- // TODO: getSequenceAsString() will be deprecated in the future
- // TODO: need to leave to SequenceI implementor to update gaps
- seq.setSequence(alignedSequences.get(0).getSequenceAsString());
+ SequenceI alignedSeq = alignedSequences.get(0);
+
+ /*
+ * gap fill for leading (5') UTR if any
+ */
+ // TODO this copies intron columns - wrong!
+ int startCol = alignedSeq.findIndex(seq.getStart()); // 1..
+ int endCol = alignedSeq.findIndex(seq.getEnd());
+ char[] seqchars = new char[endCol - leftmost + 1];
+ Arrays.fill(seqchars, gapCharacter);
+ char[] toCopy = alignedSeq.getSequence(startCol - 1, endCol);
+ System.arraycopy(toCopy, 0, seqchars, startCol - leftmost,
+ toCopy.length);
+ seq.setSequence(String.valueOf(seqchars));