#include "modelidentifier.h"
#include "genesorter.h"
#include "sortaction.h"
-
-typedef pair<ModelIdentifier::Model,double> modelpair;
-
-struct ScoreCmp {
- template<typename T>
- bool operator()(T s1, T s2){
- return s1.first < s2.first;
- }
-};
+#include "genealgorithms.h"
+#include "model.h"
int main(int argc, char** argv){
string ann = "default.ann";
+ Model model(0);
+ bool detectModel = true;
+ //Parse command line arguments
int opt;
- while ((opt = getopt(argc, argv, "n:h")) != -1) {
+ while ((opt = getopt(argc, argv, "m:n:h")) != -1) {
switch (opt) {
+ case 'm':
+ model = Model::modelFactory(optarg);
+ detectModel = false;
+ break;
case 'n':
ann = optarg;
break;
case 'h':
cout << "Usage: " << argv[0] << " [OPTION] [FILE]" << endl
+ << endl << " -m <model> Specifies which model to use for sorting: Whirl, X, Zipper, FatX or Cloud "
<< endl << " -n <ann> Specifies which artificial neural network to use for identification. '" << ann << "' is used by default"
<< endl << " -h Prints this help message"
<< endl << endl
}
}
+ //Open file, or stdin
istream* in;
ifstream file;
if (optind == argc || *argv[optind] == '-'){
}
in = &file;
}
- //TODO: Parse
+
+ //Parse the gene order permutation
vector<Gene> g;
copy(istream_iterator<int>(*in), istream_iterator<int>(),
- back_inserter(g));
+ back_inserter(g));
GeneOrder go(g.begin(),g.end());
- //TODO: Identify
+ //Identify the model
ModelIdentifier mi(ann);
- map<ModelIdentifier::Model,double> scores = mi.identify(go);
- priority_queue<pair<double,ModelIdentifier::Model>,vector<pair<double,ModelIdentifier::Model> >, ScoreCmp > pq;
- for (map<ModelIdentifier::Model,double>::iterator m = scores.begin();
- m != scores.end(); ++m){
- if (m->second > 0){
- pq.push(pair<double,ModelIdentifier::Model>(m->second,m->first));
- }
+ priority_queue<pair<double,Model> > pq = mi.identify(go);
+ if (detectModel){
+ model = pq.top().second;
}
while (pq.size() > 0){
- cout << "Model: " << mi.modelName(pq.top().second) << " score: " << pq.top().first << endl;
+ cout << "Model: " << pq.top().second.name() << " score: " << pq.top().first << endl;
pq.pop();
}
+ cout << "Using model: " << model.name() << endl;
+
+ cout << "Distance: " << inversionDistance(go) << endl;
+ //copy(go.begin(), go.end(), ostream_iterator<int>(cout, " "));
+ //cout << endl;
- //TODO: Chose a sorter
+ //Sort
GeneSorter so;
- //TODO: Sort
- GeneSorter::ActionList al = so.sort(go);
- //TODO: Print result
+ GeneSorter::ActionList al = so.sort(go,model);
+
+ //Print the result
+ double score = 0;
+ for (GeneSorter::ActionList::iterator sa = al.begin(); sa != al.end(); ++sa){
+ cout << "Action: " << sa->toString() << " model score: " << model.score(*sa,go) << endl;
+ score += model.score(*sa,go);
+ }
+ cout << "Avg score: " << score / al.size() << endl;
+
return EXIT_SUCCESS;
}