X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=fb53900320054a76c2567e91a0428211a6614b9f;hb=ad15cff29620f960119f80176f1fd443da9f6763;hp=102e46316987dd1fe9c9641e4c201890cbcff11f;hpb=c0aaf84826ff25d510846bd1099e10809c4df711;p=jalview.git

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 102e463..fb53900 100644
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 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.
  * 
@@ -27,8 +27,8 @@ import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
-import jalview.datamodel.ViewerData;
-import jalview.datamodel.ViewerData.StructureData;
+import jalview.datamodel.StructureViewerModel;
+import jalview.datamodel.StructureViewerModel.StructureData;
 import jalview.schemabinding.version2.AlcodMap;
 import jalview.schemabinding.version2.Alcodon;
 import jalview.schemabinding.version2.AlcodonFrame;
@@ -3044,7 +3044,7 @@ public class Jalview2XML
      * Run through all PDB ids on the alignment, and collect mappings between
      * distinct view ids and all sequences referring to that view.
      */
-    Map<String, ViewerData> structureViewers = new LinkedHashMap<String, ViewerData>();
+    Map<String, StructureViewerModel> structureViewers = new LinkedHashMap<String, StructureViewerModel>();
 
     for (int i = 0; i < jseqs.length; i++)
     {
@@ -3086,7 +3086,7 @@ public class Jalview2XML
             }
             if (!structureViewers.containsKey(sviewid))
             {
-              structureViewers.put(sviewid, new ViewerData(x, y, width, height,
+              structureViewers.put(sviewid, new StructureViewerModel(x, y, width, height,
                       false, false, true));
               // Legacy pre-2.7 conversion JAL-823 :
               // do not assume any view has to be linked for colour by
@@ -3097,7 +3097,7 @@ public class Jalview2XML
             // file }, orig_fileloc, SequenceI[][] {{ seqs_file 1 }, {
             // seqs_file 2}, boolean[] {
             // linkAlignPanel,superposeWithAlignpanel}} from hash
-            ViewerData jmoldat = structureViewers.get(sviewid);
+            StructureViewerModel jmoldat = structureViewers.get(sviewid);
             jmoldat.setAlignWithPanel(jmoldat.isAlignWithPanel()
                     | (structureState.hasAlignwithAlignPanel() ? structureState
                             .getAlignwithAlignPanel() : false));
@@ -3156,7 +3156,7 @@ public class Jalview2XML
       }
     }
       // Instantiate the associated structure views
-      for (Entry<String, ViewerData> entry : structureViewers.entrySet())
+      for (Entry<String, StructureViewerModel> entry : structureViewers.entrySet())
       {
         createOrLinkStructureViewer(entry, af, ap);
       }
@@ -3169,10 +3169,10 @@ public class Jalview2XML
    * @param ap
    */
   protected void createOrLinkStructureViewer(
-          Entry<String, ViewerData> viewerData, AlignFrame af,
+          Entry<String, StructureViewerModel> viewerData, AlignFrame af,
           AlignmentPanel ap)
   {
-    final ViewerData svattrib = viewerData.getValue();
+    final StructureViewerModel svattrib = viewerData.getValue();
 
     /*
      * Search for any viewer windows already open from other alignment views
@@ -3206,10 +3206,10 @@ public class Jalview2XML
    * @param viewerData
    * @param af
    */
-  protected void createChimeraViewer(Entry<String, ViewerData> viewerData,
+  protected void createChimeraViewer(Entry<String, StructureViewerModel> viewerData,
           AlignFrame af)
   {
-    final ViewerData data = viewerData.getValue();
+    final StructureViewerModel data = viewerData.getValue();
     String chimeraSession = data.getStateData();
 
     if (new File(chimeraSession).exists())
@@ -3255,9 +3255,9 @@ public class Jalview2XML
    * @param af
    */
   protected void createJmolViewer(
-          final Entry<String, ViewerData> viewerData, AlignFrame af)
+          final Entry<String, StructureViewerModel> viewerData, AlignFrame af)
   {
-    final ViewerData svattrib = viewerData.getValue();
+    final StructureViewerModel svattrib = viewerData.getValue();
     String state = svattrib.getStateData();
     List<String> pdbfilenames = new ArrayList<String>();
     List<SequenceI[]> seqmaps = new ArrayList<SequenceI[]>();
@@ -3400,10 +3400,10 @@ public class Jalview2XML
    * @return
    */
   protected StructureViewerBase findMatchingViewer(
-          Entry<String, ViewerData> viewerData)
+          Entry<String, StructureViewerModel> viewerData)
   {
     final String sviewid = viewerData.getKey();
-    final ViewerData svattrib = viewerData.getValue();
+    final StructureViewerModel svattrib = viewerData.getValue();
     StructureViewerBase comp = null;
     JInternalFrame[] frames = getAllFrames();
     for (JInternalFrame frame : frames)
@@ -3447,7 +3447,7 @@ public class Jalview2XML
    * @param viewerColouring
    */
   protected void linkStructureViewer(AlignmentPanel ap,
-          StructureViewerBase viewer, ViewerData svattrib)
+          StructureViewerBase viewer, StructureViewerModel svattrib)
   {
     // NOTE: if the jalview project is part of a shared session then
     // view synchronization should/could be done here.