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;
}
* replace parsed sequence with the realised forward reference
*/
includedseqs.set(p, dummyseq);
+
+ /*
+ * and remove from the newseqs list
+ */
+ newseqs.remove(dummyseq);
}
}