3253-omnibus save

[jalview.git] / src / jalview / bin / JalviewAppLoader.java

diff --git a/src/jalview/bin/JalviewAppLoader.java b/src/jalview/bin/JalviewAppLoader.java
index 8fe2cdc..834a30f 100644 (file)
--- 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)