public TestAnneal(
double targetTemp,
Oligo oligo,
int amplicon,
double shiftRange,
int lenMin,
int lenMax,
boolean forward,
boolean sense,
boolean modified)
throws IOException {
super(
mage.Tools.FASTA.readFFN(Constants.blastdirectory, "genome.ffn"),
targetTemp,
oligo,
amplicon,
shiftRange,
lenMin,
lenMax,
forward,
sense,
modified);
// creationTracker = new int[matrix.length][matrix[0].length];
epochTracker = new Integer[matrix.length][matrix[0].length];
mcsTracker = new Integer[matrix.length][matrix[0].length];
scoreTracker = new Double[matrix.length][matrix[0].length];
}
public static void main(String[] args) throws Exception {
String gen = mage.Tools.FASTA.readFFN(Constants.blastdirectory, "genome.ffn");
Oligo o = Oligo.InsertionFactory(gen, "TAG", 3090358, 2, true, "endA");
// Oligo o = Oligo.MismatchFactory(genome, "A", left_position, right_position, replichore, true,
// genome)
// test Move
if (false) {
TestAnneal ta = new TestAnneal(60.0, o, 400, .05, 16, 30, false, true, false);
System.out.println("TestMove in Two dimensions, T = " + ta.initialT);
ta.testGetMove(ta.initialT);
float cooledT = ta.cool(ta.initialT);
cooledT = ta.cool(cooledT);
System.out.println("Partially cooled, T = " + cooledT);
ta.testGetMove(cooledT);
System.out.println("Fully Cooled, T = " + ta.finalT);
ta.testGetMove(ta.finalT);
ta = new TestAnneal(60.0, o, 400, 0, 16, 30, false, true, false);
System.out.println("TestMove, No shifting");
ta.testGetMove(ta.initialT); // no shifting allowed
ta = new TestAnneal(60.0, o, 400, .05, 20, 20, false, true, false);
System.out.println("TestMove, Fixed length");
ta.testGetMove(ta.initialT); // fixed length
}
// test Cool
if (false) {
// Slowdown
Anneal.setCoolingType(CoolingType.SLOWDOWN);
TestAnneal ta = new TestAnneal(60.0, o, 400, .05, 16, 30, false, true, false);
ta.testCool();
// Linear
Anneal.setCoolingType(CoolingType.LINEAR);
ta = new TestAnneal(60.0, o, 400, .05, 16, 30, false, true, false);
ta.testCool();
}
// test getOptimizedPrimer
if (false) {
TestAnneal ta = new TestAnneal(60.0, o, 400, .05, 10, 30, false, true, false);
Anneal.random.setSeed(9999l);
ta.testOptimize();
ta = new TestAnneal(60.0, o, 400, .05, 10, 30, false, true, false);
Anneal.random.setSeed(8888l);
ta.testOptimize();
ta = new TestAnneal(60.0, o, 400, .05, 10, 30, false, true, false);
Anneal.random.setSeed(7777l);
ta.testOptimize();
}
// test accept
if (false) {
TestAnneal ta = new TestAnneal(60.0, o, 400, .05, 10, 30, false, true, false);
System.out.println("Test Accept at initial temp");
Anneal.random.setSeed(999l);
ta.testAccept(ta.initialT);
ta.testAccept2(ta.initialT);
System.out.println("Test Accept at final temp");
Anneal.random.setSeed(888l);
// ta.testAccept(ta.finalT);
}
// test initial temp
if (false) {
TestAnneal ta = new TestAnneal(60.0, o, 400, .05, 10, 30, false, true, false);
ta.testInitialTemp();
ta.testInitialTemp();
ta.testInitialTemp();
}
// test a particular problem primer
if (true) {
String directory = Constants.blastdirectory + "nat/";
String genome = FASTA.readFFN(directory, "genome.FASTA");
Oligo.Directory = directory;
Oligo.Genome = "genome.FASTA";
o = Oligo.MismatchFactory(genome, "A", 4572079, 4572079, 1, true, "avrII07");
TestAnneal ta = new TestAnneal(60.0, o, 500, .05, 10, 30, false, true, true);
ta.testOptimize();
}
}