JAL-1705 derive transcript sequences from gene sequence/GFF; handle CDS

[jalview.git] / src / jalview / io / FeaturesFile.java

diff --git a/src/jalview/io/FeaturesFile.java b/src/jalview/io/FeaturesFile.java
index 2d91a08..2dd5f26 100755 (executable)
--- a/src/jalview/io/FeaturesFile.java
+++ b/src/jalview/io/FeaturesFile.java
@@ -74,8 +74,6 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
 
   private static final String NOTE = "Note";
 
-  protected static final String FRAME = "FRAME";
-
   protected static final String TAB = "\t";
 
   protected static final String GFF_VERSION = "##gff-version";
@@ -1078,7 +1076,8 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
           out.append(strand == 1 ? "+" : (strand == -1 ? "-" : "."));
           out.append(TAB);
 
-          out.append(sf.getValue(FRAME, "."));
+          String phase = sf.getPhase();
+          out.append(phase == null ? "." : phase);
 
           // miscellaneous key-values (GFF column 9)
           String attributes = sf.getAttributes();