JAL-2418 patch build - broken htsjdk import

[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..cc2f636 100755 (executable)
--- a/src/jalview/gui/Jalview2XML_V1.java
+++ b/src/jalview/gui/Jalview2XML_V1.java
@@ -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());