance()) + Desktop.getStructureSelectionManager() .registerMappings(ds.getCodonFrames()); } } @@ -3264,7 +3341,9 @@ 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 @@ -3276,10 +3355,14 @@ public class Jalview2XML * data source provider * @return alignment frame created from view stored in DOM */ - AlignFrame loadFromObject(JalviewModel jalviewModel, String file, + private AlignFrame loadFromObject(JalviewModel jalviewModel, String file, boolean loadTreesAndStructures, jarInputStreamProvider jprovider) { - SequenceSet vamsasSet = jalviewModel.getVamsasModel().getSequenceSet().get(0); + + // Platform.timeCheck("Jalview2XML.loadFromObject0", Platform.TIME_MARK); + + SequenceSet vamsasSet = jalviewModel.getVamsasModel().getSequenceSet() + .get(0); List vamsasSeqs = vamsasSet.getSequence(); // JalviewModelSequence jms = object.getJalviewModelSequence(); @@ -3312,6 +3395,7 @@ public class Jalview2XML : view.getId() + uniqueSetSuffix); } + // Platform.timeCheck("Jalview2XML.loadFromObject1", Platform.TIME_MARK); // //////////////////////////////// // LOAD SEQUENCES @@ -3332,6 +3416,7 @@ 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 @@ -3396,6 +3481,8 @@ public class Jalview2XML } } + // Platform.timeCheck("Jalview2XML.loadFromObject-seq", + // Platform.TIME_MARK); // / // Create the alignment object from the sequence set // /////////////////////////////// @@ -3436,6 +3523,8 @@ public class Jalview2XML recoverDatasetFor(vamsasSet, al, isdsal, uniqueSeqSetId); } + // Platform.timeCheck("Jalview2XML.loadFromObject-align", + // Platform.TIME_MARK); if (referenceseqForView != null) { al.setSeqrep(referenceseqForView); @@ -3448,6 +3537,8 @@ 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?? @@ -3461,6 +3552,7 @@ 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); @@ -3515,7 +3607,9 @@ 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) @@ -3575,9 +3669,7 @@ public class Jalview2XML { entry.setProperty(prop.getName(), prop.getValue()); } - StructureSelectionManager - .getStructureSelectionManager(Desktop.getInstance()) - .registerPDBEntry(entry); + Desktop.getStructureSelectionManager().registerPDBEntry(entry); // adds PDBEntry to datasequence's set (since Jalview 2.10) if (al.getSequenceAt(i).getDatasetSequence() != null) { @@ -3589,7 +3681,12 @@ public class Jalview2XML } } } + } + + // Platform.timeCheck("features done", Platform.TIME_GET); + // Platform.timeCheck("Jalview2XML.loadFromObject-endmultiview", + // Platform.TIME_MARK); } // end !multipleview // /////////////////////////////// @@ -3623,14 +3720,16 @@ public class Jalview2XML else { // defer to later - frefedSequence.add( - newAlcodMapRef(map.getDnasq(), cf, mapping)); + frefedSequence + .add(newAlcodMapRef(map.getDnasq(), cf, mapping)); } } } al.addCodonFrame(cf); } } + // Platform.timeCheck("Jalview2XML.loadFromObject-seqmap", + // Platform.TIME_MARK); } // //////////////////////////////// @@ -3691,6 +3790,9 @@ 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; @@ -3726,6 +3828,7 @@ public class Jalview2XML } } } + // create the new AlignmentAnnotation jalview.datamodel.AlignmentAnnotation jaa = null; if (annotation.isGraph()) @@ -3762,6 +3865,7 @@ 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); @@ -3832,8 +3936,7 @@ public class Jalview2XML jaa.setCalcId(annotation.getCalcId()); if (annotation.getProperty().size() > 0) { - for (Annotation.Property prop : annotation - .getProperty()) + for (Annotation.Property prop : annotation.getProperty()) { jaa.setProperty(prop.getName(), prop.getValue()); } @@ -3850,6 +3953,8 @@ public class Jalview2XML al.addAnnotation(jaa); } } + // Platform.timeCheck("Jalview2XML.loadFromObject-annot", + // Platform.TIME_MARK); } // /////////////////////// // LOAD GROUPS @@ -3914,9 +4019,9 @@ public class Jalview2XML sg.setShowNonconserved(safeBoolean(jGroup.isShowUnconserved())); sg.thresholdTextColour = safeInt(jGroup.getTextColThreshold()); // attributes with a default in the schema are never null - sg.setShowConsensusHistogram(jGroup.isShowConsensusHistogram()); - sg.setshowSequenceLogo(jGroup.isShowSequenceLogo()); - sg.setNormaliseSequenceLogo(jGroup.isNormaliseSequenceLogo()); + sg.setShowConsensusHistogram(jGroup.isShowConsensusHistogram()); + sg.setshowSequenceLogo(jGroup.isShowSequenceLogo()); + sg.setNormaliseSequenceLogo(jGroup.isNormaliseSequenceLogo()); sg.setIgnoreGapsConsensus(jGroup.isIgnoreGapsinConsensus()); if (jGroup.getConsThreshold() != null && jGroup.getConsThreshold().intValue() != 0) @@ -3960,10 +4065,13 @@ public class Jalview2XML if (addAnnotSchemeGroup) { // reconstruct the annotation colourscheme - sg.setColourScheme(constructAnnotationColour( - jGroup.getAnnotationColours(), null, al, jalviewModel, false)); + sg.setColourScheme( + constructAnnotationColour(jGroup.getAnnotationColours(), + null, al, jalviewModel, false)); } } + // Platform.timeCheck("Jalview2XML.loadFromObject-groups", + // Platform.TIME_MARK); } if (view == null) { @@ -3973,8 +4081,6 @@ 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) { @@ -4005,6 +4111,8 @@ public class Jalview2XML } } + // Platform.timeCheck("Jalview2XML.loadFromObject-viewport", + // Platform.TIME_MARK); } /** * indicate that annotation colours are applied across all groups (pre @@ -4013,8 +4121,9 @@ 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 @@ -4024,25 +4133,27 @@ 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; } @@ -4051,14 +4162,62 @@ 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()) + { + Jalview.execRunnable(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()) + { + Jalview.execRunnable(new Runnable() + { + @Override + public void run() + { + // Platform.timeCheck(null, Platform.TIME_MARK); + loadPCAViewers(jalviewModel, ap0); + // Platform.timeCheck("Jalview2XML.loadPCA", Platform.TIME_MARK); + } + }); + } + Jalview.execRunnable(new Runnable() + { + @Override + public void run() + { + // Platform.timeCheck(null, Platform.TIME_MARK); + loadPDBStructures(jprovider, jseqs, af0, ap0); + // Platform.timeCheck("Jalview2XML.loadPDB", Platform.TIME_MARK); + } + }); + Jalview.execRunnable(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; } @@ -4075,7 +4234,7 @@ public class Jalview2XML * @param jseqs * @param ap */ - private void loadRnaViewers(jarInputStreamProvider jprovider, + protected void loadRnaViewers(jarInputStreamProvider jprovider, List jseqs, AlignmentPanel ap) { /* @@ -4613,9 +4772,9 @@ 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 + // { + Jalview.execRunnable(new Runnable() { @Override public void run() @@ -4641,15 +4800,16 @@ public class Jalview2XML } } } - }); - } catch (InvocationTargetException ex) - { - warn("Unexpected error when opening Jmol view.", ex); - - } catch (InterruptedException e) - { - // e.printStackTrace(); - } + }); + // javax.swing.SwingUtilities.invokeLater(r); + // } catch (InvocationTargetException ex) + // { + // warn("Unexpected error when opening Jmol view.", ex); + // + // } catch (InterruptedException e) + // { + // // e.printStackTrace(); + // } } @@ -4848,27 +5008,28 @@ public class Jalview2XML } } - AlignFrame loadViewport(String file, List JSEQ, - List hiddenSeqs, AlignmentI al, - JalviewModel jm, Viewport view, String uniqueSeqSetId, - String viewId, List autoAlan) + AlignFrame loadViewport(String fileName, List JSEQ, + 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) -// { -// -// @Override -// protected void processKeyEvent(java.awt.event.KeyEvent e) { -// System.out.println("Jalview2XML AF " + e); -// super.processKeyEvent(e); -// -// } -// -// } + 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); + af.alignPanel.setHoldRepaint(true); + af.setFileName(fileName, FileFormat.Jalview); + af.setFileObject(jarFile); // BH 2019 JAL-3436 final AlignViewport viewport = af.getViewport(); for (int i = 0; i < JSEQ.size(); i++) @@ -4943,9 +5104,8 @@ 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())); @@ -4976,8 +5136,18 @@ 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; @@ -5021,9 +5191,8 @@ public class Jalview2XML 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); @@ -5044,13 +5213,13 @@ 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(); @@ -5062,8 +5231,8 @@ 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); @@ -5095,8 +5264,7 @@ public class Jalview2XML float max = setting.getMax() == null ? 1f : setting.getMax().floatValue(); FeatureColourI gc = new FeatureColour(maxColour, minColour, - maxColour, - noValueColour, min, max); + maxColour, noValueColour, min, max); if (setting.getAttributeName().size() > 0) { gc.setAttributeName(setting.getAttributeName().toArray( @@ -5130,8 +5298,7 @@ public class Jalview2XML } else { - featureColours.put(featureType, - new FeatureColour(maxColour)); + featureColours.put(featureType, new FeatureColour(maxColour)); } renderOrder[fs] = featureType; if (setting.getOrder() != null) @@ -5199,8 +5366,9 @@ 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); @@ -5467,7 +5635,7 @@ public class Jalview2XML return false; } - public void addToSkipList(AlignFrame af) + protected void addToSkipList(AlignFrame af) { if (skipList == null) { @@ -5476,7 +5644,7 @@ public class Jalview2XML skipList.put(af.getViewport().getSequenceSetId(), af); } - public void clearSkipList() + protected void clearSkipList() { if (skipList != null) { @@ -5545,8 +5713,8 @@ 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. @@ -5960,14 +6128,8 @@ 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