X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fproject%2FJalview2XML.java;h=336ea47a2e11f5bd11b29effd5c786aad0203ab2;hb=13f26fb9d1c8d6f27fcedbf5c760f8e3947fd145;hp=e546789a97fe1e51889e75a222b2a39e7bb9b3ca;hpb=c9f40e367fcb287b5b8a85ff63a37cdac3bcce4f;p=jalview.git

diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java
index e546789..336ea47 100644
--- a/src/jalview/project/Jalview2XML.java
+++ b/src/jalview/project/Jalview2XML.java
@@ -29,6 +29,7 @@ import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.GraphLine;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.RnaViewerModel;
@@ -130,6 +131,7 @@ 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;
@@ -186,6 +188,27 @@ 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_";
@@ -1595,6 +1618,7 @@ public class Jalview2XML
       // using save and then load
       try
       {
+    	fileName = fileName.replace('\\', '/');
         System.out.println("Writing jar entry " + fileName);
         JarEntry entry = new JarEntry(fileName);
         jout.putNextEntry(entry);
@@ -1775,6 +1799,7 @@ public class Jalview2XML
   {
     if (jout != null)
     {
+      jarEntryName = jarEntryName.replace('\\','/');
       System.out.println("Writing jar entry " + jarEntryName);
       jout.putNextEntry(new JarEntry(jarEntryName));
       DataOutputStream dout = new DataOutputStream(jout);
@@ -2235,7 +2260,7 @@ public class Jalview2XML
     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()));
@@ -2253,15 +2278,16 @@ public class Jalview2XML
     }
     if (dbrefs != null)
     {
-      for (int d = 0; d < dbrefs.length; d++)
+      for (int d = 0, nd = dbrefs.size(); d < nd; d++)
       {
         DBRef dbref = new DBRef();
-        dbref.setSource(dbrefs[d].getSource());
-        dbref.setVersion(dbrefs[d].getVersion());
-        dbref.setAccessionId(dbrefs[d].getAccessionId());
-        if (dbrefs[d].hasMap())
+        DBRefEntry ref = dbrefs.get(d);
+        dbref.setSource(ref.getSource());
+        dbref.setVersion(ref.getVersion());
+        dbref.setAccessionId(ref.getAccessionId());
+        if (ref.hasMap())
         {
-          Mapping mp = createVamsasMapping(dbrefs[d].getMap(), parentseq,
+          Mapping mp = createVamsasMapping(ref.getMap(), parentseq,
                   jds, recurse);
           dbref.setMapping(mp);
         }
@@ -2457,7 +2483,7 @@ public class Jalview2XML
    * @param file
    *          - HTTP URL or filename
    */
-  public AlignFrame loadJalviewAlign(final String file)
+  public AlignFrame loadJalviewAlign(final Object file)
   {
 
     jalview.gui.AlignFrame af = null;
@@ -2501,44 +2527,52 @@ public class Jalview2XML
     return af;
   }
 
-  private jarInputStreamProvider createjarInputStreamProvider(
-          final String file) throws MalformedURLException
-  {
-    URL url = null;
-    errorMessage = null;
-    uniqueSetSuffix = null;
-    seqRefIds = null;
-    viewportsAdded.clear();
-    frefedSequence = null;
-
-    if (file.startsWith("http://"))
-    {
-      url = new URL(file);
-    }
-    final URL _url = url;
-    return new jarInputStreamProvider()
-    {
-
-      @Override
-      public JarInputStream getJarInputStream() throws IOException
-      {
-        if (_url != null)
-        {
-          return new JarInputStream(_url.openStream());
-        }
-        else
-        {
-          return new JarInputStream(new FileInputStream(file));
-        }
-      }
-
-      @Override
-      public String getFilename()
-      {
-        return file;
-      }
-    };
-  }
+	@SuppressWarnings("unused")
+	private jarInputStreamProvider createjarInputStreamProvider(final Object ofile) throws MalformedURLException {
+
+		// BH 2018 allow for bytes already attached to File object
+		try {
+			String file = (ofile instanceof File ? ((File) ofile).getCanonicalPath() : ofile.toString());
+			byte[] bytes = /** @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
@@ -2580,9 +2614,6 @@ public class Jalview2XML
 
         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()
@@ -2592,11 +2623,6 @@ public class Jalview2XML
                   .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);
@@ -4578,7 +4604,18 @@ public class Jalview2XML
   {
     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);