X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML_V1.java;h=aefc233db286d963a1e691ca96703df912a40637;hb=7d6bf4ac01167499c0f4e07de63edcdd72a6d595;hp=9182a83cfea8e02e8be83e47c48a422b9a59a318;hpb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;p=jalview.git

diff --git a/src/jalview/gui/Jalview2XML_V1.java b/src/jalview/gui/Jalview2XML_V1.java
index 9182a83..aefc233 100755
--- a/src/jalview/gui/Jalview2XML_V1.java
+++ b/src/jalview/gui/Jalview2XML_V1.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,6 +20,7 @@
  */
 package jalview.gui;
 
+import jalview.analysis.Conservation;
 import jalview.binding.Annotation;
 import jalview.binding.AnnotationElement;
 import jalview.binding.Features;
@@ -35,15 +36,17 @@ import jalview.binding.Tree;
 import jalview.binding.UserColours;
 import jalview.binding.Viewport;
 import jalview.datamodel.PDBEntry;
+import jalview.io.FileFormat;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
-import jalview.schemes.ResidueProperties;
 import jalview.structure.StructureSelectionManager;
 import jalview.util.MessageManager;
 import jalview.util.jarInputStreamProvider;
 import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
 
 import java.io.InputStreamReader;
+import java.io.Reader;
+import java.net.UnknownHostException;
 import java.util.Hashtable;
 import java.util.Vector;
 import java.util.jar.JarEntry;
@@ -51,8 +54,6 @@ import java.util.jar.JarInputStream;
 
 import javax.swing.JOptionPane;
 
-import org.exolab.castor.xml.IDResolver;
-
 /**
  * DOCUMENT ME!
  * 
@@ -127,43 +128,39 @@ public class Jalview2XML_V1
           jarentry = jin.getNextJarEntry();
         }
 
-        class NoDescIDResolver implements IDResolver
-        {
-          public Object resolve(String idref)
-          {
-            System.out.println(idref + " used");
-            return null;
-          }
-        }
-
         if (jarentry != null)
         {
-          InputStreamReader in = new InputStreamReader(jin, "UTF-8");
-          JalviewModel object = new JalviewModel();
+          entryCount++;
+          if (jarentry.getName().endsWith(".xml"))
+          {
+            Reader in = new InputStreamReader(jin, "UTF-8");
+            JalviewModel object = new JalviewModel();
 
-          object = object.unmarshal(in);
+            object = object.unmarshal(in);
 
-          af = LoadFromObject(object, file);
-          entryCount++;
+            af = LoadFromObject(object, file);
+          }
         }
+        jin.close();
       } while (jarentry != null);
-    } catch (final java.net.UnknownHostException ex)
+    } catch (final UnknownHostException ex)
     {
       ex.printStackTrace();
       if (raiseGUI)
       {
         javax.swing.SwingUtilities.invokeLater(new Runnable()
         {
+          @Override
           public void run()
           {
 
             System.err.println("Couldn't locate Jalview XML file : " + ex
                     + "\n");
-            JOptionPane.showInternalMessageDialog(Desktop.desktop,
+            JvOptionPane.showInternalMessageDialog(Desktop.desktop,
                     MessageManager.formatMessage("label.couldnt_locate",
                             new String[] { file }), MessageManager
                             .getString("label.url_not_found"),
-                    JOptionPane.WARNING_MESSAGE);
+                    JvOptionPane.WARNING_MESSAGE);
           }
         });
       }
@@ -176,15 +173,16 @@ public class Jalview2XML_V1
       {
         javax.swing.SwingUtilities.invokeLater(new Runnable()
         {
+          @Override
           public void run()
           {
 
-            JOptionPane.showInternalMessageDialog(Desktop.desktop,
+            JvOptionPane.showInternalMessageDialog(Desktop.desktop,
                     MessageManager.formatMessage(
                             "label.error_loading_file_params", new String[]
                             { file }), MessageManager
                             .getString("label.error_loading_jalview_file"),
-                    JOptionPane.WARNING_MESSAGE);
+                    JvOptionPane.WARNING_MESSAGE);
           }
         });
       }
@@ -308,7 +306,7 @@ public class Jalview2XML_V1
 
     AlignFrame af = new AlignFrame(al, view.getWidth(), view.getHeight());
 
-    af.setFileName(file, "Jalview");
+    af.setFileName(file, FileFormat.Jalview);
 
     for (int i = 0; i < JSEQ.length; i++)
     {
@@ -335,7 +333,7 @@ public class Jalview2XML_V1
           }
           else
           {
-            cs = ColourSchemeProperty.getColour(al, groups[i].getColour());
+            cs = ColourSchemeProperty.getColourScheme(al, groups[i].getColour());
           }
 
           if (cs != null)
@@ -362,9 +360,8 @@ public class Jalview2XML_V1
 
         if (groups[i].getConsThreshold() != 0)
         {
-          jalview.analysis.Conservation c = new jalview.analysis.Conservation(
-                  "All", ResidueProperties.propHash, 3,
-                  sg.getSequences(null), 0, sg.getWidth() - 1);
+          Conservation c = new Conservation("All", sg.getSequences(null),
+                  0, sg.getWidth() - 1);
           c.calculate();
           c.verdict(false, 25);
           sg.cs.setConservation(c);
@@ -404,7 +401,7 @@ public class Jalview2XML_V1
       }
       else
       {
-        cs = ColourSchemeProperty.getColour(al, view.getBgColour());
+        cs = ColourSchemeProperty.getColourScheme(al, view.getBgColour());
       }
 
       if (cs != null)