X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fproject%2FJalview2XML.java;h=985aece519bf73c7d2b4be10186b7c080fea140d;hb=48a66195bf4aee8b2c479d3bbbf4c1fb8b824f5a;hp=8bbe20c0cb440b49d94d4c11387b002067bb40d9;hpb=7720585dc8cc56cdad2486b330ed37ddd0133531;p=jalview.git

diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java
index 8bbe20c..985aece 100644
--- a/src/jalview/project/Jalview2XML.java
+++ b/src/jalview/project/Jalview2XML.java
@@ -29,7 +29,6 @@ import java.awt.Font;
 import java.awt.Rectangle;
 import java.io.BufferedReader;
 import java.io.ByteArrayInputStream;
-import java.io.DataOutputStream;
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.FileOutputStream;
@@ -55,6 +54,7 @@ import java.util.IdentityHashMap;
 import java.util.Iterator;
 import java.util.LinkedHashMap;
 import java.util.List;
+import java.util.Locale;
 import java.util.Map;
 import java.util.Map.Entry;
 import java.util.Set;
@@ -134,6 +134,7 @@ import jalview.schemes.UserColourScheme;
 import jalview.structure.StructureSelectionManager;
 import jalview.structures.models.AAStructureBindingModel;
 import jalview.util.Format;
+import jalview.util.HttpUtils;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
 import jalview.util.StringUtils;
@@ -758,8 +759,8 @@ public class Jalview2XML
       // 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);
+      FileOutputStream fos = new FileOutputStream(
+              doBackup ? backupfiles.getTempFilePath() : jarFile);
 
       JarOutputStream jout = new JarOutputStream(fos);
       List<AlignFrame> frames = new ArrayList<>();
@@ -913,13 +914,12 @@ public class Jalview2XML
     }
     if (jal.getProperties() != null)
     {
-      Enumeration en = jal.getProperties().keys();
-      while (en.hasMoreElements())
+      for (Entry<Object, Object> prop : jal.getProperties().entrySet())
       {
-        String key = en.nextElement().toString();
+        String key = prop.getKey().toString();
         SequenceSetProperties ssp = new SequenceSetProperties();
         ssp.setKey(key);
-        ssp.setValue(jal.getProperties().get(key).toString());
+        ssp.setValue(prop.getValue().toString());
         // vamsasSet.addSequenceSetProperties(ssp);
         vamsasSet.getSequenceSetProperties().add(ssp);
       }
@@ -958,7 +958,7 @@ public class Jalview2XML
         else
         {
           vamsasSeq = createVamsasSequence(id, jds);
-//          vamsasSet.addSequence(vamsasSeq);
+          // vamsasSet.addSequence(vamsasSeq);
           vamsasSet.getSequence().add(vamsasSeq);
           vamsasSetIds.put(id, vamsasSeq);
           seqRefIds.put(id, jds);
@@ -1089,13 +1089,14 @@ public class Jalview2XML
             if (frames[f] instanceof StructureViewerBase)
             {
               StructureViewerBase viewFrame = (StructureViewerBase) frames[f];
-              matchedFile = saveStructureState(ap, jds, pdb, entry, viewIds,
-                      matchedFile, viewFrame);
+              matchedFile = saveStructureViewer(ap, jds, pdb, entry,
+                      viewIds, matchedFile, viewFrame);
               /*
                * Only store each structure viewer's state once in the project
                * jar. First time through only (storeDS==false)
                */
               String viewId = viewFrame.getViewId();
+              String viewerType = viewFrame.getViewerType().toString();
               if (!storeDS && !viewIds.contains(viewId))
               {
                 viewIds.add(viewId);
@@ -1103,13 +1104,12 @@ public class Jalview2XML
                 if (viewerState != null)
                 {
                   copyFileToJar(jout, viewerState.getPath(),
-                          getViewerJarEntryName(viewId));
+                          getViewerJarEntryName(viewId), viewerType);
                 }
                 else
                 {
-                  Cache.log.error("Failed to save viewer state for "
-                          +
-                          viewFrame.getViewerType().toString());
+                  Cache.log.error(
+                          "Failed to save viewer state for " + viewerType);
                 }
               }
             }
@@ -1131,7 +1131,7 @@ public class Jalview2XML
             if (!pdbfiles.contains(pdbId))
             {
               pdbfiles.add(pdbId);
-              copyFileToJar(jout, matchedFile, pdbId);
+              copyFileToJar(jout, matchedFile, pdbId, pdbId);
             }
           }
 
@@ -1353,9 +1353,8 @@ public class Jalview2XML
 
             if (colourScheme instanceof jalview.schemes.UserColourScheme)
             {
-              jGroup.setColour(
-                      setUserColourScheme(colourScheme, userColours,
-                              object));
+              jGroup.setColour(setUserColourScheme(colourScheme,
+                      userColours, object));
             }
             else
             {
@@ -1401,7 +1400,7 @@ public class Jalview2XML
         }
       }
 
-      //jms.setJGroup(groups);
+      // jms.setJGroup(groups);
       Object group;
       for (JGroup grp : groups)
       {
@@ -1538,11 +1537,13 @@ public class Jalview2XML
              * save any filter for the feature type
              */
             FeatureMatcherSetI filter = fr.getFeatureFilter(featureType);
-            if (filter != null)  {
-              Iterator<FeatureMatcherI> filters = filter.getMatchers().iterator();
+            if (filter != null)
+            {
+              Iterator<FeatureMatcherI> filters = filter.getMatchers()
+                      .iterator();
               FeatureMatcherI firstFilter = filters.next();
-              setting.setMatcherSet(Jalview2XML.marshalFilter(
-                      firstFilter, filters, filter.isAnded()));
+              setting.setMatcherSet(Jalview2XML.marshalFilter(firstFilter,
+                      filters, filter.isAnded()));
             }
 
             /*
@@ -1591,8 +1592,7 @@ public class Jalview2XML
 
             setting.setDisplay(
                     av.getFeaturesDisplayed().isVisible(featureType));
-            float rorder = fr
-                    .getOrder(featureType);
+            float rorder = fr.getOrder(featureType);
             if (rorder > -1)
             {
               setting.setOrder(rorder);
@@ -1616,7 +1616,7 @@ public class Jalview2XML
           Group g = new Group();
           g.setName(grp);
           g.setDisplay(((Boolean) fr.checkGroupVisibility(grp, false))
-                          .booleanValue());
+                  .booleanValue());
           // fs.addGroup(g);
           fs.getGroup().add(g);
           groupsAdded.addElement(grp);
@@ -1678,7 +1678,7 @@ public class Jalview2XML
       // using save and then load
       try
       {
-    	fileName = fileName.replace('\\', '/');
+        fileName = fileName.replace('\\', '/');
         System.out.println("Writing jar entry " + fileName);
         JarEntry entry = new JarEntry(fileName);
         jout.putNextEntry(entry);
@@ -1979,7 +1979,7 @@ public class Jalview2XML
 
                 String varnaStateFile = varna.getStateInfo(model.rna);
                 jarEntryName = RNA_PREFIX + viewId + "_" + nextCounter();
-                copyFileToJar(jout, varnaStateFile, jarEntryName);
+                copyFileToJar(jout, varnaStateFile, jarEntryName, "Varna");
                 rnaSessions.put(model, jarEntryName);
               }
               SecondaryStructure ss = new SecondaryStructure();
@@ -2003,16 +2003,19 @@ public class Jalview2XML
    * @param jout
    * @param infilePath
    * @param jarEntryName
+   * @param msg
+   *          additional identifying info to log to the console
    */
   protected void copyFileToJar(JarOutputStream jout, String infilePath,
-          String jarEntryName)
+          String jarEntryName, String msg)
   {
     try (InputStream is = new FileInputStream(infilePath))
     {
       File file = new File(infilePath);
       if (file.exists() && jout != null)
       {
-        System.out.println("Writing jar entry " + jarEntryName);
+        System.out.println(
+                "Writing jar entry " + jarEntryName + " (" + msg + ")");
         jout.putNextEntry(new JarEntry(jarEntryName));
         copyAll(is, jout);
         jout.closeEntry();
@@ -2028,29 +2031,6 @@ public class Jalview2XML
   }
 
   /**
-   * Write the data to a new entry of given name in the output jar file
-   * 
-   * @param jout
-   * @param jarEntryName
-   * @param data
-   * @throws IOException
-   */
-  protected void writeJarEntry(JarOutputStream jout, String jarEntryName,
-          byte[] data) throws IOException
-  {
-    if (jout != null)
-    {
-      jarEntryName = jarEntryName.replace('\\','/');
-      System.out.println("Writing jar entry " + jarEntryName);
-      jout.putNextEntry(new JarEntry(jarEntryName));
-      DataOutputStream dout = new DataOutputStream(jout);
-      dout.write(data, 0, data.length);
-      dout.flush();
-      jout.closeEntry();
-    }
-  }
-
-  /**
    * Copies input to output, in 4K buffers; handles any data (text or binary)
    * 
    * @param in
@@ -2081,7 +2061,7 @@ public class Jalview2XML
    * @param viewFrame
    * @return
    */
-  protected String saveStructureState(AlignmentPanel ap, SequenceI jds,
+  protected String saveStructureViewer(AlignmentPanel ap, SequenceI jds,
           Pdbids pdb, PDBEntry entry, List<String> viewIds,
           String matchedFile, StructureViewerBase viewFrame)
   {
@@ -2095,9 +2075,9 @@ public class Jalview2XML
     {
       final PDBEntry pdbentry = bindingModel.getPdbEntry(peid);
       final String pdbId = pdbentry.getId();
-      if (!pdbId.equals(entry.getId())
-              && !(entry.getId().length() > 4 && entry.getId().toLowerCase()
-                      .startsWith(pdbId.toLowerCase())))
+      if (!pdbId.equals(entry.getId()) && !(entry.getId().length() > 4
+              && entry.getId().toLowerCase(Locale.ROOT)
+                      .startsWith(pdbId.toLowerCase(Locale.ROOT))))
       {
         /*
          * not interested in a binding to a different PDB entry here
@@ -2393,7 +2373,8 @@ public class Jalview2XML
   {
     if (calcIdParam.getVersion().equals("1.0"))
     {
-      final String[] calcIds = calcIdParam.getServiceURL().toArray(new String[0]);
+      final String[] calcIds = calcIdParam.getServiceURL()
+              .toArray(new String[0]);
       Jws2Instance service = Jws2Discoverer.getDiscoverer()
               .getPreferredServiceFor(calcIds);
       if (service != null)
@@ -2548,14 +2529,15 @@ public class Jalview2XML
         dbref.setSource(ref.getSource());
         dbref.setVersion(ref.getVersion());
         dbref.setAccessionId(ref.getAccessionId());
+        dbref.setCanonical(ref.isCanonical());
         if (ref instanceof GeneLocus)
         {
           dbref.setLocus(true);
         }
         if (ref.hasMap())
         {
-          Mapping mp = createVamsasMapping(ref.getMap(), parentseq,
-                  jds, recurse);
+          Mapping mp = createVamsasMapping(ref.getMap(), parentseq, jds,
+                  recurse);
           dbref.setMapping(mp);
         }
         vamsasSeq.getDBRef().add(dbref);
@@ -2663,7 +2645,7 @@ public class Jalview2XML
         for (int i = 0; i < colours.length; i++)
         {
           Colour col = new Colour();
-          col.setName(ResidueProperties.aa[i].toLowerCase());
+          col.setName(ResidueProperties.aa[i].toLowerCase(Locale.ROOT));
           col.setRGB(jalview.util.Format.getHexString(colours[i]));
           // jbucs.addColour(col);
           jbucs.getColour().add(col);
@@ -2679,12 +2661,12 @@ public class Jalview2XML
     return id;
   }
 
-  jalview.schemes.UserColourScheme getUserColourScheme(
-          JalviewModel jm, String id)
+  jalview.schemes.UserColourScheme getUserColourScheme(JalviewModel jm,
+          String id)
   {
     List<UserColours> uc = jm.getUserColours();
     UserColours colours = null;
-/*
+    /*
     for (int i = 0; i < uc.length; i++)
     {
       if (uc[i].getId().equals(id))
@@ -2693,7 +2675,7 @@ public class Jalview2XML
         break;
       }
     }
-*/
+    */
     for (UserColours c : uc)
     {
       if (c.getId().equals(id))
@@ -2721,10 +2703,9 @@ public class Jalview2XML
       newColours = new java.awt.Color[23];
       for (int i = 0; i < 23; i++)
       {
-        newColours[i] = new java.awt.Color(Integer.parseInt(
-                colours.getUserColourScheme().getColour().get(i + 24)
-                        .getRGB(),
-                16));
+        newColours[i] = new java.awt.Color(
+                Integer.parseInt(colours.getUserColourScheme().getColour()
+                        .get(i + 24).getRGB(), 16));
       }
       ucs.setLowerCaseColours(newColours);
     }
@@ -2793,52 +2774,69 @@ public class Jalview2XML
     return af;
   }
 
-	@SuppressWarnings("unused")
-	private jarInputStreamProvider createjarInputStreamProvider(final Object ofile) throws MalformedURLException {
+  @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());
+    // 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;
-		}
-	}
+      URL url = null;
+      errorMessage = null;
+      uniqueSetSuffix = null;
+      seqRefIds = null;
+      viewportsAdded.clear();
+      frefedSequence = null;
+
+      if (HttpUtils.startsWithHttpOrHttps(file))
+      {
+        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
@@ -2885,8 +2883,8 @@ public class Jalview2XML
           XMLStreamReader streamReader = XMLInputFactory.newInstance()
                   .createXMLStreamReader(jin);
           javax.xml.bind.Unmarshaller um = jc.createUnmarshaller();
-          JAXBElement<JalviewModel> jbe = um
-                  .unmarshal(streamReader, JalviewModel.class);
+          JAXBElement<JalviewModel> jbe = um.unmarshal(streamReader,
+                  JalviewModel.class);
           JalviewModel object = jbe.getValue();
 
           if (true) // !skipViewport(object))
@@ -2922,6 +2920,7 @@ public class Jalview2XML
           entryCount++;
         }
       } while (jarentry != null);
+      jin.close();
       resolveFrefedSequences();
     } catch (IOException ex)
     {
@@ -3274,7 +3273,8 @@ public class Jalview2XML
   AlignFrame loadFromObject(JalviewModel jalviewModel, String file,
           boolean loadTreesAndStructures, jarInputStreamProvider jprovider)
   {
-    SequenceSet vamsasSet = jalviewModel.getVamsasModel().getSequenceSet().get(0);
+    SequenceSet vamsasSet = jalviewModel.getVamsasModel().getSequenceSet()
+            .get(0);
     List<Sequence> vamsasSeqs = vamsasSet.getSequence();
 
     // JalviewModelSequence jms = object.getJalviewModelSequence();
@@ -3333,11 +3333,10 @@ public class Jalview2XML
           if (tmpSeq.getStart() != jseq.getStart()
                   || tmpSeq.getEnd() != jseq.getEnd())
           {
-            System.err.println(
-                    String.format("Warning JAL-2154 regression: updating start/end for sequence %s from %d/%d to %d/%d",
-                            tmpSeq.getName(), tmpSeq.getStart(),
-                            tmpSeq.getEnd(), jseq.getStart(),
-                            jseq.getEnd()));
+            System.err.println(String.format(
+                    "Warning JAL-2154 regression: updating start/end for sequence %s from %d/%d to %d/%d",
+                    tmpSeq.getName(), tmpSeq.getStart(), tmpSeq.getEnd(),
+                    jseq.getStart(), jseq.getEnd()));
           }
         }
         else
@@ -3620,8 +3619,8 @@ public class Jalview2XML
               else
               {
                 // defer to later
-                frefedSequence.add(
-                        newAlcodMapRef(map.getDnasq(), cf, mapping));
+                frefedSequence
+                        .add(newAlcodMapRef(map.getDnasq(), cf, mapping));
               }
             }
           }
@@ -3829,8 +3828,7 @@ 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());
           }
@@ -3911,9 +3909,9 @@ 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)
@@ -3957,8 +3955,9 @@ 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));
         }
       }
     }
@@ -4164,8 +4163,8 @@ public class Jalview2XML
    * @param av
    * @param ap
    */
-  protected void loadTrees(JalviewModel jm, Viewport view,
-          AlignFrame af, AlignViewport av, AlignmentPanel ap)
+  protected void loadTrees(JalviewModel jm, Viewport view, AlignFrame af,
+          AlignViewport av, AlignmentPanel ap)
   {
     // TODO result of automated refactoring - are all these parameters needed?
     try
@@ -4273,8 +4272,8 @@ public class Jalview2XML
           for (int s = 0; s < structureStateCount; s++)
           {
             // check to see if we haven't already created this structure view
-            final StructureState structureState = pdbid
-                    .getStructureState().get(s);
+            final StructureState structureState = pdbid.getStructureState()
+                    .get(s);
             String sviewid = (structureState.getViewId() == null) ? null
                     : structureState.getViewId() + uniqueSetSuffix;
             jalview.datamodel.PDBEntry jpdb = new jalview.datamodel.PDBEntry();
@@ -4342,8 +4341,8 @@ public class Jalview2XML
             colourByViewer &= structureState.isColourByJmol();
             jmoldat.setColourByViewer(colourByViewer);
 
-            if (jmoldat.getStateData().length() < structureState
-                    .getValue()/*Content()*/.length())
+            if (jmoldat.getStateData().length() < structureState.getValue()
+                    /*Content()*/.length())
             {
               jmoldat.setStateData(structureState.getValue());// Content());
             }
@@ -4421,8 +4420,7 @@ public class Jalview2XML
     } catch (IllegalArgumentException | NullPointerException e)
     {
       // TODO JAL-3619 show error dialog / offer an alternative viewer
-      Cache.log.error(
-              "Invalid structure viewer type: " + type);
+      Cache.log.error("Invalid structure viewer type: " + type);
     }
   }
 
@@ -4622,23 +4620,23 @@ public class Jalview2XML
   }
 
   AlignFrame loadViewport(String file, List<JSeq> JSEQ,
-          List<SequenceI> hiddenSeqs, AlignmentI al,
-          JalviewModel jm, Viewport view, String uniqueSeqSetId,
-          String viewId, List<JvAnnotRow> autoAlan)
+          List<SequenceI> hiddenSeqs, AlignmentI al, JalviewModel jm,
+          Viewport view, String uniqueSeqSetId, String viewId,
+          List<JvAnnotRow> 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);
@@ -4716,9 +4714,8 @@ 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()));
@@ -4794,9 +4791,8 @@ 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);
@@ -4820,13 +4816,13 @@ 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<String, FeatureColourI> featureColours = new Hashtable<>();
       Map<String, Float> 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();
@@ -4838,8 +4834,8 @@ 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);
@@ -4871,8 +4867,7 @@ 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(
@@ -4906,8 +4901,7 @@ public class Jalview2XML
         }
         else
         {
-          featureColours.put(featureType,
-                  new FeatureColour(maxColour));
+          featureColours.put(featureType, new FeatureColour(maxColour));
         }
         renderOrder[fs] = featureType;
         if (setting.getOrder() != null)
@@ -5380,6 +5374,7 @@ public class Jalview2XML
       }
     }
   }
+
   /**
    * 
    * @param vamsasSeq
@@ -5629,6 +5624,7 @@ public class Jalview2XML
       {
         entry.setMap(addMapping(dr.getMapping()));
       }
+      entry.setCanonical(dr.isCanonical());
       datasetSequence.addDBRef(entry);
     }
   }
@@ -6128,8 +6124,8 @@ public class Jalview2XML
    * @param af
    * @param jprovider
    */
-  protected void createStructureViewer(
-          ViewerType viewerType, final Entry<String, StructureViewerModel> viewerData,
+  protected void createStructureViewer(ViewerType viewerType,
+          final Entry<String, StructureViewerModel> viewerData,
           AlignFrame af, jarInputStreamProvider jprovider)
   {
     final StructureViewerModel viewerModel = viewerData.getValue();
@@ -6143,8 +6139,7 @@ public class Jalview2XML
     {
       String viewerJarEntryName = getViewerJarEntryName(
               viewerModel.getViewId());
-      sessionFilePath = copyJarEntry(jprovider,
-              viewerJarEntryName,
+      sessionFilePath = copyJarEntry(jprovider, viewerJarEntryName,
               "viewerSession", ".tmp");
     }
     final String sessionPath = sessionFilePath;
@@ -6164,8 +6159,7 @@ public class Jalview2XML
             addNewStructureViewer(sview);
           } catch (OutOfMemoryError ex)
           {
-            new OOMWarning("Restoring structure view for "
-                    + viewerType,
+            new OOMWarning("Restoring structure view for " + viewerType,
                     (OutOfMemoryError) ex.getCause());
             if (sview != null && sview.isVisible())
             {
@@ -6198,8 +6192,8 @@ public class Jalview2XML
     String state = svattrib.getStateData(); // Jalview < 2.9
     if (state == null || state.isEmpty()) // Jalview >= 2.9
     {
-      state = readJarEntry(jprovider,
-              getViewerJarEntryName(svattrib.getViewId()));
+      String jarEntryName = getViewerJarEntryName(svattrib.getViewId());
+      state = readJarEntry(jprovider, jarEntryName);
     }
     // TODO or simpler? for each key in oldFiles,
     // replace key.getPath() in state with oldFiles.get(key).getFilePath()
@@ -6225,8 +6219,7 @@ public class Jalview2XML
           String reformatedOldFilename = oldfilenam.replaceAll("/", "\\\\");
           filedat = oldFiles.get(new File(reformatedOldFilename));
         }
-        rewritten
-                .append(Platform.escapeBackslashes(filedat.getFilePath()));
+        rewritten.append(Platform.escapeBackslashes(filedat.getFilePath()));
         rewritten.append("\"");
         cp = ecp + 1; // advance beyond last \" and set cursor so we can
                       // look for next file statement.
@@ -6246,8 +6239,7 @@ public class Jalview2XML
       {
         // add pdb files that should be present in the viewer
         StructureData filedat = oldFiles.get(id);
-        rewritten.append(filedat.getFilePath()).append(" \"")
-                .append(filedat.getFilePath()).append("\"");
+        rewritten.append(" \"").append(filedat.getFilePath()).append("\"");
       }
       rewritten.append(";");
     }
@@ -6299,8 +6291,8 @@ public class Jalview2XML
    * @param fcol
    * @return
    */
-  public static Colour marshalColour(
-          String featureType, FeatureColourI fcol)
+  public static Colour marshalColour(String featureType,
+          FeatureColourI fcol)
   {
     Colour col = new Colour();
     if (fcol.isSimpleColour())
@@ -6361,7 +6353,7 @@ public class Jalview2XML
           boolean and)
   {
     jalview.xml.binding.jalview.FeatureMatcherSet result = new jalview.xml.binding.jalview.FeatureMatcherSet();
-  
+
     if (filters.hasNext())
     {
       /*
@@ -6411,7 +6403,7 @@ public class Jalview2XML
       }
       result.setMatchCondition(matcherModel);
     }
-  
+
     return result;
   }
 
@@ -6422,8 +6414,7 @@ public class Jalview2XML
    * @param matcherSetModel
    * @return
    */
-  public static FeatureMatcherSetI parseFilter(
-          String featureType,
+  public static FeatureMatcherSetI parseFilter(String featureType,
           jalview.xml.binding.jalview.FeatureMatcherSet matcherSetModel)
   {
     FeatureMatcherSetI result = new FeatureMatcherSet();
@@ -6438,7 +6429,7 @@ public class Jalview2XML
                       featureType, e.getMessage()));
       // return as much as was parsed up to the error
     }
-  
+
     return result;
   }
 
@@ -6453,8 +6444,7 @@ public class Jalview2XML
    * @throws IllegalStateException
    *           if AND and OR conditions are mixed
    */
-  protected static void parseFilterConditions(
-          FeatureMatcherSetI matcherSet,
+  protected static void parseFilterConditions(FeatureMatcherSetI matcherSet,
           jalview.xml.binding.jalview.FeatureMatcherSet matcherSetModel,
           boolean and)
   {
@@ -6476,7 +6466,7 @@ public class Jalview2XML
       else if (filterBy == FilterBy.BY_SCORE)
       {
         matchCondition = FeatureMatcher.byScore(cond, pattern);
-  
+
       }
       else if (filterBy == FilterBy.BY_ATTRIBUTE)
       {
@@ -6486,7 +6476,7 @@ public class Jalview2XML
         matchCondition = FeatureMatcher.byAttribute(cond, pattern,
                 attNames);
       }
-  
+
       /*
        * note this throws IllegalStateException if AND-ing to a 
        * previously OR-ed compound condition, or vice versa
@@ -6529,13 +6519,13 @@ public class Jalview2XML
   public static FeatureColourI parseColour(Colour colourModel)
   {
     FeatureColourI colour = null;
-  
+
     if (colourModel.getMax() != null)
     {
       Color mincol = null;
       Color maxcol = null;
       Color noValueColour = null;
-  
+
       try
       {
         mincol = new Color(Integer.parseInt(colourModel.getMinRGB(), 16));
@@ -6544,7 +6534,7 @@ public class Jalview2XML
       {
         Cache.log.warn("Couldn't parse out graduated feature color.", e);
       }
-  
+
       NoValueColour noCol = colourModel.getNoValueColour();
       if (noCol == NoValueColour.MIN)
       {
@@ -6554,7 +6544,7 @@ public class Jalview2XML
       {
         noValueColour = maxcol;
       }
-  
+
       colour = new FeatureColour(maxcol, mincol, maxcol, noValueColour,
               safeFloat(colourModel.getMin()),
               safeFloat(colourModel.getMax()));
@@ -6593,7 +6583,7 @@ public class Jalview2XML
       Color color = new Color(Integer.parseInt(colourModel.getRGB(), 16));
       colour = new FeatureColour(color);
     }
-  
+
     return colour;
   }
 }