X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fproject%2FJalview2XML.java;h=2c93ee52d0f156c7de70fca6871c48163084067b;hb=14bfc6fb57f123b815f08dbf5b35544abd33b3af;hp=0291a0a31d0389533454420eff8bdb2b8f977b32;hpb=0031ee4b6a42ad328e417cb65c7a840183e62e87;p=jalview.git diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java index 0291a0a..2c93ee5 100644 --- a/src/jalview/project/Jalview2XML.java +++ b/src/jalview/project/Jalview2XML.java @@ -35,6 +35,7 @@ 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; @@ -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; @@ -160,6 +162,7 @@ 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; @@ -187,7 +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; @@ -265,6 +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. @@ -424,7 +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") @@ -446,7 +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) { @@ -478,7 +499,7 @@ public class Jalview2XML return fref; } - public void resolveFrefedSequences() + protected void resolveFrefedSequences() { Iterator nextFref = frefedSequence.iterator(); int toresolve = frefedSequence.size(); @@ -846,7 +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); @@ -868,7 +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) @@ -2730,17 +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 @@ -2774,8 +2784,9 @@ public class Jalview2XML { try { + // BH 2019 -- can't wait - SwingUtilities.invokeLater(new Runnable() + Jalview.execRunnable(new Runnable() { @Override public void run() @@ -2788,55 +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 @@ -2862,12 +2873,16 @@ 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); @@ -2879,9 +2894,14 @@ public class Jalview2XML jarentry = jin.getNextJarEntry(); } String name = (jarentry == null ? null : jarentry.getName()); + +// 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 @@ -2911,8 +2931,14 @@ public class Jalview2XML _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) { @@ -2979,6 +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); + } + } /* @@ -2998,7 +3031,7 @@ public class Jalview2XML { if (ds.getCodonFrames() != null) { - Desktop.getInstance().getStructureSelectionManager() + Desktop.getStructureSelectionManager() .registerMappings(ds.getCodonFrames()); } } @@ -3322,16 +3355,16 @@ 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) { -// Platform.timeCheck("Jalview2XML.loadFromObject0", Platform.TIME_MARK); + // Platform.timeCheck("Jalview2XML.loadFromObject0", Platform.TIME_MARK); - SequenceSet vamsasSet = jalviewModel.getVamsasModel().getSequenceSet().get(0); + SequenceSet vamsasSet = jalviewModel.getVamsasModel().getSequenceSet() + .get(0); List vamsasSeqs = vamsasSet.getSequence(); - // JalviewModelSequence jms = object.getJalviewModelSequence(); // Viewport view = (jms.getViewportCount() > 0) ? jms.getViewport(0) @@ -3362,7 +3395,7 @@ public class Jalview2XML : view.getId() + uniqueSetSuffix); } -// Platform.timeCheck("Jalview2XML.loadFromObject1", Platform.TIME_MARK); + // Platform.timeCheck("Jalview2XML.loadFromObject1", Platform.TIME_MARK); // //////////////////////////////// // LOAD SEQUENCES @@ -3448,8 +3481,8 @@ public class Jalview2XML } } -// Platform.timeCheck("Jalview2XML.loadFromObject-seq", -// Platform.TIME_MARK); + // Platform.timeCheck("Jalview2XML.loadFromObject-seq", + // Platform.TIME_MARK); // / // Create the alignment object from the sequence set // /////////////////////////////// @@ -3490,8 +3523,8 @@ public class Jalview2XML recoverDatasetFor(vamsasSet, al, isdsal, uniqueSeqSetId); } -// Platform.timeCheck("Jalview2XML.loadFromObject-align", -// Platform.TIME_MARK); + // Platform.timeCheck("Jalview2XML.loadFromObject-align", + // Platform.TIME_MARK); if (referenceseqForView != null) { al.setSeqrep(referenceseqForView); @@ -3504,8 +3537,8 @@ public class Jalview2XML al.setProperty(ssp.getKey(), ssp.getValue()); } -// Platform.timeCheck("Jalview2XML.loadFromObject-setseqprop", -// Platform.TIME_MARK); + // Platform.timeCheck("Jalview2XML.loadFromObject-setseqprop", + // Platform.TIME_MARK); // /////////////////////////////// Hashtable pdbloaded = new Hashtable(); // TODO nothing writes to this?? @@ -3519,7 +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_MARK); + // Platform.timeCheck("J2XML features0", Platform.TIME_RESET); for (int i = 0; i < vamsasSeqs.size(); i++) { JSeq jseq = jseqs.get(i); @@ -3574,11 +3607,11 @@ 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); } } - Platform.timeCheck("J2XML features done", Platform.TIME_MARK); - if (vamsasSeqs.get(i).getDBRef().size() > 0) { // adds dbrefs to datasequence's set (since Jalview 2.10) @@ -3636,8 +3669,7 @@ public class Jalview2XML { entry.setProperty(prop.getName(), prop.getValue()); } - Desktop.getInstance().getStructureSelectionManager() - .registerPDBEntry(entry); + Desktop.getStructureSelectionManager().registerPDBEntry(entry); // adds PDBEntry to datasequence's set (since Jalview 2.10) if (al.getSequenceAt(i).getDatasetSequence() != null) { @@ -3649,9 +3681,12 @@ public class Jalview2XML } } } + } -// Platform.timeCheck("Jalview2XML.loadFromObject-endmultiview", -// Platform.TIME_MARK); + + // Platform.timeCheck("features done", Platform.TIME_GET); + // Platform.timeCheck("Jalview2XML.loadFromObject-endmultiview", + // Platform.TIME_MARK); } // end !multipleview // /////////////////////////////// @@ -3685,16 +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); + // Platform.timeCheck("Jalview2XML.loadFromObject-seqmap", + // Platform.TIME_MARK); } // //////////////////////////////// @@ -3755,8 +3790,8 @@ public class Jalview2XML } // Construct new annotation from model. List ae = annotation.getAnnotationElement(); -// System.err.println( -// "Jalview2XML processing " + ae.size() + " annotations"); + // System.err.println( + // "Jalview2XML processing " + ae.size() + " annotations"); jalview.datamodel.Annotation[] anot = null; java.awt.Color firstColour = null; @@ -3901,8 +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()); } @@ -3919,8 +3953,8 @@ public class Jalview2XML al.addAnnotation(jaa); } } -// Platform.timeCheck("Jalview2XML.loadFromObject-annot", -// Platform.TIME_MARK); + // Platform.timeCheck("Jalview2XML.loadFromObject-annot", + // Platform.TIME_MARK); } // /////////////////////// // LOAD GROUPS @@ -3985,9 +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) @@ -4031,12 +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); + // Platform.timeCheck("Jalview2XML.loadFromObject-groups", + // Platform.TIME_MARK); } if (view == null) { @@ -4076,8 +4111,8 @@ public class Jalview2XML } } -// Platform.timeCheck("Jalview2XML.loadFromObject-viewport", -// Platform.TIME_MARK); + // Platform.timeCheck("Jalview2XML.loadFromObject-viewport", + // Platform.TIME_MARK); } /** * indicate that annotation colours are applied across all groups (pre @@ -4130,47 +4165,47 @@ public class Jalview2XML final AlignFrame af0 = af; final AlignViewport av0 = av; final AlignmentPanel ap0 = ap; -// Platform.timeCheck("Jalview2XML.loadFromObject-beforetree", -// Platform.TIME_MARK); + // Platform.timeCheck("Jalview2XML.loadFromObject-beforetree", + // Platform.TIME_MARK); if (loadTreesAndStructures) { if (!jalviewModel.getTree().isEmpty()) { - SwingUtilities.invokeLater(new Runnable() + Jalview.execRunnable(new Runnable() { @Override public void run() { -// Platform.timeCheck(null, Platform.TIME_MARK); + // Platform.timeCheck(null, Platform.TIME_MARK); loadTrees(jalviewModel, view, af0, av0, ap0); -// Platform.timeCheck("Jalview2XML.loadTrees", Platform.TIME_MARK); + // Platform.timeCheck("Jalview2XML.loadTrees", Platform.TIME_MARK); } }); } if (!jalviewModel.getPcaViewer().isEmpty()) { - SwingUtilities.invokeLater(new Runnable() + Jalview.execRunnable(new Runnable() { @Override public void run() { -// Platform.timeCheck(null, Platform.TIME_MARK); + // Platform.timeCheck(null, Platform.TIME_MARK); loadPCAViewers(jalviewModel, ap0); -// Platform.timeCheck("Jalview2XML.loadPCA", Platform.TIME_MARK); + // Platform.timeCheck("Jalview2XML.loadPCA", Platform.TIME_MARK); } }); } - SwingUtilities.invokeLater(new Runnable() + Jalview.execRunnable(new Runnable() { @Override public void run() { -// Platform.timeCheck(null, Platform.TIME_MARK); + // Platform.timeCheck(null, Platform.TIME_MARK); loadPDBStructures(jprovider, jseqs, af0, ap0); -// Platform.timeCheck("Jalview2XML.loadPDB", Platform.TIME_MARK); + // Platform.timeCheck("Jalview2XML.loadPDB", Platform.TIME_MARK); } }); - SwingUtilities.invokeLater(new Runnable() + Jalview.execRunnable(new Runnable() { @Override public void run() @@ -4178,8 +4213,11 @@ public class Jalview2XML 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; } @@ -4736,7 +4774,7 @@ public class Jalview2XML svattrib.getWidth(), svattrib.getHeight()); // try // { - javax.swing.SwingUtilities.invokeLater(new Runnable() + Jalview.execRunnable(new Runnable() { @Override public void run() @@ -4762,7 +4800,8 @@ public class Jalview2XML } } } - }); + }); + // javax.swing.SwingUtilities.invokeLater(r); // } catch (InvocationTargetException ex) // { // warn("Unexpected error when opening Jmol view.", ex); @@ -4969,27 +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++) @@ -5064,9 +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())); @@ -5152,9 +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); @@ -5175,13 +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(); @@ -5193,8 +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); @@ -5226,8 +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( @@ -5261,8 +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) @@ -5330,8 +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); @@ -5598,7 +5635,7 @@ public class Jalview2XML return false; } - public void addToSkipList(AlignFrame af) + protected void addToSkipList(AlignFrame af) { if (skipList == null) { @@ -5607,7 +5644,7 @@ public class Jalview2XML skipList.put(af.getViewport().getSequenceSetId(), af); } - public void clearSkipList() + protected void clearSkipList() { if (skipList != null) { @@ -5676,8 +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. @@ -6091,14 +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