#include "command.hpp"
#include "parsimony.h"
#include "treemap.h"
+#include "progress.hpp"
+#include "sharedutilities.h"
+#include "fileoutput.h"
-using namespace std;
class GlobalData;
class ParsimonyCommand : public Command {
+
+public:
+ ParsimonyCommand(string);
+ ParsimonyCommand();
+ ~ParsimonyCommand() { if (abort == false) { delete pars; delete util; delete output; } }
+ vector<string> getRequiredParameters();
+ vector<string> getValidParameters();
+ vector<string> getRequiredFiles();
+ map<string, vector<string> > getOutputFiles() { return outputTypes; }
+ int execute();
+ void help();
+
+private:
+ GlobalData* globaldata;
+ SharedUtil* util;
+ FileOutput* output;
+ vector<Tree*> T; //user trees
+ Tree* randT; //random tree
+ Tree* copyUserTree;
+ TreeMap* tmap;
+ TreeMap* savetmap;
+ Parsimony* pars;
+ vector<string> groupComb; // AB. AC, BC...
+ string sumFile, randomtree, allGroups, outputDir;
+ int iters, numGroups, numComp, counter, processors;
+ vector<int> numEachGroup; //vector containing the number of sequences in each group the users wants for random distrib.
+ vector< vector<float> > userTreeScores; //scores for users trees for each comb.
+ vector< vector<float> > UScoreSig; //tree score signifigance when compared to random trees - percentage of random trees with that score or lower.
+ EstOutput userData; //pscore info for user tree
+ EstOutput randomData; //pscore info for random trees
+ map<int, double> validScores; //map contains scores from both user and random
+ vector< map<int, double> > rscoreFreq; //map <pscore, number of random trees with that score.> -vector entry for each combination.
+ vector< map<int, double> > uscoreFreq; //map <pscore, number of user trees with that score.> -vector entry for each combination.
+ vector< map<int, double> > rCumul; //map <pscore, cumulative percentage of number of random trees with that score or lower.> -vector entry for each combination.
+ vector< map<int, double> > uCumul; //map <pscore, cumulative percentage of number of user trees with that score or lower .> -vector entry for each combination.
+
+ ofstream outSum;
- public:
- ParsimonyCommand();
- ~ParsimonyCommand() { delete pars; }
- int execute();
+
+ bool abort;
+ string groups, itersString;
+ vector<string> Groups, outputNames; //holds groups to be used
+ map<string, vector<string> > outputTypes;
+
+ void printParsimonyFile();
+ int printUSummaryFile();
+ void getUserInput();
- private:
- GlobalData* globaldata;
- vector<Tree*> T; //user trees
- Tree* randT; //random tree
- Tree* copyUserTree;
- TreeMap* tmap;
- TreeMap* savetmap;
- Parsimony* pars;
- vector<string> groupComb; // AB. AC, BC...
- string parsFile, sumFile, randomtree;
- int iters, numGroups, numComp;
- vector<int> numEachGroup; //vector containing the number of sequences in each group the users wants for random distrib.
- vector< vector<float> > userTreeScores; //scores for users trees for each comb.
- vector< vector<float> > UScoreSig; //tree score signifigance when compared to random trees - percentage of random trees with that score or lower.
- EstOutput userData; //pscore info for user tree
- EstOutput randomData; //pscore info for random trees
- vector< map<int, double> > validScores; //map contains scores from both user and random
- vector< map<int, double> > rscoreFreq; //map <pscore, number of random trees with that score.> -vector entry for each combination.
- vector< map<int, double> > uscoreFreq; //map <pscore, number of user trees with that score.> -vector entry for each combination.
- vector< map<int, double> > rCumul; //map <pscore, cumulative percentage of number of random trees with that score or lower.> -vector entry for each combination.
- vector< map<int, double> > uCumul; //map <pscore, cumulative percentage of number of user trees with that score or lower .> -vector entry for each combination.
- map<int, double>::iterator it;
- map<int, double>::iterator it2;
-
- ofstream out, outSum;
-
- void printParsimonyFile();
- void printUSummaryFile();
- void getUserInput();
- void setGroups();
-
};