X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=12f2cb20640daf23751f617cd02c13317b8e049d;hb=339c2de5fce77a1e1518df6df0c2d894352d6648;hp=008be21188ac3dbb809014943462fe666b309df9;hpb=c901bd1778574b5792a7ee168bfe3e1addd3e181;p=jalview.git

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 008be21..12f2cb2 100755
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -12,12 +12,17 @@ import javax.swing.JInternalFrame;
 public class Jalview2XML
 {
 
+  // SAVES SEVERAL ALIGNEMENT WINDOWS TO SAME JARFILE
   public static void SaveState(File statefile)
   {
       long creation = System.currentTimeMillis();
       JInternalFrame[] frames = Desktop.desktop.getAllFrames();
       try{
-        JalviewState state = new JalviewState();
+        FileOutputStream fos = new FileOutputStream(statefile);
+        JarOutputStream jout = new JarOutputStream(fos);
+        //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
+        ////////////////////////////////////////////////////
+        PrintWriter out = new PrintWriter(new OutputStreamWriter(jout, "UTF-8"));
 
         Vector shortNames = new Vector();
         for (int i = 0; i < frames.length; i++)
@@ -30,7 +35,6 @@ public class Jalview2XML
 
             shortName = shortName.replace('/', '_');
             shortName = shortName.replace('\\', '_');
-            String jarFile = statefile.getParent()+File.separatorChar+shortName+".jar";
 
             int count=1;
             while( shortNames.contains(shortName) )
@@ -46,22 +50,33 @@ public class Jalview2XML
             if(!shortName.endsWith(".xml"))
               shortName = shortName+".xml";
 
-            jarFile = statefile.getParent()+File.separatorChar+shortName+".jar";
-
-            SaveState( af, creation, shortName, jarFile);
-            state.addFile(jarFile);
-          }
+            SaveState( af, creation, shortName, jout, out);
+           }
         }
-
-        PrintWriter out = new PrintWriter(new FileWriter(statefile));
-        state.marshal(out);
         out.close();
+        jout.close();
       }
       catch(Exception ex){ex.printStackTrace();}
   }
 
+  // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW
+  public static void SaveState( AlignFrame af, String jarFile, String fileName)
+  {
+    try{
+      FileOutputStream fos = new FileOutputStream(jarFile);
+      JarOutputStream jout = new JarOutputStream(fos);
+      //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
+      ////////////////////////////////////////////////////
+      PrintWriter out = new PrintWriter(new OutputStreamWriter(jout, "UTF-8"));
+
+      SaveState(af, System.currentTimeMillis(), fileName, jout, out);
+      out.close();
+      jout.close();
+    }catch(Exception ex){}
+  }
 
-  public static void SaveState( AlignFrame af, long timeStamp, String fileName, String jarFile)
+  public static void SaveState( AlignFrame af, long timeStamp,
+      String fileName, JarOutputStream jout, PrintWriter out)
   {
 
     Vector seqids = new Vector();
@@ -240,16 +255,6 @@ public class Jalview2XML
 
     try
     {
-    // NAME OF FILE
-     FileOutputStream fos = new FileOutputStream(jarFile);
-
-     //PUT IT IN THIS JARFILE
-     JarOutputStream jout = new JarOutputStream(fos);
-
-     //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
-     ////////////////////////////////////////////////////
-     PrintWriter out = new PrintWriter(new OutputStreamWriter(jout, "UTF-8"));
-
      if(!fileName.endsWith(".xml"))
               fileName = fileName+".xml";
 
@@ -257,9 +262,6 @@ public class Jalview2XML
      jout.putNextEntry(entry);
 
       object.marshal(out);
-      out.close();
-      fos.close();
-      jout.close();
     }
     catch (Exception ex)
     {
@@ -267,37 +269,38 @@ public class Jalview2XML
     }
   }
 
-  public static void LoadState(String file)
-  {
-    try{
-       JalviewState state = new JalviewState();
-       BufferedReader in = new BufferedReader(new FileReader(file));
-       state = (JalviewState)state.unmarshal(in);
-       Enumeration en = state.enumerateFile();
-       while( en.hasMoreElements() )
-       {
-         LoadJalviewAlign( en.nextElement().toString());
-       }
-    }
-    catch(Exception ex)
-    {   ex.printStackTrace(); return; }
-  }
 
   public static void LoadJalviewAlign(String file)
   {
     JalviewModel object = new JalviewModel();
-    Vector seqids = new Vector();
     try{
-      FileInputStream fis = new FileInputStream(file);
-      JarInputStream jin = new JarInputStream(fis);
-      jin.getNextJarEntry();
-      InputStreamReader in = new InputStreamReader(jin, "UTF-8");
-      object = (JalviewModel) object.unmarshal(in);
+      //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
+      JarInputStream jin = new JarInputStream(new FileInputStream(file));
+      JarEntry jarentry=null;
+      int entryCount = 1;
+      do{
+        jin = new JarInputStream(new FileInputStream(file));
+        for(int i=0; i<entryCount; i++)
+          jarentry = jin.getNextJarEntry();
+
+        if(jarentry!=null)
+        {
+          InputStreamReader in = new InputStreamReader(jin, "UTF-8");
+          object = (JalviewModel) object.unmarshal(in);
+          LoadFromObject(object);
+          entryCount++;
+        }
+      }while(jarentry!=null);
+
     }
     catch(Exception ex)
-    {   System.out.println(ex); return; }
+    {   System.out.println("HERE"+ex); return; }
 
+  }
 
+  static void LoadFromObject(JalviewModel object)
+  {
+     Vector seqids = new Vector();
      SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
      Sequence [] vamsasSeq = vamsasSet.getSequence();
 
@@ -411,6 +414,9 @@ public class Jalview2XML
     af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(), view.getHeight());
     af.viewport.setStartRes( view.getStartRes() );
     af.viewport.setStartSeq( view.getStartSeq() );
+    af.viewport.showConservation = view.getShowConservation();
+    af.viewport.showQuality = view.getShowQuality();
+    af.viewport.showIdentity= view.getShowIdentity();
     af.viewport.setAbovePIDThreshold( view.getPidSelected() );
     af.viewport.setColourText( view.getShowColourText() );
     af.viewport.setConservationSelected( view.getConservationSelected());
@@ -456,7 +462,6 @@ public class Jalview2XML
         af.ShowNewickTree(new jalview.io.NewickFile(
             (String)object.getVamsasModel().getTree(0)), "Tree");
       }catch(Exception ex){ex.printStackTrace();}
-
     }
 
   }