public class ContactGeometryTest
{
- @Test(groups="Functional")
+ @Test(groups = "Functional")
public void testCoverageofRange()
{
// a really dumb test to make sure we really cover the requested pixel and
}
}
}
+
@Test(groups = "Functional")
public void testContactGeometry()
{
SequenceI sq = new Sequence("a", "SSSQ");
MappableContactMatrixI cm = new SeqDistanceContactMatrix(4);
AlignmentAnnotation cm_aan = sq.addContactList(cm);
- checkConsistencyFor(sq,cm_aan);
+ checkConsistencyFor(sq, cm_aan);
// Also check all is good when there's a sequence mapping involved
- MappableContactMatrixI newcm=cm.liftOver(sq,
+ MappableContactMatrixI newcm = cm.liftOver(sq,
new Mapping(sq, new MapList(new int[]
{ 1, 4 }, new int[] { 1, 4 }, 1, 1)));
AlignmentAnnotation mapped_cm = sq.addContactList(newcm);
- checkConsistencyFor(sq,mapped_cm);
+ checkConsistencyFor(sq, mapped_cm);
}
+
// Do some asserts for a sequence and a contact matrix
private void checkConsistencyFor(SequenceI sq, AlignmentAnnotation cm_aan)
{
- int col=1;
+ int col = 1;
ContactListI cl = sq.getContactListFor(cm_aan, col);
assertNotNull(cl);
- assertEquals(cl.getContactHeight(),4);
-
- // Map contacts 0 to 3 to a tiny range and check
- ContactGeometry testee = new ContactGeometry(cl,2);
- assertEquals(testee.contacts_per_pixel,2d);
+ assertEquals(cl.getContactHeight(), 4);
+
+ // Map contacts 0 to 3 to a tiny range and check
+ ContactGeometry testee = new ContactGeometry(cl, 2);
+ assertEquals(testee.contacts_per_pixel, 2d);
ContactGeometry.contactInterval lastInterval = testee.mapFor(1);
- assertEquals(lastInterval.cStart,2);
- assertEquals(lastInterval.cEnd,3);
- assertEquals(lastInterval.pStart,1);
- assertEquals(lastInterval.pEnd,1);
- ContactGeometry.contactInterval another = testee.mapFor(1,2);
- assertEquals(lastInterval,another);
+ assertEquals(lastInterval.cStart, 2);
+ assertEquals(lastInterval.cEnd, 3);
+ assertEquals(lastInterval.pStart, 1);
+ assertEquals(lastInterval.pEnd, 1);
+ ContactGeometry.contactInterval another = testee.mapFor(1, 2);
+ assertEquals(lastInterval, another);
// Also check for a big pixel range
testee = new ContactGeometry(cl, 395);
lastInterval = testee.mapFor(390, 395); // 395 is one over limit.
assertNotNull(lastInterval);
- assertEquals(lastInterval.cEnd,3);
- assertEquals(lastInterval.pEnd,394);
+ assertEquals(lastInterval.cEnd, 3);
+ assertEquals(lastInterval.pEnd, 394);
// Map contacts 0 to 3 to Pixels 0-9, 10-19, 20-29, 30-39
testee = new ContactGeometry(cl, 40);
// verify mapping from pixel to contacts
-
+
// renderer thinks base 0 for pixel coordinates
// contact coordinates are base 1
for (int p = 0; p < 40; p++)
{
- int expectC=(p / 10);
- int expectP=(expectC)*10;
+ int expectC = (p / 10);
+ int expectP = (expectC) * 10;
ContactGeometry.contactInterval ci_at = testee.mapFor(p),
ci_from = testee.mapFor(p, p);
assertNotNull(ci_at);
// mapFor and map should locate the same pixel window
- assertEquals(ci_at.cStart, expectC,"Different cStart at position "+p);
- assertEquals(ci_at.cEnd, expectC,"Different cEnd at position "+p);
- assertEquals(ci_at.pStart,expectP, "Different pStart at position "+p);
- assertEquals(ci_at.pEnd,expectP+9, "Different pEnd at position "+p);
-
- assertEquals(ci_from,ci_at, "Different contactIntervals at position "+p);
+ assertEquals(ci_at.cStart, expectC,
+ "Different cStart at position " + p);
+ assertEquals(ci_at.cEnd, expectC, "Different cEnd at position " + p);
+ assertEquals(ci_at.pStart, expectP,
+ "Different pStart at position " + p);
+ assertEquals(ci_at.pEnd, expectP + 9,
+ "Different pEnd at position " + p);
+
+ assertEquals(ci_from, ci_at,
+ "Different contactIntervals at position " + p);
// also test getRangeFor
ContactRange cr = cl.getRangeFor(ci_at.cStart, ci_at.cEnd);
- assertEquals(cr.getFrom_column(),cr.getTo_column());
- assertEquals((double) cr.getMean(),(double)Math.abs(col-cr.getFrom_column()), "Didn't resolve expected value at position "+p);
+ assertEquals(cr.getFrom_column(), cr.getTo_column());
+ assertEquals((double) cr.getMean(),
+ (double) Math.abs(col - cr.getFrom_column()),
+ "Didn't resolve expected value at position " + p);
}
-
+
ContactGeometry.contactInterval ci_at0 = testee.mapFor(0);
ContactGeometry.contactInterval ci_at9 = testee.mapFor(9);
assertNotNull(ci_at9);
-
- assertEquals(ci_at0,ci_at9);
+
+ assertEquals(ci_at0, ci_at9);
// Adjacent cell
ContactGeometry.contactInterval ci_at10 = testee.mapFor(10);
ContactGeometry.contactInterval ci_at11 = testee.mapFor(11);
assertNotNull(ci_at11);
- assertEquals(ci_at11,ci_at10,"Off-by-one in ContactGeometry mapping.");
+ assertEquals(ci_at11, ci_at10,
+ "Off-by-one in ContactGeometry mapping.");
+
+ assertNotEquals(ci_at0, ci_at10,
+ "Expected adjacent cells to be not equal.");
- assertNotEquals(ci_at0,ci_at10,"Expected adjacent cells to be not equal.");
-
// verify adjacent window is mapped
- assertEquals(ci_at11.cStart,ci_at9.cStart+1);
-
- assertEquals(ci_at9.cEnd+1,ci_at11.cStart);
- assertEquals(ci_at9.cEnd+1,ci_at11.cEnd);
-
+ assertEquals(ci_at11.cStart, ci_at9.cStart + 1);
+
+ assertEquals(ci_at9.cEnd + 1, ci_at11.cStart);
+ assertEquals(ci_at9.cEnd + 1, ci_at11.cEnd);
+
// verify interval/intersection
// column selection is base 0
ColumnSelection cs = new ColumnSelection();
cs.removeElement(2);
assertFalse(testee.intersects(testee.mapFor(21), cs, null, mask));
mask = !mask;
- } while (!mask);
-
+ } while (!mask);
+
}
}
git://source.jalview.org / jalview.git / blobdiff