merge

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

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index a448d19..fc96edc 100644 (file)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -1092,15 +1092,26 @@ 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);
@@ -1937,16 +1948,16 @@ 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)
     {
@@ -2453,6 +2464,11 @@ 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);
 
     /*