X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=sffmultiplecommand.h;h=ee83d727ad3b3a1e910f4b3cb633eae53938f87a;hp=ecf33b7b87b04890479ef41ce2cc09dd6048e658;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=b866e1519a60681527244036428104ad1cb90c93

diff --git a/sffmultiplecommand.h b/sffmultiplecommand.h
index ecf33b7..ee83d72 100644
--- a/sffmultiplecommand.h
+++ b/sffmultiplecommand.h
@@ -10,6 +10,11 @@
 //
 
 #include "command.hpp"
+#include "sffinfocommand.h"
+#include "seqsummarycommand.h"
+#include "trimflowscommand.h"
+#include "shhhercommand.h"
+#include "trimseqscommand.h"
 
 class SffMultipleCommand : public Command {
 	
@@ -21,8 +26,9 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "sff.multiple";			}
 	string getCommandCategory()		{ return "Sequence Processing";		}
-	string getOutputFileNameTag(string, string);
+	
 	string getHelpString();	
+    string getOutputPattern(string);	
 	string getCitation() { return "http://www.mothur.org/wiki/Sff.multiple"; }
 	string getDescription()		{ return "run multiple sff files through, sffinfo, trim.flow, shhh.flows and trim.seqs combining the results"; }
     
@@ -37,21 +43,21 @@ private:
 		linePair(int i, int j) : start(i), end(j) {}
 	};
 
-	string filename, outputDir, flowOrder;
+	string filename, outputDir, flowOrder, lookupFileName, minDelta;
 	vector<string> outputNames;
-	bool abort, trim, large, flip, qtrim, allFiles, keepforward;
-	int maxFlows, minFlows, minLength, maxLength, maxHomoP, tdiffs, bdiffs, pdiffs, sdiffs, ldiffs, numLinkers, numSpacers;
-	int numFlows, numFPrimers, numRPrimers, processors, maxIters, largeSize;
-	float signal, noise, cutoff, sigma, minDelta;
-    int qWindowSize, qWindowStep, keepFirst, removeLast, maxAmbig;
-	double qRollAverage, qThreshold, qWindowAverage, qAverage;
+	bool abort, trim, large, flip, allFiles, keepforward, append, makeGroup;
+	int maxFlows, minFlows, minLength, maxLength, maxHomoP, tdiffs, bdiffs, pdiffs, sdiffs, ldiffs;
+	int processors, maxIters, largeSize;
+	float signal, noise, cutoff, sigma;
+    int keepFirst, removeLast, maxAmbig;
     
     int readFile(vector<string>& sffFiles, vector<string>& oligosFiles);
-    int createProcesses(vector<string> sffFiles, vector<string> oligosFiles);
-    int driver(vector<string> sffFiles, vector<string> oligosFiles, int start, int end);
+    int createProcesses(vector<string> sffFiles, vector<string> oligosFiles, string, string, string);
+    int driver(vector<string> sffFiles, vector<string> oligosFiles, int start, int end, string, string, string);
+    int mergeOutputFileList(map<string, vector<string> >& files, map<string, vector<string> >& temp);
+
 
     
 };
 
-
 #endif