X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalviewAppLoader.java;h=834a30fc4299599c31f707a335f03bd5d5fe5f01;hb=6200addf078b7f7ace90597dc056dafc7fc602c1;hp=8fe2cdc2860f35acafc5e4cfe2abf33e55c8d9e5;hpb=4b1c969e87feaefd4fb9c49ba3d6b828b3ce1a9c;p=jalview.git

diff --git a/src/jalview/bin/JalviewAppLoader.java b/src/jalview/bin/JalviewAppLoader.java
index 8fe2cdc..834a30f 100644
--- a/src/jalview/bin/JalviewAppLoader.java
+++ b/src/jalview/bin/JalviewAppLoader.java
@@ -1370,7 +1370,8 @@ public class JalviewAppLoader
     return true;
   }
 
-  public String getFeaturesFrom(AlignFrameI alf, String format)
+  public String getFeaturesFrom(AlignFrameI alf, String format,
+          boolean includeNonpositionsFeatures, boolean includeComplement)
   {
     AlignFrame f = ((AlignFrame) alf);
 
@@ -1380,13 +1381,15 @@ public class JalviewAppLoader
     {
       features = formatter.printJalviewFormat(
               f.getViewport().getAlignment().getSequencesArray(),
-              f.alignPanel.getFeatureRenderer(), true);
+              f.alignPanel.getFeatureRenderer(),
+              includeNonpositionsFeatures, includeComplement);
     }
     else
     {
       features = formatter.printGffFormat(
               f.getViewport().getAlignment().getSequencesArray(),
-              f.alignPanel.getFeatureRenderer(), true);
+              f.alignPanel.getFeatureRenderer(),
+              includeNonpositionsFeatures, includeComplement);
     }
 
     if (features == null)