X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=2799a7e2921d5867352c63a98e0fe635b57ce2d7;hb=b2cedc8371f6624859f107581e6d84e841d4114b;hp=2f90e915ec479326cb93ceef877de0b45f44a39f;hpb=4316d4573368e1c5455f84c6fcb96aa3a1e48045;p=jalview.git

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 2f90e91..2799a7e 100644
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -163,7 +163,7 @@ public class Jalview2XML
    */
   Map<String, SequenceI> seqRefIds = null;
 
-  Vector frefedSequence = null;
+  Vector<Object[]> frefedSequence = null;
 
   boolean raiseGUI = true; // whether errors are raised in dialog boxes or not
 
@@ -258,7 +258,7 @@ public class Jalview2XML
       int r = 0, rSize = frefedSequence.size();
       while (r < rSize)
       {
-        Object[] ref = (Object[]) frefedSequence.elementAt(r);
+        Object[] ref = frefedSequence.elementAt(r);
         if (ref != null)
         {
           String sref = (String) ref[0];
@@ -761,10 +761,11 @@ public class Jalview2XML
           if (sf[index].otherDetails != null)
           {
             String key;
-            Enumeration keys = sf[index].otherDetails.keys();
-            while (keys.hasMoreElements())
+            Iterator<String> keys = sf[index].otherDetails.keySet()
+                    .iterator();
+            while (keys.hasNext())
             {
-              key = keys.nextElement().toString();
+              key = keys.next();
               OtherData keyValue = new OtherData();
               keyValue.setKey(key);
               keyValue.setValue(sf[index].otherDetails.get(key).toString());
@@ -879,7 +880,7 @@ public class Jalview2XML
     // SAVE MAPPINGS
     if (jal.getCodonFrames() != null)
     {
-      Set<AlignedCodonFrame> jac = jal.getCodonFrames();
+      List<AlignedCodonFrame> jac = jal.getCodonFrames();
       for (AlignedCodonFrame acf : jac)
       {
         AlcodonFrame alc = new AlcodonFrame();
@@ -1092,15 +1093,26 @@ public class Jalview2XML
       view.setViewName(av.viewName);
       view.setGatheredViews(av.isGatherViewsHere());
 
-      Rectangle position = ap.av.getExplodedGeometry();
-      if (position == null)
+      Rectangle size = ap.av.getExplodedGeometry();
+      Rectangle position = size;
+      if (size == null)
       {
-        position = ap.alignFrame.getBounds();
+        size = ap.alignFrame.getBounds();
+        if (av.getCodingComplement() != null)
+        {
+          position = ((SplitFrame) ap.alignFrame.getSplitViewContainer())
+                  .getBounds();
+        }
+        else
+        {
+          position = size;
+        }
       }
       view.setXpos(position.x);
       view.setYpos(position.y);
-      view.setWidth(position.width);
-      view.setHeight(position.height);
+
+      view.setWidth(size.width);
+      view.setHeight(size.height);
 
       view.setStartRes(av.startRes);
       view.setStartSeq(av.startSeq);
@@ -1854,8 +1866,8 @@ public class Jalview2XML
       }
     }
     throw new Error(MessageManager.formatMessage(
-            "error.unsupported_version_calcIdparam", new Object[]
-            { calcIdParam.toString() }));
+            "error.unsupported_version_calcIdparam",
+            new Object[] { calcIdParam.toString() }));
   }
 
   /**
@@ -1937,16 +1949,16 @@ public class Jalview2XML
     if (jds.getDatasetSequence() != null)
     {
       vamsasSeq.setDsseqid(seqHash(jds.getDatasetSequence()));
-      if (jds.getDatasetSequence().getDBRef() != null)
+      if (jds.getDatasetSequence().getDBRefs() != null)
       {
-        dbrefs = jds.getDatasetSequence().getDBRef();
+        dbrefs = jds.getDatasetSequence().getDBRefs();
       }
     }
     else
     {
       vamsasSeq.setDsseqid(id); // so we can tell which sequences really are
       // dataset sequences only
-      dbrefs = jds.getDBRef();
+      dbrefs = jds.getDBRefs();
     }
     if (dbrefs != null)
     {
@@ -2167,6 +2179,7 @@ public class Jalview2XML
       {
         SwingUtilities.invokeAndWait(new Runnable()
         {
+          @Override
           public void run()
           {
             setLoadingFinishedForNewStructureViewers();
@@ -2241,7 +2254,7 @@ public class Jalview2XML
     }
     if (frefedSequence == null)
     {
-      frefedSequence = new Vector();
+      frefedSequence = new Vector<Object[]>();
     }
 
     AlignFrame af = null, _af = null;
@@ -2453,6 +2466,11 @@ public class Jalview2XML
     int width = (int) dnaFrame.getBounds().getWidth();
     int height = (int) (dnaFrame.getBounds().getHeight()
             + proteinFrame.getBounds().getHeight() + 50);
+
+    /*
+     * SplitFrame location is saved to both enclosed frames
+     */
+    splitFrame.setLocation(dnaFrame.getX(), dnaFrame.getY());
     Desktop.addInternalFrame(splitFrame, title, width, height);
 
     /*
@@ -2832,15 +2850,15 @@ public class Jalview2XML
             {
               mapping = addMapping(maps[m].getMapping());
             }
-            if (dnaseq != null)
+            if (dnaseq != null && mapping.getTo() != null)
             {
               cf.addMap(dnaseq, mapping.getTo(), mapping.getMap());
             }
             else
             {
               // defer to later
-              frefedSequence.add(new Object[]
-              { maps[m].getDnasq(), cf, mapping });
+              frefedSequence.add(new Object[] { maps[m].getDnasq(), cf,
+                  mapping });
             }
           }
         }
@@ -3250,8 +3268,8 @@ public class Jalview2XML
      * indicate that annotation colours are applied across all groups (pre
      * Jalview 2.8.1 behaviour)
      */
-    boolean doGroupAnnColour = isVersionStringLaterThan("2.8.1",
-            object.getVersion());
+    boolean doGroupAnnColour = Jalview2XML.isVersionStringLaterThan(
+            "2.8.1", object.getVersion());
 
     AlignmentPanel ap = null;
     boolean isnewview = true;
@@ -4037,7 +4055,7 @@ public class Jalview2XML
    * @return true if version is development/null or evaluates to the same or
    *         later X.Y.Z (where X,Y,Z are like [0-9]+b?[0-9]*)
    */
-  protected boolean isVersionStringLaterThan(String supported,
+  public static boolean isVersionStringLaterThan(String supported,
           String version)
   {
     if (version == null || version.equalsIgnoreCase("DEVELOPMENT BUILD")
@@ -4060,11 +4078,18 @@ public class Jalview2XML
         String fileT = fileV.nextToken().toLowerCase().replace('b', '.');
         try
         {
-          if (Float.valueOf(curT) > Float.valueOf(fileT))
+          float supportedVersionToken = Float.parseFloat(curT);
+          float myVersiontoken = Float.parseFloat(fileT);
+          if (supportedVersionToken > myVersiontoken)
           {
             // current version is newer than the version that wrote the file
             return false;
           }
+          if (supportedVersionToken < myVersiontoken)
+          {
+            // current version is older than the version that wrote the file
+            return true;
+          }
         } catch (NumberFormatException nfe)
         {
           System.err
@@ -4583,8 +4608,8 @@ 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)
@@ -4994,8 +5019,7 @@ public class Jalview2XML
         }
         else
         {
-          frefedSequence.add(new Object[]
-          { dsfor, jmap });
+          frefedSequence.add(new Object[] { dsfor, jmap });
         }
       }
       else