seqs.add(new Sequence("seq3", "V-IW-"));
seqs.add(new Sequence("seq4", "VGLH-"));
seqs.add(new Sequence("seq5", "VGLH-"));
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
/*
* 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();
// but it is treated as percentage threshold in calculate() ?
Conservation cons = new Conservation("", 50, seqs, 0, 4);
cons.calculate();
assertEquals(colCons.get("polar").intValue(), 0);
assertEquals(colCons.get("positive").intValue(), 0);
assertEquals(colCons.get("aromatic").intValue(), 0);
assertEquals(colCons.get("polar").intValue(), 0);
assertEquals(colCons.get("positive").intValue(), 0);
assertEquals(colCons.get("aromatic").intValue(), 0);
assertEquals(colCons.get("polar").intValue(), 0);
assertEquals(colCons.get("positive").intValue(), 0);
assertEquals(colCons.get("aromatic").intValue(), 0);
assertEquals(colCons.get("polar").intValue(), 0);
assertEquals(colCons.get("positive").intValue(), 0);
assertEquals(colCons.get("aromatic").intValue(), 0);
assertEquals(colCons.get("polar").intValue(), 0);
assertEquals(colCons.get("positive").intValue(), 0);
assertEquals(colCons.get("aromatic").intValue(), 0);
assertEquals(colCons.get("polar").intValue(), 0);
assertEquals(colCons.get("positive").intValue(), 0);
assertEquals(colCons.get("aromatic").intValue(), 0);
* verify tooltips; conserved properties are sorted alphabetically within
* positive followed by negative
*/
* verify tooltips; conserved properties are sorted alphabetically within
* positive followed by negative
*/
assertEquals(cons.getTooltip(4), "hydrophobic");
assertEquals(cons.getTooltip(5), "");
assertEquals(cons.getTooltip(6), "");
assertEquals(cons.getTooltip(4), "hydrophobic");
assertEquals(cons.getTooltip(5), "");
assertEquals(cons.getTooltip(6), "");