X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=trimflowscommand.h;h=0514a53edc62362d3b95118d5d5e501fd2ef0b2e;hb=0d4b21e5ccc56276b0c18d17d8e75d94ce1df4e7;hp=99103ba25af92565be2e0879c0904603aea5990c;hpb=902e0fcab76e75009ac43d3f4537e08182628d6f;p=mothur.git

diff --git a/trimflowscommand.h b/trimflowscommand.h
index 99103ba..0514a53 100644
--- a/trimflowscommand.h
+++ b/trimflowscommand.h
@@ -20,13 +20,15 @@ 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();	
+	
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
 	
 private:
 	bool abort;
@@ -44,13 +46,9 @@ private:
 	int createProcessesCreateTrim(string, string, string, string, vector<vector<string> >); 
 	int driverCreateTrim(string, string, string, string, vector<vector<string> >, linePair*);
 
-	
-	map<string, vector<string> > outputTypes;
 	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
 	int stripForward(Sequence&, int&);				//largely redundant with trimseqscommand.h
@@ -65,7 +63,7 @@ private:
 	int numFlows;
 	float signal, noise;
 	bool fasta;
-	
+	string flowOrder;	
 	
 	string flowFileName, oligoFileName, outputDir;