+
+ //@formatter:on
+
+ /**
+ * Test case where the declared gap character is one Jalview does not support;
+ * it should be converted to a '-'
+ *
+ * @throws IOException
+ */
+ @Test(groups = { "Functional" })
+ public void testParse_weirdGapCharacter() throws IOException
+ {
+ //@formatter:off
+ String data = "#MEGA\n"+
+ "!TITLE Interleaved sequence data;\n" +
+ "!Format Identical=. Indel=%;\n\n" +
+ "#U455 %BC%EF\n" +
+ "#CPZANT M..P.R\n\n" +
+ "#U455 KLMNOP\n" +
+ "#CPZANT .%%Z..";
+ AppletFormatAdapter fa = new AppletFormatAdapter();
+ AlignmentI al = fa.readFile(data,
+ AppletFormatAdapter.PASTE, "MEGA");
+ //@formatter:on
+ List<SequenceI> seqs = al.getSequences();
+ assertEquals("First sequence data wrong", "-BC-EFKLMNOP", seqs.get(0)
+ .getSequenceAsString());
+ assertEquals("Second sequence data wrong", "MBCPERK--ZOP", seqs.get(1)
+ .getSequenceAsString());
+ assertEquals('-', al.getGapCharacter());
+ }