X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=trimflowscommand.h;h=5affc3fbdf7fedc366f7c8294c762e28681d7625;hb=a44542a3c740cf957cff72ac71742f2fe48b0eaf;hp=215b1a2f69bf717e11e2a8f25ce1761e7c0951f9;hpb=d635b39347cd81943ea50de7b813a0a5d743b0c0;p=mothur.git

diff --git a/trimflowscommand.h b/trimflowscommand.h
index 215b1a2..5affc3f 100644
--- a/trimflowscommand.h
+++ b/trimflowscommand.h
@@ -20,19 +20,22 @@ class TrimFlowsCommand : public Command {
 public:
 	TrimFlowsCommand(string);
 	TrimFlowsCommand();
-	~TrimFlowsCommand();
-	vector<string> getRequiredParameters();
-	vector<string> getValidParameters();
-	vector<string> getRequiredFiles();
-	map<string, vector<string> > getOutputFiles() { return outputTypes; }
-	int execute();
-	void help();
+	~TrimFlowsCommand() {}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "trim.flows";	}
+	string getCommandCategory()		{ return "Hidden";		}
+	string getHelpString();	
+	string getCitation() { return "no citation"; }
+	string getDescription()		{ return "trim.flows"; }
+
+	
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
 	
 private:
 	bool abort;
 
-//	GroupMap* groupMap;
-	
 	struct linePair {
 		unsigned long int start;
 		unsigned long int end;
@@ -41,12 +44,13 @@ private:
 	int comboStarts;
 	vector<int> processIDS;   //processid
 	vector<linePair*> lines;
-	vector<linePair*> qLines;
-	map<string, vector<string> > outputTypes;
+
+	vector<unsigned long int> getFlowFileBreaks();
+	int createProcessesCreateTrim(string, string, string, string, vector<vector<string> >); 
+	int driverCreateTrim(string, string, string, string, vector<vector<string> >, linePair*);
+
 	vector<string> outputNames;
 	set<string> filesToRemove;
-
-	
 	
 	void getOligos(vector<vector<string> >&);		//a rewrite of what is in trimseqscommand.h
 	int stripBarcode(Sequence&, int&);				//largely redundant with trimseqscommand.h
@@ -54,15 +58,15 @@ private:
 	bool stripReverse(Sequence&);					//largely redundant with trimseqscommand.h
 	bool compareDNASeq(string, string);				//largely redundant with trimseqscommand.h
 	int countDiffs(string, string);					//largely redundant with trimseqscommand.h
-
 	
 	bool allFiles;
-//	int processors;
+	int processors;
 	int numFPrimers, numRPrimers;
-	int totalFlows, minFlows, minLength, maxLength, maxHomoP, tdiffs, bdiffs, pdiffs;
+	int maxFlows, minFlows, minLength, maxLength, maxHomoP, tdiffs, bdiffs, pdiffs;
+	int numFlows;
 	float signal, noise;
 	bool fasta;
-	
+	string flowOrder;	
 	
 	string flowFileName, oligoFileName, outputDir;
 
@@ -77,12 +81,6 @@ private:
 	map<string, int> combos;			//needed here?
 	map<string, int> groupToIndex;		//needed here?
 	
-	
-	int driverCreateTrim(string, string, string, string);
-	
-//	int createProcessesCreateTrim(string, string, string, string, string, string, string, vector<string>, vector<string>){};
-	int setLines(string, string, vector<unsigned long int>&, vector<unsigned long int>&){};
-	
 };