seqs.add(new Sequence("seq3", "V-IW-"));
seqs.add(new Sequence("seq4", "VGLH-"));
seqs.add(new Sequence("seq5", "VGLH-"));
-
+
/*
* threshold 50% means a residue has to occur 3 or more times
* in a column to be counted for conservation
// but it is treated as percentage threshold in calculate() ?
Conservation cons = new Conservation("", 50, seqs, 0, 4);
cons.calculate();
-
+
/*
* column 0: all V (hydrophobic/aliphatic/small)
*/
assertEquals(colCons.get("polar").intValue(), 0);
assertEquals(colCons.get("positive").intValue(), 0);
assertEquals(colCons.get("aromatic").intValue(), 0);
-
+
/*
* column 1: all G (hydrophobic/small/tiny)
* gaps are ignored as not above threshold
assertEquals(colCons.get("polar").intValue(), 0);
assertEquals(colCons.get("positive").intValue(), 0);
assertEquals(colCons.get("aromatic").intValue(), 0);
-
+
/*
* column 2: I/L (aliphatic/hydrophobic), all others negatively conserved
*/
assertEquals(colCons.get("polar").intValue(), 0);
assertEquals(colCons.get("positive").intValue(), 0);
assertEquals(colCons.get("aromatic").intValue(), 0);
-
+
/*
* column 3: nothing above threshold
*/
colCons = cons.total[3];
assertTrue(colCons.isEmpty());
-
+
/*
* column 4: all gaps - counted as having all properties
*/
* verify tooltips; conserved properties are sorted alphabetically within
* positive followed by negative
*/
- assertEquals(
- cons.getTooltip(0),
+ assertEquals(cons.getTooltip(0),
"aliphatic hydrophobic small !aromatic !charged !negative !polar !positive !proline !tiny");
- assertEquals(
- cons.getTooltip(1),
+ assertEquals(cons.getTooltip(1),
"hydrophobic small tiny !aliphatic !aromatic !charged !negative !polar !positive !proline");
- assertEquals(
- cons.getTooltip(2),
+ assertEquals(cons.getTooltip(2),
"aliphatic hydrophobic !aromatic !charged !negative !polar !positive !proline !small !tiny");
- assertEquals(cons.getTooltip(3), "hydrophobic !negative !proline !tiny");
+ assertEquals(cons.getTooltip(3),
+ "hydrophobic !negative !proline !tiny");
assertEquals(cons.getTooltip(4), "hydrophobic");
assertEquals(cons.getTooltip(5), "");
assertEquals(cons.getTooltip(6), "");