Null sequence check

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

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 08b3903..8406299 100755 (executable)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -308,7 +308,9 @@ public class Jalview2XML
 \r
                 Annotation an = new Annotation();\r
                 an.setDescription(aa[i].description);\r
-                an.setGraph(aa[i].isGraph);\r
+                if(aa[i].graph>0)\r
+                  an.setGraph(true);\r
+\r
                 an.setLabel(aa[i].label);\r
 \r
                 AnnotationElement ae;\r
@@ -717,7 +719,8 @@ public class Jalview2XML
                 if (an[i].getGraph())\r
                 {\r
                     jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),\r
-                            an[i].getDescription(), anot, 0, 0, 1);\r
+                            an[i].getDescription(), anot, 0, 0,\r
+                            jalview.datamodel.AlignmentAnnotation.BAR_GRAPH);\r
                 }\r
                 else\r
                 {\r
@@ -799,6 +802,7 @@ public class Jalview2XML
             view.getHeight());\r
         af.viewport.setStartRes(view.getStartRes());\r
         af.viewport.setStartSeq(view.getStartSeq());\r
+        af.viewport.setShowAnnotation(view.getShowAnnotation());\r
         af.viewport.showConservation = view.getShowConservation();\r
         af.viewport.showQuality = view.getShowQuality();\r
         af.viewport.showIdentity = view.getShowIdentity();\r