X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML_V1.java;h=74728777344e97fdc6e18f2ab87dcc2306cd7943;hb=24680a271861e9309a2241c8884874656ac111b1;hp=b551f5d66902843951952d10316c059f7ae03835;hpb=4d7f98a6dd54d9863ba449ec79dcd95d25ed863d;p=jalview.git

diff --git a/src/jalview/gui/Jalview2XML_V1.java b/src/jalview/gui/Jalview2XML_V1.java
index b551f5d..7472877 100755
--- a/src/jalview/gui/Jalview2XML_V1.java
+++ b/src/jalview/gui/Jalview2XML_V1.java
@@ -20,6 +20,7 @@
  */
 package jalview.gui;
 
+import jalview.analysis.Conservation;
 import jalview.binding.Annotation;
 import jalview.binding.AnnotationElement;
 import jalview.binding.Features;
@@ -35,24 +36,22 @@ 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;
 import java.util.jar.JarInputStream;
 
-import javax.swing.JOptionPane;
-
-import org.exolab.castor.xml.IDResolver;
-
 /**
  * DOCUMENT ME!
  * 
@@ -127,43 +126,39 @@ 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 +171,16 @@ 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 +304,7 @@ 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++)
     {
@@ -335,15 +331,10 @@ public class Jalview2XML_V1
           }
           else
           {
-            cs = ColourSchemeProperty.getColour(al, groups[i].getColour());
-          }
-
-          if (cs != null)
-          {
-            cs.setThreshold(groups[i].getPidThreshold(), true);
+            cs = ColourSchemeProperty.getColourScheme(al, groups[i].getColour());
           }
-
         }
+        int pidThreshold = groups[i].getPidThreshold();
 
         Vector seqs = new Vector();
         int[] ids = groups[i].getSeq();
@@ -357,14 +348,14 @@ public class Jalview2XML_V1
                 seqs, groups[i].getName(), cs, groups[i].getDisplayBoxes(),
                 groups[i].getDisplayText(), groups[i].getColourText(),
                 groups[i].getStart(), groups[i].getEnd());
+        sg.getGroupColourScheme().setThreshold(pidThreshold, true);
 
         sg.setOutlineColour(new java.awt.Color(groups[i].getOutlineColour()));
 
         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);
@@ -404,23 +395,27 @@ public class Jalview2XML_V1
       }
       else
       {
-        cs = ColourSchemeProperty.getColour(al, view.getBgColour());
+        cs = ColourSchemeProperty.getColourScheme(al, view.getBgColour());
       }
 
-      if (cs != null)
-      {
-        cs.setThreshold(view.getPidThreshold(), true);
-        cs.setConsensus(af.viewport.getSequenceConsensusHash());
-      }
+      // if (cs != null)
+      // {
+      // cs.setThreshold(view.getPidThreshold(), true);
+      // cs.setConsensus(af.viewport.getSequenceConsensusHash());
+      // }
     }
 
-    af.viewport.setGlobalColourScheme(cs);
+    af.viewport.getViewportColourScheme().setThreshold(
+            view.getPidThreshold(), true);
+    af.viewport.getViewportColourScheme().setConsensus(
+            af.viewport.getSequenceConsensusHash());
     af.viewport.setColourAppliesToAllGroups(false);
     af.alignPanel.updateLayout();
     af.changeColour(cs);
     if (view.getConservationSelected() && cs != null)
     {
-      cs.setConservationInc(view.getConsThreshold());
+      af.viewport.getViewportColourScheme().setConservationInc(
+              view.getConsThreshold());
     }
 
     af.viewport.setColourAppliesToAllGroups(true);