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 22b0601..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";
@@ -271,6 +269,17 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
       return false;
     }
 
+    /*
+     * experimental - add any dummy sequences with features to the alignment
+     * - we need them for Ensembl feature extraction - though maybe not otherwise
+     */
+    for (SequenceI newseq : newseqs)
+    {
+      if (newseq.getSequenceFeatures() != null)
+      {
+        align.addSequence(newseq);
+      }
+    }
     return true;
   }
 
@@ -1067,7 +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();
@@ -1319,6 +1329,11 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
          * replace parsed sequence with the realised forward reference
          */
         includedseqs.set(p, dummyseq);
+
+        /*
+         * and remove from the newseqs list
+         */
+        newseqs.remove(dummyseq);
       }
     }