X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=3c070dcdf523b4b65ffb0e4d1f294f64a0997b39;hb=26b115b0a77d521da92a06572d9b7819c2d0d49a;hp=fdc28470cd5ab6760c2e67d7fbf6f9b4b64a91c0;hpb=aa4e99f8937ce22963cf32f1e92f174ee52ad7ee;p=jalview.git

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index fdc2847..3c070dc 100644
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -29,6 +29,7 @@ import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.GraphLine;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.RnaViewerModel;
@@ -52,7 +53,6 @@ import jalview.schemabinding.version2.Annotation;
 import jalview.schemabinding.version2.AnnotationColours;
 import jalview.schemabinding.version2.AnnotationElement;
 import jalview.schemabinding.version2.CalcIdParam;
-import jalview.schemabinding.version2.Colour;
 import jalview.schemabinding.version2.CompoundMatcher;
 import jalview.schemabinding.version2.DBRef;
 import jalview.schemabinding.version2.Features;
@@ -1102,13 +1102,13 @@ public class Jalview2XML
           {
             TreePanel tp = (TreePanel) frames[t];
 
-            if (tp.treeCanvas.av.getAlignment() == jal)
+            if (tp.getTreeCanvas().getViewport().getAlignment() == jal)
             {
               Tree tree = new Tree();
               tree.setTitle(tp.getTitle());
               tree.setCurrentTree((av.getCurrentTree() == tp.getTree()));
               tree.setNewick(tp.getTree().print());
-              tree.setThreshold(tp.treeCanvas.threshold);
+              tree.setThreshold(tp.getTreeCanvas().getThreshold());
 
               tree.setFitToWindow(tp.fitToWindow.getState());
               tree.setFontName(tp.getTreeFont().getName());
@@ -1247,7 +1247,7 @@ public class Jalview2XML
       {
         view.setComplementId(av.getCodingComplement().getViewId());
       }
-      view.setViewName(av.viewName);
+      view.setViewName(av.getViewName());
       view.setGatheredViews(av.isGatherViewsHere());
 
       Rectangle size = ap.av.getExplodedGeometry();
@@ -1450,9 +1450,10 @@ public class Jalview2XML
         }
         else
         {
-          ArrayList<int[]> hiddenRegions = hidden.getHiddenColumnsCopy();
-          for (int[] region : hiddenRegions)
+          Iterator<int[]> hiddenRegions = hidden.iterator();
+          while (hiddenRegions.hasNext())
           {
+            int[] region = hiddenRegions.next();
             HiddenColumns hc = new HiddenColumns();
             hc.setStart(region[0]);
             hc.setEnd(region[1]);
@@ -2109,7 +2110,7 @@ public class Jalview2XML
     vamsasSeq.setName(jds.getName());
     vamsasSeq.setSequence(jds.getSequenceAsString());
     vamsasSeq.setDescription(jds.getDescription());
-    jalview.datamodel.DBRefEntry[] dbrefs = null;
+    List<DBRefEntry> dbrefs = null;
     if (jds.getDatasetSequence() != null)
     {
       vamsasSeq.setDsseqid(seqHash(jds.getDatasetSequence()));
@@ -2127,15 +2128,16 @@ public class Jalview2XML
     }
     if (dbrefs != null)
     {
-      for (int d = 0; d < dbrefs.length; d++)
+      for (int d = 0, n = dbrefs.size(); d < n; d++)
       {
         DBRef dbref = new DBRef();
-        dbref.setSource(dbrefs[d].getSource());
-        dbref.setVersion(dbrefs[d].getVersion());
-        dbref.setAccessionId(dbrefs[d].getAccessionId());
-        if (dbrefs[d].hasMap())
+        DBRefEntry e = dbrefs.get(d);
+        dbref.setSource(e.getSource());
+        dbref.setVersion(e.getVersion());
+        dbref.setAccessionId(e.getAccessionId());
+        if (e.hasMap())
         {
-          Mapping mp = createVamsasMapping(dbrefs[d].getMap(), parentseq,
+          Mapping mp = createVamsasMapping(e.getMap(), parentseq,
                   jds, recurse);
           dbref.setMapping(mp);
         }
@@ -2677,6 +2679,7 @@ public class Jalview2XML
     if (errorMessage != null)
     {
       final String finalErrorMessage = errorMessage;
+      errorMessage = null;
       if (raiseGUI)
       {
         javax.swing.SwingUtilities.invokeLater(new Runnable()
@@ -2694,10 +2697,10 @@ public class Jalview2XML
       }
       else
       {
-        System.err.println("Problem loading Jalview file: " + errorMessage);
+        System.err.println(
+                "Problem loading Jalview file: " + finalErrorMessage);
       }
     }
-    errorMessage = null;
   }
 
   Map<String, String> alreadyLoadedPDB = new HashMap<>();
@@ -3762,11 +3765,11 @@ public class Jalview2XML
           tp.setTitle(tree.getTitle());
           tp.setBounds(new Rectangle(tree.getXpos(), tree.getYpos(),
                   tree.getWidth(), tree.getHeight()));
-          tp.av = av; // af.viewport; // TODO: verify 'associate with all
+          tp.setViewport(av); // af.viewport; // TODO: verify 'associate with all
           // views'
           // works still
-          tp.treeCanvas.av = av; // af.viewport;
-          tp.treeCanvas.ap = ap; // af.alignPanel;
+          tp.getTreeCanvas().setViewport(av); // af.viewport;
+          tp.getTreeCanvas().setAssociatedPanel(ap); // af.alignPanel;
 
         }
         if (tp == null)
@@ -3794,7 +3797,7 @@ public class Jalview2XML
         tp.showBootstrap(tree.getShowBootstrap());
         tp.showDistances(tree.getShowDistances());
 
-        tp.treeCanvas.threshold = tree.getThreshold();
+        tp.getTreeCanvas().setThreshold(tree.getThreshold());
 
         if (tree.getCurrentTree())
         {
@@ -4527,7 +4530,7 @@ public class Jalview2XML
 
     if (view.getViewName() != null)
     {
-      af.viewport.viewName = view.getViewName();
+      af.viewport.setViewName(view.getViewName());
       af.setInitialTabVisible();
     }
     af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),