Merge branch 'develop' into Jalview-JS/develop

diff --combined src/jalview/project/Jalview2XML.java
index 5049443,02b405e..fa104a6
--- 1/src/jalview/project/Jalview2XML.java
--- 2/src/jalview/project/Jalview2XML.java
+++ b/src/jalview/project/Jalview2XML.java
@@@ -38,7 -38,6 +38,7 @@@ import jalview.datamodel.AlignedCodonFr
  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;
@@@ -153,7 -152,6 +153,7 @@@ import java.awt.Color
  import java.awt.Font;
  import java.awt.Rectangle;
  import java.io.BufferedReader;
 +import java.io.ByteArrayInputStream;
  import java.io.DataInputStream;
  import java.io.DataOutputStream;
  import java.io.File;
@@@ -210,27 -208,6 +210,27 @@@ 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
 +
 +  private static void addJ2SBinaryType(String ext)
 +  {
 +    ext = "." + ext + "?";
 +
 +    /**
 +     * @j2sNative
 +     * 
 +     *            J2S._binaryTypes.push(ext);
 +     * 
 +     */
 +  }
 +
 +  static
 +  {
 +    addJ2SBinaryType(".jvp?");
 +  }
 +
    private static final String VIEWER_PREFIX = "viewer_";
  
    private static final String RNA_PREFIX = "rna_";
@@@ -768,10 -745,9 +768,10 @@@
      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<AlignFrame> frames = new ArrayList<>();
@@@ -796,11 -772,8 +796,11 @@@
        jout.close();
        boolean success = true;
  
 -      backupfiles.setWriteSuccess(success);
 -      success = backupfiles.rollBackupsAndRenameTempFile();
 +      if (doBackup)
 +      {
 +        backupfiles.setWriteSuccess(success);
 +        success = backupfiles.rollBackupsAndRenameTempFile();
 +      }
  
        return success;
      } catch (Exception ex)
@@@ -1686,7 -1659,6 +1686,7 @@@
        // using save and then load
        try
        {
 +      fileName = fileName.replace('\\', '/');
          System.out.println("Writing jar entry " + fileName);
          JarEntry entry = new JarEntry(fileName);
          jout.putNextEntry(entry);
@@@ -2057,7 -2029,6 +2057,7 @@@
    {
      if (jout != null)
      {
 +      jarEntryName = jarEntryName.replace('\\','/');
        System.out.println("Writing jar entry " + jarEntryName);
        jout.putNextEntry(new JarEntry(jarEntryName));
        DataOutputStream dout = new DataOutputStream(jout);
@@@ -2518,7 -2489,7 +2518,7 @@@
      vamsasSeq.setName(jds.getName());
      vamsasSeq.setSequence(jds.getSequenceAsString());
      vamsasSeq.setDescription(jds.getDescription());
 -    jalview.datamodel.DBRefEntry[] dbrefs = null;
 +    List<DBRefEntry> dbrefs = null;
      if (jds.getDatasetSequence() != null)
      {
        vamsasSeq.setDsseqid(seqHash(jds.getDatasetSequence()));
@@@ -2536,16 -2507,15 +2536,16 @@@
      }
      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);
          }
@@@ -2741,7 -2711,7 +2741,7 @@@
     * @param file
     *          - HTTP URL or filename
     */
 -  public AlignFrame loadJalviewAlign(final String file)
 +  public AlignFrame loadJalviewAlign(final Object file)
    {
  
      jalview.gui.AlignFrame af = null;
@@@ -2785,52 -2755,44 +2785,52 @@@
      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 = /** @j2sNative ofile._bytes || */
 +                                      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
@@@ -2872,6 -2834,9 +2872,6 @@@
  
          if (jarentry != null && jarentry.getName().endsWith(".xml"))
          {
 -          InputStreamReader in = new InputStreamReader(jin, UTF_8);
 -          // JalviewModel object = new JalviewModel();
 -
            JAXBContext jc = JAXBContext
                    .newInstance("jalview.xml.binding.jalview");
            XMLStreamReader streamReader = XMLInputFactory.newInstance()
@@@ -2881,6 -2846,11 +2881,6 @@@
                    .unmarshal(streamReader, JalviewModel.class);
            JalviewModel object = jbe.getValue();
  
 -          /*
 -          Unmarshaller unmar = new Unmarshaller(object);
 -          unmar.setValidation(false);
 -          object = (JalviewModel) unmar.unmarshal(in);
 -          */
            if (true) // !skipViewport(object))
            {
              _af = loadFromObject(object, file, true, jprovider);
@@@ -4217,10 -4187,8 +4217,8 @@@
            // 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"
@@@ -4871,18 -4839,7 +4869,18 @@@
    {
      AlignFrame af = null;
      af = new AlignFrame(al, safeInt(view.getWidth()),
 -            safeInt(view.getHeight()), uniqueSeqSetId, viewId);
 +            safeInt(view.getHeight()), uniqueSeqSetId, viewId) 
 +//    {
 +//            
 +//            @Override
 +//            protected void processKeyEvent(java.awt.event.KeyEvent e) {
 +//                    System.out.println("Jalview2XML   AF " + e);
 +//                    super.processKeyEvent(e);
 +//                    
 +//            }
 +//            
 +//    }
 +    ;
  
      af.setFileName(file, FileFormat.Jalview);