*/
package jalview.datamodel;
+import static org.testng.Assert.assertTrue;
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertFalse;
+import jalview.gui.JvOptionPane;
+import jalview.util.Comparison;
+
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
/**
*/
public class SeqCigarTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
+ @Test(groups = { "Functional" })
+ public void testFindPosition()
+ {
+ SequenceI oseq = new Sequence("MySeq", "ASD---ASD---ASD", 37, 45);
+ oseq.createDatasetSequence();
+ SeqCigar cs = new SeqCigar(oseq);
+ assertEquals(oseq.getSequenceAsString(), cs.getSequenceString('-'));
+ for (int c = 0, cLen = oseq.getLength(); c < cLen; c++)
+ {
+ int os_p = oseq.findPosition(c);
+ int cigar_p = cs.findPosition(c);
+ if (Comparison.isGap(oseq.getCharAt(c)))
+ {
+ assertEquals("Expected gap at position " + os_p + " column " + c,
+ -1, cigar_p);
+ }
+ else
+ {
+ assertEquals("Positions don't match for at column " + c, os_p,
+ cigar_p);
+ }
+ }
+ }
+
/*
* refactored 'as is' from main method
*
assertEquals("Failed parseCigar", ex_cs_gapped,
gen_sgapped.getCigarstring());
- testSeqRecovery(gen_sgapped, s_gapped);
+ assertTrue(testSeqRecovery(gen_sgapped, s_gapped,true));
/*
* Test dataset resolution
*/
SeqCigar sub_gapped = new SeqCigar(s_subsequence_gapped);
- testSeqRecovery(sub_gapped, s_subsequence_gapped);
+ assertTrue(testSeqRecovery(sub_gapped, s_subsequence_gapped,true));
/*
* Test width functions
/*
* TODO: can we add assertions to the sysouts that follow?
*/
- System.out.println("Original sequence align:\n" + sub_gapped_s
+ System.out.println("\nOriginal sequence align:\n" + sub_gapped_s
+ "\nReconstructed window from 8 to 48\n" + "XXXXXXXX"
+ sub_se_gp.getSequenceString('-') + "..." + "\nCigar String:"
+ sub_se_gp.getCigarstring() + "\n");
assertEquals("Failed getCigarstring", ex_cs_gapped, cs_gapped);
}
- protected void testSeqRecovery(SeqCigar gen_sgapped, SequenceI s_gapped)
+ protected boolean testSeqRecovery(SeqCigar gen_sgapped, SequenceI s_gapped,boolean startEndCheck)
{
// this is non-rigorous - start and end recovery is not tested.
SequenceI gen_sgapped_s = gen_sgapped.getSeq('-');
// assertEquals("Couldn't reconstruct sequence", s_gapped.getSequence(),
// gen_sgapped_s);
- if (!gen_sgapped_s.getSequence().equals(s_gapped.getSequence()))
+ if (!gen_sgapped_s.getSequenceAsString().equals(
+ s_gapped.getSequenceAsString()))
{
// TODO: investigate errors reported here, to allow full conversion to
// passing JUnit assertion form
System.err.println("Couldn't reconstruct sequence.\n"
+ gen_sgapped_s.getSequenceAsString() + "\n"
+ s_gapped.getSequenceAsString());
+ return false;
+ }
+ if (startEndCheck)
+ {
+ assertEquals("Start not conserved in reconstructed sequence",s_gapped.getStart(),gen_sgapped_s.getStart());
+ assertEquals("End not conserved in reconstructed sequence",s_gapped.getEnd(),gen_sgapped_s.getEnd());
}
+ return true;
}
}