Example #1
0
  @Test(dataProvider = "dataLines")
  public void testDecode1(
      String str, String contig, int start, int end, List<String> header, List<String> vals) {
    TableCodec tc = new TableCodec();
    final TableFeature decode = tc.decode(str);
    Assert.assertEquals(decode.getContig(), contig, "contig");
    Assert.assertEquals(decode.getStart(), start, "start");
    Assert.assertEquals(decode.getEnd(), end, "end");
    Assert.assertEquals(decode.getHeader(), header, decode.getHeader().toString());

    Assert.assertEquals(decode.columnCount(), vals.size());
    for (int i = 0; i < decode.columnCount(); i++) {
      Assert.assertEquals(decode.getValue(i), vals.get(i), "i:" + i);
    }
  }
Example #2
0
  @Test
  public void testDecodeHeader2() {
    TableCodec tc = new TableCodec();
    final String str2 = "1:1  1   2   3";
    LineReader reader = makeReader(asList("HEADER a b c", str2));
    LineIterator li = new LineIteratorImpl(reader);
    List<String> hd = tc.readActualHeader(li);
    Assert.assertEquals(hd, asList("HEADER", "a", "b", "c"));

    final TableFeature decode = tc.decode(str2);
    Assert.assertEquals(decode.get("a"), "1");
    Assert.assertEquals(decode.get("b"), "2");
    Assert.assertEquals(decode.get("c"), "3");
    Assert.assertEquals(decode.getLocation().getContig(), "1");
    Assert.assertEquals(decode.getContig(), "1");
    Assert.assertEquals(decode.getLocation().getStart(), 1);
    Assert.assertEquals(decode.getLocation().getEnd(), 1);
  }