X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=parsimonycommand.h;h=9e756b884fb087f95ca0d43c23027c8caaa33b3f;hb=c53ef46b40b97c00e32bfd8c3924ce8c51b5cd7b;hp=6fa1914f31e320517ff89389a34fc3e5a1cd6dc6;hpb=aa9238c0a9e6e7aa0ed8b8b606b08ad4fd7dcfe3;p=mothur.git

diff --git a/parsimonycommand.h b/parsimonycommand.h
index 6fa1914..9e756b8 100644
--- a/parsimonycommand.h
+++ b/parsimonycommand.h
@@ -23,7 +23,12 @@ 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();
 
@@ -39,7 +44,7 @@ private:
 	Parsimony* pars;
 	vector<string> groupComb; // AB. AC, BC...
 	string sumFile, randomtree, allGroups, outputDir;
-	int iters, numGroups, numComp, counter;
+	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.
@@ -57,6 +62,7 @@ private:
 	bool abort;
 	string groups, itersString;
 	vector<string> Groups, outputNames; //holds groups to be used
+	map<string, vector<string> > outputTypes;
 
 	void printParsimonyFile();  
 	int printUSummaryFile();