JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensing glob

[jalview.git] / src / jalview / gui / Jalview2XML.java

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 5366820..d920c7f 100644 (file)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,6 +20,7 @@
  */
 package jalview.gui;
 
+import jalview.api.ViewStyleI;
 import jalview.api.structures.JalviewStructureDisplayI;
 import jalview.bin.Cache;
 import jalview.datamodel.AlignedCodonFrame;
@@ -776,9 +777,9 @@ public class Jalview2XML
         }
       }
 
-      if (jdatasq.getPDBId() != null)
+      if (jdatasq.getAllPDBEntries() != null)
       {
-        Enumeration en = jdatasq.getPDBId().elements();
+        Enumeration en = jdatasq.getAllPDBEntries().elements();
         while (en.hasMoreElements())
         {
           Pdbids pdb = new Pdbids();
@@ -1149,6 +1150,7 @@ public class Jalview2XML
       view.setFontName(av.font.getName());
       view.setFontSize(av.font.getSize());
       view.setFontStyle(av.font.getStyle());
+      view.setScaleProteinAsCdna(av.getViewStyle().isScaleProteinAsCdna());
       view.setRenderGaps(av.isRenderGaps());
       view.setShowAnnotation(av.isShowAnnotation());
       view.setShowBoxes(av.getShowBoxes());
@@ -1367,6 +1369,10 @@ public class Jalview2XML
           final SequenceI jds, List<String> viewIds, AlignmentPanel ap,
           boolean storeDataset)
   {
+    if (Desktop.desktop == null)
+    {
+      return;
+    }
     JInternalFrame[] frames = Desktop.desktop.getAllFrames();
     for (int f = frames.length - 1; f > -1; f--)
     {
@@ -1848,8 +1854,8 @@ public class Jalview2XML
       }
     }
     throw new Error(MessageManager.formatMessage(
-            "error.unsupported_version_calcIdparam", new Object[]
-            { calcIdParam.toString() }));
+            "error.unsupported_version_calcIdparam",
+            new Object[] { calcIdParam.toString() }));
   }
 
   /**
@@ -2833,8 +2839,8 @@ public class Jalview2XML
             else
             {
               // defer to later
-              frefedSequence.add(new Object[]
-              { maps[m].getDnasq(), cf, mapping });
+              frefedSequence.add(new Object[] { maps[m].getDnasq(), cf,
+                  mapping });
             }
           }
         }
@@ -3832,53 +3838,53 @@ public class Jalview2XML
       }
     }
 
-      final String[] pdbf = pdbfilenames.toArray(new String[pdbfilenames
-              .size()]);
-      final String[] id = pdbids.toArray(new String[pdbids.size()]);
-      final SequenceI[][] sq = seqmaps
-              .toArray(new SequenceI[seqmaps.size()][]);
-      final String fileloc = newFileLoc.toString();
-      final String sviewid = viewerData.getKey();
-      final AlignFrame alf = af;
-      final Rectangle rect = new Rectangle(svattrib.getX(),
-              svattrib.getY(), svattrib.getWidth(), svattrib.getHeight());
-      try
+    final String[] pdbf = pdbfilenames.toArray(new String[pdbfilenames
+            .size()]);
+    final String[] id = pdbids.toArray(new String[pdbids.size()]);
+    final SequenceI[][] sq = seqmaps
+            .toArray(new SequenceI[seqmaps.size()][]);
+    final String fileloc = newFileLoc.toString();
+    final String sviewid = viewerData.getKey();
+    final AlignFrame alf = af;
+    final Rectangle rect = new Rectangle(svattrib.getX(), svattrib.getY(),
+            svattrib.getWidth(), svattrib.getHeight());
+    try
+    {
+      javax.swing.SwingUtilities.invokeAndWait(new Runnable()
       {
-        javax.swing.SwingUtilities.invokeAndWait(new Runnable()
+        @Override
+        public void run()
         {
-          @Override
-          public void run()
+          JalviewStructureDisplayI sview = null;
+          try
           {
-            JalviewStructureDisplayI sview = null;
-            try
-            {
-              sview = new StructureViewer(alf.alignPanel
-                      .getStructureSelectionManager()).createView(
-                      StructureViewer.ViewerType.JMOL, pdbf, id, sq,
-                      alf.alignPanel, svattrib, fileloc, rect, sviewid);
-              addNewStructureViewer(sview);
-            } catch (OutOfMemoryError ex)
+            sview = new StructureViewer(alf.alignPanel
+                    .getStructureSelectionManager()).createView(
+                    StructureViewer.ViewerType.JMOL, pdbf, id, sq,
+                    alf.alignPanel, svattrib, fileloc, rect, sviewid);
+            addNewStructureViewer(sview);
+          } catch (OutOfMemoryError ex)
+          {
+            new OOMWarning("restoring structure view for PDB id " + id,
+                    (OutOfMemoryError) ex.getCause());
+            if (sview != null && sview.isVisible())
             {
-              new OOMWarning("restoring structure view for PDB id " + id,
-                      (OutOfMemoryError) ex.getCause());
-              if (sview != null && sview.isVisible())
-              {
-                sview.closeViewer(false);
-                sview.setVisible(false);
-                sview.dispose();
-              }
+              sview.closeViewer(false);
+              sview.setVisible(false);
+              sview.dispose();
             }
           }
-        });
-      } catch (InvocationTargetException ex)
-      {
-        warn("Unexpected error when opening Jmol view.", ex);
+        }
+      });
+    } catch (InvocationTargetException ex)
+    {
+      warn("Unexpected error when opening Jmol view.", ex);
 
-      } catch (InterruptedException e)
-      {
-        // e.printStackTrace();
-      }
+    } catch (InterruptedException e)
+    {
+      // e.printStackTrace();
     }
+
   }
 
   /**
@@ -4190,6 +4196,9 @@ public class Jalview2XML
     af.viewport.setFont(
             new java.awt.Font(view.getFontName(), view.getFontStyle(), view
                     .getFontSize()), true);
+    ViewStyleI vs = af.viewport.getViewStyle();
+    vs.setScaleProteinAsCdna(view.isScaleProteinAsCdna());
+    af.viewport.setViewStyle(vs);
     // TODO: allow custom charWidth/Heights to be restored by updating them
     // after setting font - which means set above to false
     af.viewport.setRenderGaps(view.getRenderGaps());
@@ -4574,8 +4583,8 @@ public class Jalview2XML
       /**
        * Kludge for magic autoannotation names (see JAL-811)
        */
-      String[] magicNames = new String[]
-      { "Consensus", "Quality", "Conservation" };
+      String[] magicNames = new String[] { "Consensus", "Quality",
+          "Conservation" };
       JvAnnotRow nullAnnot = new JvAnnotRow(-1, null);
       Hashtable<String, JvAnnotRow> visan = new Hashtable<String, JvAnnotRow>();
       for (String nm : magicNames)
@@ -4985,8 +4994,7 @@ public class Jalview2XML
         }
         else
         {
-          frefedSequence.add(new Object[]
-          { dsfor, jmap });
+          frefedSequence.add(new Object[] { dsfor, jmap });
         }
       }
       else