/**
* This method test the 'return copy of enzyme' functionality when requesting an enzyme instance.
*/
public void testCopyOfEnzyme() {
final String inputFile = TestCaseLM.getFullFilePath("enzymes_test.txt").replace("%20", " ");
// Try it for a regular Enzyme.
try {
MascotEnzymeReader mer = new MascotEnzymeReader(inputFile);
Enzyme mod = mer.getEnzyme(mer.getEnzymeNames()[0]);
int mc = mod.getMiscleavages();
String cleave = new String(mod.getCleavage());
mod.setMiscleavages(mc + 1);
mod.setCleavage(cleave + "H");
// Make sure 'mod' has changed.
Assert.assertEquals(mc + 1, mod.getMiscleavages());
Assert.assertEquals(cleave + "H", new String(mod.getCleavage()));
// Now get another copy of the same enzyme, and see if it has retained the original values.
Enzyme original = mer.getEnzyme(mer.getEnzymeNames()[0]);
Assert.assertEquals(mc, original.getMiscleavages());
Assert.assertEquals(cleave, new String(original.getCleavage()));
} catch (IOException ioe) {
fail(
"IOException while testing whether a received Enzyme is in fact a copy: '"
+ ioe.getMessage()
+ "'.");
}
// Try it for a DualEnzyme.
try {
MascotEnzymeReader mer = new MascotEnzymeReader(inputFile);
DualEnzyme mod = (DualEnzyme) mer.getEnzyme("dualTrypCathep");
int mc = mod.getMiscleavages();
String ntermCleave = new String(mod.getCleavage(DualEnzyme.NTERMINAL));
String ctermCleave = new String(mod.getCleavage(DualEnzyme.CTERMINAL));
mod.setMiscleavages(mc + 1);
mod.setCleavage(ntermCleave + "H", DualEnzyme.NTERMINAL);
mod.setCleavage(ctermCleave + "W", DualEnzyme.CTERMINAL);
// Make sure 'mod' has changed.
Assert.assertEquals(mc + 1, mod.getMiscleavages());
Assert.assertEquals(ntermCleave + "H", new String(mod.getCleavage(DualEnzyme.NTERMINAL)));
Assert.assertEquals(ctermCleave + "W", new String(mod.getCleavage(DualEnzyme.CTERMINAL)));
// Now get another copy of the same enzyme, and see if it has retained the original values.
DualEnzyme original = (DualEnzyme) mer.getEnzyme("dualTrypCathep");
Assert.assertEquals(mc, original.getMiscleavages());
Assert.assertEquals(ntermCleave, new String(original.getCleavage(DualEnzyme.NTERMINAL)));
Assert.assertEquals(ctermCleave, new String(original.getCleavage(DualEnzyme.CTERMINAL)));
} catch (IOException ioe) {
fail(
"IOException while testing whether a received Enzyme is in fact a copy: '"
+ ioe.getMessage()
+ "'.");
}
// Try it for a RegExEnzyme.
try {
MascotEnzymeReader mer = new MascotEnzymeReader(inputFile);
RegExEnzyme mod = (RegExEnzyme) mer.getEnzyme("regexTrypCathep2");
int mc = mod.getMiscleavages();
String cleave = new String(mod.getCleavage());
mod.setMiscleavages(mc + 1);
mod.setCleavage(cleave + "H");
// Make sure 'mod' has changed.
Assert.assertEquals(mc + 1, mod.getMiscleavages());
Assert.assertEquals(cleave + "H", new String(mod.getCleavage()));
// Now get another copy of the same enzyme, and see if it has retained the original values.
Enzyme original = mer.getEnzyme("regexTrypCathep2");
Assert.assertEquals(mc, original.getMiscleavages());
Assert.assertEquals(cleave, new String(original.getCleavage()));
} catch (IOException ioe) {
fail(
"IOException while testing whether a received Enzyme is in fact a copy: '"
+ ioe.getMessage()
+ "'.");
}
}
