private static final String AA_SEQS_2 =
">Seq1Name/5-8\n" +
- "K-QY--L\n" +
+ "K-QY-L\n" +
">Seq2Name/12-15\n" +
- "-R-FP-W-\n";
+ "-R-FPW\n";
private static final String AA_SEQS_2_DS =
">Seq1Name/5-8\n" +
"KQYL\n" +
AlignmentI al1 = loadAlignment(TD_SEQS_2, FileFormat.Fasta);
AlignmentI al2 = loadAlignment(AA_SEQS_2_DS, FileFormat.Fasta);
al1.setDataset(null);
- al2.setDataset(null);
+ al2.setDataset(al1.getDataset());
AlignmentI al1copy = new Alignment(al1);
AlignmentI al2copy = new Alignment(al2);
AlignmentUtils.map3diPeptideToProteinAligment(al2, al1);
}
/**
+ * Recover TdI MSA from protein msa
+ *
+ * @throws IOException
+ */
+ @Test(groups = { "Functional" })
+ public void testAlignAs_tdi_prot() throws Exception
+ {
+ // see also AlignmentUtilsTests
+ AlignmentI al1 = loadAlignment(AA_SEQS_2, FileFormat.Fasta);
+ AlignmentI al2 = loadAlignment(TD_SEQS_2_DS, FileFormat.Fasta);
+ al1.setDataset(null);
+ al2.setDataset(al1.getDataset());
+ AlignmentI al1copy = new Alignment(al1);
+ AlignmentI al2copy = new Alignment(al2);
+ AlignmentUtils.map3diPeptideToProteinAligment(al1, al2);
+ if (al2.getCodonFrames().isEmpty()) {al2.getCodonFrames().addAll(al1.getCodonFrames()); }
+ else {al1.getCodonFrames().addAll(al2.getCodonFrames()); };
+
+ ((Alignment) al2).alignAs(al1);
+ assertEquals("K-QY-L", al1.getSequenceAt(0).getSequenceAsString());
+ assertEquals("-R-FPW", al1.getSequenceAt(1).getSequenceAsString());
+ assertEquals("N-MP-R", al2.getSequenceAt(0).getSequenceAsString());
+ assertEquals("-V-XYA", al2.getSequenceAt(1).getSequenceAsString());
+
+ }
+ /**
* Test aligning cdna as per protein alignment.
*
* @throws IOException