Merge branch 'features/pca_jaxb_datasetrefs_JAL-3171_JAL-3063_JAL-1767' into develop

[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 e94ee0e..9548839 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;
@@ -226,11 +227,10 @@ 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);
         }
       }
@@ -493,7 +493,7 @@ public class Jalview2XML_V1
           tp.showBootstrap(tree.getShowBootstrap());
           tp.showDistances(tree.getShowDistances());
 
-          tp.treeCanvas.threshold = tree.getThreshold();
+          tp.getTreeCanvas().setThreshold(tree.getThreshold());
 
           if (tree.getCurrentTree())
           {