X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fproject%2FJalview2XML.java;h=47a07a006f4ac8aa6bd632a2b3b6182ab0c4456a;hb=a0c8e3d13060b488169f1398933e0d8c8c72364f;hp=42328b8cff42625407eafc872a8515bda94ed2cd;hpb=da5decd141e510a3a5ffb0b0e315c61c1ceb39a4;p=jalview.git

diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java
index 42328b8..47a07a0 100644
--- a/src/jalview/project/Jalview2XML.java
+++ b/src/jalview/project/Jalview2XML.java
@@ -130,6 +130,7 @@ 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;
@@ -1616,6 +1617,7 @@ 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);
@@ -1796,6 +1798,7 @@ 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);
@@ -2478,7 +2481,7 @@ 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;
@@ -2522,44 +2525,52 @@ 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
@@ -2597,6 +2608,7 @@ public class Jalview2XML
         for (int i = 0; i < entryCount; i++)
         {
           jarentry = jin.getNextJarEntry();
+          System.out.println("Jalview2XML#loadJalviewAlign: jarentry=" + (jarentry == null ? null : jarentry.getName()));
         }
 
         if (jarentry != null && jarentry.getName().endsWith(".xml"))
@@ -2612,7 +2624,7 @@ public class Jalview2XML
           JAXBElement<JalviewModel> jbe = um
                   .unmarshal(streamReader, JalviewModel.class);
           JalviewModel object = jbe.getValue();
-
+          System.out.println("processing JalviewModel object=" + object);
           /*
           Unmarshaller unmar = new Unmarshaller(object);
           unmar.setValidation(false);
@@ -2959,6 +2971,7 @@ public class Jalview2XML
       do
       {
         entry = jin.getNextJarEntry();
+      	System.out.println("Jalview2XML#copyJarEntry: jarentry=" + (entry == null ? null : entry.getName()));
       } while (entry != null && !entry.getName().equals(jarEntryName));
       if (entry != null)
       {
@@ -5796,6 +5809,7 @@ public class Jalview2XML
       do
       {
         entry = jin.getNextJarEntry();
+      	System.out.println("Jalview2XML#readJarEntry: jarentry=" + (entry == null ? null : entry.getName()));
       } while (entry != null && !entry.getName().equals(jarEntryName));
 
       if (entry != null)