import jalview.datamodel.Mapping;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
import java.io.PrintStream;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
public class TestAlignSeq
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
SequenceI s1, s2, s3;
/**
* @throws java.lang.Exception
*/
- @BeforeMethod
+ @BeforeMethod(alwaysRun = true)
public void setUp() throws Exception
{
s1 = new Sequence("Seq1", "ASDFAQQQRRRSSS");
s2 = new Sequence("Seq2", "ASDFA");
s2.setStart(5);
s2.setEnd(9);
- s3 = new Sequence("Seq1", "SDFAQQQSSS");
+ s3 = new Sequence("Seq3", "SDFAQQQSSS");
}
- @Test
+ @Test(groups = { "Functional" })
/**
* simple test that mapping from alignment corresponds identical positions.
*/
public void testGetMappingForS1()
{
- AlignSeq as = AlignSeq
- .doGlobalNWAlignment(s1, s2, AlignSeq.PEP);
+ AlignSeq as = AlignSeq.doGlobalNWAlignment(s1, s2, AlignSeq.PEP);
System.out.println("s1: " + as.getAStr1());
System.out.println("s2: " + as.getAStr2());
}
}
- @Test
+ @Test(groups = { "Functional" })
public void testExtractGaps()
{
assertNull(AlignSeq.extractGaps(null, null));
assertEquals("ABCD", AlignSeq.extractGaps(" .-", ". -A-B.C D."));
}
- @Test
+ @Test(groups = { "Functional" })
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\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);
}
}