JAL-3202 reduced scope of rendering flags

[jalview.git] / src / jalview / project / Jalview2XML.java

diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java
index 194cbf2..336ea47 100644 (file)
--- 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;
@@ -1617,6 +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);
@@ -1797,6 +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);
@@ -2257,7 +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()));
@@ -2275,15 +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);
         }
@@ -2523,68 +2527,52 @@ public class Jalview2XML
     return af;
   }
 
-  @SuppressWarnings("unused")
-private jarInputStreamProvider createjarInputStreamProvider(
-          final Object ofile) throws MalformedURLException
-  {
-       
-         // BH 2018 allow for bytes already attached to File object
-       final String file = ofile.toString();
-       byte[] bytes = /** @j2sNative ofile._bytes ||*/null;
-       if (bytes != null) {
-
-           return new jarInputStreamProvider()
-           {
-
-             @Override
-             public JarInputStream getJarInputStream() throws IOException
-             {
-                 return new JarInputStream(new ByteArrayInputStream(bytes));
-             }
-
-             @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;
+               }
        }
-    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;
-      }
-    };
-  }
 
   /**
    * Recover jalview session from a jalview project archive. Caller may
@@ -2626,9 +2614,6 @@ private jarInputStreamProvider createjarInputStreamProvider(
 
         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()
@@ -2638,11 +2623,6 @@ private jarInputStreamProvider createjarInputStreamProvider(
                   .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);
@@ -4624,7 +4604,18 @@ private jarInputStreamProvider createjarInputStreamProvider(
   {
     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);