/**
* Gets a list of the affected genes.
*
* @param selected is the list of selected genes.
* @return the list of affected genes.
*/
public ArrayList<ArrayList<Gene>> getAffected(ArrayList<Gene> selected) {
ArrayList<ArrayList<Gene>> results = new ArrayList<ArrayList<Gene>>();
for (ArrayList<Gene> x : causes) {
boolean conditions = true;
// check if the list of conditions are met.
int j = 0;
while (conditions == true && j < x.size()) {
boolean gene_found = false;
int i = 0;
Gene gene_x = x.get(j);
// check input list against condision
while (gene_found == false && i < selected.size()) {
if (gene_x.equals(selected.get(i))) {
gene_found = true;
}
i++;
}
if (gene_found == false) {
conditions = false;
}
j++;
}
if (conditions == true) {
results.add(x);
}
}
return results;
}
/**
* Checks if any of the conditions for the disease are met.
*
* @param selected is the list of selected genes.
* @return true if conditions met.
*/
public boolean isAffected(ArrayList<Gene> selected) {
for (ArrayList<Gene> x : causes) {
boolean conditions = true;
// check if the list of conditions are met.
int j = 0;
while (conditions == true && j < x.size()) { // goes through sub list
Gene gene_x = x.get(j); // gets current gene
boolean gene_found = false;
int i = 0;
// check input list against condition
while (gene_found == false && i < selected.size()) {
if (gene_x.equals(selected.get(i))) {
gene_found = true;
}
i++;
}
if (gene_found == false) {
conditions = false;
}
j++;
}
if (conditions == true) {
return true;
}
}
return false;
}
public int addLink(int historicalID) {
int attempts = 0;
int maxAttempts = 5;
boolean success = false;
int input;
int output;
Gene link;
do {
input = rand.nextInt(numInputs + neurons.size() - numOutputs);
if (rand.nextDouble() < GeneticAlgorithm.biasRate) {
input = numInputs - 1;
} else if (input >= numInputs) {
input += numOutputs;
}
do {
output = rand.nextInt(neurons.size()) + numInputs;
} while (output == input);
// make sure link is not backwards
if (neuronType(input) == 1 && neuronType(output) == 1) {
if (getNeuron(input).getx() > getNeuron(output).getx()) {
// if input is ahead of output, swap
int temp = input;
input = output;
output = temp;
} else if (getNeuron(input).getx() == getNeuron(output).getx()) {
// if input is same as output, move one
getNeuron(output).setx(getNeuron(output).getx() + 0.1);
}
}
link = new Gene(input, output, historicalID, false);
success = true;
for (Gene l : links) {
if (l.equals(link)) {
success = false;
}
}
attempts++;
} while (attempts < maxAttempts && !success);
if (success) {
addLink(link);
return historicalID + 1;
} else {
return historicalID;
}
}