JAL-2480 move ContiguousI and Range to jalview.datamodel

[jalview.git] / src / jalview / gui / Jalview2XML_V1.java

diff --git a/src/jalview/gui/Jalview2XML_V1.java b/src/jalview/gui/Jalview2XML_V1.java
index e751a2c..b17d060 100755 (executable)
--- a/src/jalview/gui/Jalview2XML_V1.java
+++ b/src/jalview/gui/Jalview2XML_V1.java
@@ -36,6 +36,7 @@ import jalview.binding.Tree;
 import jalview.binding.UserColours;
 import jalview.binding.Viewport;
 import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceFeature;
 import jalview.io.FileFormat;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
@@ -224,11 +225,10 @@ public class Jalview2XML_V1
         Features[] features = JSEQ[i].getFeatures();
         for (int f = 0; f < features.length; f++)
         {
-          jalview.datamodel.SequenceFeature sf = new jalview.datamodel.SequenceFeature(
-                  features[f].getType(), features[f].getDescription(),
-                  features[f].getStatus(), features[f].getBegin(),
+          SequenceFeature sf = new SequenceFeature(features[f].getType(),
+                  features[f].getDescription(), features[f].getBegin(),
                   features[f].getEnd(), null);
-
+          sf.setStatus(features[f].getStatus());
           al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
         }
       }
@@ -367,8 +367,8 @@ public class Jalview2XML_V1
 
     af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
             view.getHeight());
-    af.viewport.setStartRes(view.getStartRes());
-    af.viewport.setStartSeq(view.getStartSeq());
+    af.viewport.getRanges().setStartRes(view.getStartRes());
+    af.viewport.getRanges().setStartSeq(view.getStartSeq());
     af.viewport.setShowAnnotation(view.getShowAnnotation());
     af.viewport.setAbovePIDThreshold(view.getPidSelected());
     af.viewport.setColourText(view.getShowColourText());
@@ -464,7 +464,7 @@ public class Jalview2XML_V1
 
           Tree tree = jms.getTree(t);
 
-          TreePanel tp = af.ShowNewickTree(
+          TreePanel tp = af.showNewickTree(
                   new jalview.io.NewickFile(tree.getNewick()),
                   tree.getTitle(), tree.getWidth(), tree.getHeight(),
                   tree.getXpos(), tree.getYpos());