/**
* Prints an entire subpopulation in a form readable by humans but also parseable by the computer
* using readSubpopulation(EvolutionState, LineNumberReader).
*/
public void printSubpopulation(final EvolutionState state, final PrintWriter writer) {
writer.println(NUM_INDIVIDUALS_PREAMBLE + Code.encode(individuals.length));
for (int i = 0; i < individuals.length; i++) {
writer.println(INDIVIDUAL_INDEX_PREAMBLE + Code.encode(i));
individuals[i].printIndividual(state, writer);
}
}
/**
* Prints an entire subpopulation in a form readable by humans but also parseable by the computer
* using readSubpopulation(EvolutionState, LineNumberReader) with a verbosity of
* Output.V_NO_GENERAL.
*/
public void printSubpopulation(final EvolutionState state, final int log) {
state.output.println(NUM_INDIVIDUALS_PREAMBLE + Code.encode(individuals.length), log);
for (int i = 0; i < individuals.length; i++) {
state.output.println(INDIVIDUAL_INDEX_PREAMBLE + Code.encode(i), log);
individuals[i].printIndividual(state, log);
}
}
protected void parseGenotype(final EvolutionState state, final LineNumberReader reader)
throws IOException {
// read in the next line. The first item is the number of genes
String s = reader.readLine();
DecodeReturn d = new DecodeReturn(s);
Code.decode(d);
if (d.type != DecodeReturn.T_INTEGER) // uh oh
state.output.fatal(
"Individual with genome:\n"
+ s
+ "\n... does not have an integer at the beginning indicating the genome count.");
int lll = (int) (d.l);
genome = new boolean[lll];
// read in the genes
for (int i = 0; i < genome.length; i++) {
Code.decode(d);
genome[i] = (boolean) (d.l != 0);
}
}
/**
* Reads a subpopulation from the format generated by printSubpopulation(....). If the number of
* individuals is not identical, the individuals array will be deleted and replaced with a new
* array, and a warning will be generated as individuals will have to be created using
* newIndividual(...) rather than readIndividual(...).
*/
public void readSubpopulation(final EvolutionState state, final LineNumberReader reader)
throws IOException {
// read in number of individuals and check to see if this appears to be a valid subpopulation
int numIndividuals = Code.readIntegerWithPreamble(NUM_INDIVIDUALS_PREAMBLE, state, reader);
// read in individuals
if (numIndividuals != individuals.length) {
state.output.warnOnce(
"On reading subpopulation from text stream, the subpopulation size didn't match.\n"
+ "Had to resize and use newIndividual() instead of readIndividual().");
individuals = new Individual[numIndividuals];
for (int i = 0; i < individuals.length; i++) {
int j = Code.readIntegerWithPreamble(INDIVIDUAL_INDEX_PREAMBLE, state, reader);
// sanity check
if (j != i)
state.output.warnOnce(
"On reading subpopulation from text stream, some individual indexes in the subpopulation did not match.");
individuals[i] = species.newIndividual(state, reader);
}
} else
for (int i = 0; i < individuals.length; i++) {
int j = Code.readIntegerWithPreamble(INDIVIDUAL_INDEX_PREAMBLE, state, reader);
// sanity check
if (j != i)
state.output.warnOnce(
"On reading subpopulation from text stream, some individual indexes in the subpopulation did not match.");
if (individuals[i] != null) individuals[i].readIndividual(state, reader);
else {
state.output.warnOnce(
"On reading subpopulation from text stream, some of the preexisting subpopulation's slots were null.\n"
+ "Had to use newIndividual() instead of readIndividual(). If you're starting an evolutionary run by reading an\n"
+ "existing population from a file, this is expected -- ignore this message.");
individuals[i] = species.newIndividual(state, reader);
}
}
}
public String genotypeToString() {
StringBuilder s = new StringBuilder();
s.append(Code.encode(genome.length));
for (int i = 0; i < genome.length; i++) s.append(Code.encode(genome[i]));
return s.toString();
}