X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=f1f7db19d93985d2172c77d728052518f351e99b;hb=451619e33c0a90c8130c7d79ffa38161af1c6e0f;hp=0f0889697aec8cdb97cbdbd4f89471dc9ccf21df;hpb=35426f122a3db9e75360f2692c26a5452ec54460;p=jalview.git

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 0f08896..f1f7db1 100755
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -21,8 +21,6 @@ package jalview.gui;
 
 import jalview.schemes.*;
 
-import jalview.gui.*;
-
 import java.io.*;
 
 import java.net.*;
@@ -142,7 +140,7 @@ public class Jalview2XML
     }
 
     // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW
-    public void SaveAlignment(AlignFrame af, String jarFile,
+    public boolean SaveAlignment(AlignFrame af, String jarFile,
         String fileName)
     {
         try
@@ -163,10 +161,12 @@ public class Jalview2XML
 
           out.close();
           jout.close();
+          return true;
         }
         catch (Exception ex)
         {
           ex.printStackTrace();
+          return false;
         }
     }
 
@@ -230,7 +230,7 @@ public class Jalview2XML
               vamsasSeq = new Sequence();
               vamsasSeq.setId(id + "");
               vamsasSeq.setName(jds.getName());
-              vamsasSeq.setSequence(jds.getSequence());
+              vamsasSeq.setSequence(jds.getSequenceAsString());
               vamsasSeq.setDescription(jds.getDescription());
 
               if (jds.getDatasetSequence().getDBRef() != null)
@@ -335,19 +335,20 @@ public class Jalview2XML
                 pdb.setId(entry.getId());
                 pdb.setType(entry.getType());
 
+
                 if(entry.getFile()!=null)
                 {
+                  pdb.setFile(entry.getFile());
                   if(pdbfiles==null)
                     pdbfiles = new Vector();
 
-
                   if(!pdbfiles.contains(entry.getId()))
                   {
                     pdbfiles.addElement(entry.getId());
                     try
                     {
                       File file = new File(entry.getFile());
-                      if(file.exists())
+                      if(file.exists() && jout!=null)
                       {
                         byte[] data = new byte[ (int) file.length()];
                         jout.putNextEntry(new JarEntry(entry.getId()));
@@ -669,6 +670,7 @@ public class Jalview2XML
         view.setShowBoxes(av.getShowBoxes());
         view.setShowColourText(av.getColourText());
         view.setShowFullId(av.getShowJVSuffix());
+        view.setRightAlignIds(av.rightAlignIds);
         view.setShowSequenceFeatures(av.showSequenceFeatures);
         view.setShowText(av.getShowText());
         view.setWrapAlignment(av.getWrapAlignment());
@@ -980,6 +982,7 @@ public class Jalview2XML
 
     String loadPDBFile(String file, String pdbId)
     {
+      System.out.println(file +" "+pdbId);
       try
       {
         JarInputStream jin = null;
@@ -1402,11 +1405,14 @@ public class Jalview2XML
           af.alignPanel.adjustAnnotationHeight();
         }
 
-        af.viewport.viewName = view.getViewName();
+        if(view.getViewName()!=null)
+        {
+          af.viewport.viewName = view.getViewName();
+          af.setInitialTabVisible();
+        }
         af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
             view.getHeight());
-        af.viewport.setStartRes(view.getStartRes());
-        af.viewport.setStartSeq(view.getStartSeq());
+
         af.viewport.setShowAnnotation(view.getShowAnnotation());
         af.viewport.setAbovePIDThreshold(view.getPidSelected());
 
@@ -1414,6 +1420,7 @@ public class Jalview2XML
 
         af.viewport.setConservationSelected(view.getConservationSelected());
         af.viewport.setShowJVSuffix(view.getShowFullId());
+        af.viewport.rightAlignIds=view.getRightAlignIds();
         af.viewport.setFont(new java.awt.Font(view.getFontName(),
                 view.getFontStyle(), view.getFontSize()));
         af.alignPanel.fontChanged();
@@ -1431,6 +1438,8 @@ public class Jalview2XML
         af.viewport.textColour2 = new java.awt.Color(view.getTextCol2());
         af.viewport.thresholdTextColour = view.getTextColThreshold();
 
+        af.viewport.setStartRes(view.getStartRes());
+        af.viewport.setStartSeq(view.getStartSeq());
 
         ColourSchemeI cs = null;