s2 = new Sequence("Seq2", "ASDFA");
s2.setStart(5);
s2.setEnd(9);
- s3 = new Sequence("Seq1", "SDFAQQQSSS");
+ s3 = new Sequence("Seq3", "SDFAQQQSSS");
}
public void testPrintAlignment()
{
AlignSeq as = AlignSeq.doGlobalNWAlignment(s1, s3, AlignSeq.PEP);
+
+ // s1 = new Sequence("Seq1", "ASDFAQQQRRRSSS");
+ // s1.setStart(3);
+ // s1.setEnd(18);
+ // s3 = new Sequence("Seq3", "SDFAQQQSSS");
+ //
final StringBuilder baos = new StringBuilder();
PrintStream ps = new PrintStream(System.out)
{
@Override
public void print(String x)
{
- baos.append(x);
+ baos.append(x.replaceAll("\r", ""));
}
@Override
};
as.printAlignment(ps);
- String expected = "Score = 320\nLength of alignment = 10\nSequence Seq1 : 3 - 18 (Sequence length = 14)\nSequence Seq1 : 1 - 10 (Sequence length = 10)\n\n"
- + "Seq1 SDFAQQQRRR\n"
- + " ||||||| \n"
- + "Seq1 SDFAQQQSSS\n\n" + "Percentage ID = 70.00\n";
- assertEquals(expected, baos.toString());
+ String expected = "Score = 320.0\n" + "Length of alignment = 10\n"
+ + "Sequence Seq1/4-13 (Sequence length = 14)\n"
+ + "Sequence Seq3/1-10 (Sequence length = 10)\n" + "\n"
+ + "Seq1/4-13 SDFAQQQRRR\n"
+ + " ||||||| \n"
+ + "Seq3/1-10 SDFAQQQSSS\n" + "\n" + "Percentage ID = 70.00\n"
+ + "\n";
+
+ String s = baos.toString();
+ System.out.println(s);
+
+ assertEquals(expected, s);
}
}