import jalview.gui.JvOptionPane;
import java.io.PrintStream;
+import java.nio.charset.Charset;
+import java.util.Locale;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
+import com.google.common.base.Charsets;
+
/**
* Test the alignment -> Mapping routines
*
assertEquals(as.getAStr1(), as.getAStr2());
Mapping s1tos2 = as.getMappingFromS1(false);
+ checkMapping(s1tos2, s1, s2);
+ }
+
+ public void checkMapping(Mapping s1tos2, SequenceI _s1, SequenceI _s2)
+ {
System.out.println(s1tos2.getMap().toString());
- for (int i = s2.getStart(); i < s2.getEnd(); i++)
+ for (int i = _s2.getStart(); i < _s2.getEnd(); i++)
{
- System.out.println("Position in s2: " + i
- + " maps to position in s1: " + s1tos2.getPosition(i));
- // TODO fails: getCharAt doesn't allow for the start position??
- // assertEquals(String.valueOf(s2.getCharAt(i)),
- // String.valueOf(s1.getCharAt(s1tos2.getPosition(i))));
+ int p = s1tos2.getPosition(i);
+ char s2c = _s2.getCharAt(i - _s2.getStart());
+ char s1c = _s1.getCharAt(p - _s1.getStart());
+ System.out.println("Position in s2: " + i + s2c
+ + " maps to position in s1: " + p + s1c);
+ assertEquals(s1c, s2c);
}
}
@Test(groups = { "Functional" })
+ /**
+ * simple test that mapping from alignment corresponds identical positions.
+ */
+ public void testGetMappingForS1_withLowerCase()
+ {
+ // make one of the sequences lower case
+ SequenceI ns2 = new Sequence(s2);
+ ns2.replace('D', 'd');
+ AlignSeq as = AlignSeq.doGlobalNWAlignment(s1, ns2, AlignSeq.PEP);
+ System.out.println("s1: " + as.getAStr1());
+ System.out.println("s2: " + as.getAStr2());
+
+ // aligned results match
+ assertEquals("ASDFA", as.getAStr1());
+ assertEquals(as.getAStr1(), as.getAStr2().toUpperCase(Locale.ROOT));
+
+ Mapping s1tos2 = as.getMappingFromS1(false);
+ assertEquals("ASdFA", as.getAStr2());
+ // verify mapping is consistent between original all-caps sequences
+ checkMapping(s1tos2, s1, s2);
+ }
+
+ @Test(groups = { "Functional" })
public void testExtractGaps()
{
assertNull(AlignSeq.extractGaps(null, null));
as.printAlignment(ps);
String expected = "Score = 320.0\nLength of alignment = 10\nSequence Seq1/4-13 (Sequence length = 14)\nSequence Seq3/1-10 (Sequence length = 10)\n\n"
- + "Seq1/4-13 SDFAQQQRRR\n"
- + " ||||||| \n"
+ + "Seq1/4-13 SDFAQQQRRR\n" + " ||||||| \n"
+ "Seq3/1-10 SDFAQQQSSS\n\n" + "Percentage ID = 70.00\n\n";
assertEquals(expected, baos.toString());
}