X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sffmultiplecommand.h;h=4ab2c972557500c059b48ef38f712483f5731231;hb=cc19310422f125d6628980bd1148e1e816792382;hp=ae881aa7fcacb2aab09224d204f301db0531fa35;hpb=dc383fb61b6d165a8d36e6108df8bc7129243ae6;p=mothur.git

diff --git a/sffmultiplecommand.h b/sffmultiplecommand.h
index ae881aa..4ab2c97 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 {
 	
@@ -30,16 +35,28 @@ public:
 	void help() { m->mothurOut(getHelpString()); }	
 	
 private:
-	string filename, outputDir, flowOrder;
+    
+    struct linePair {
+		int start;
+		int end;
+		linePair(int i, int j) : start(i), end(j) {}
+	};
+
+	string filename, outputDir, flowOrder, lookupFileName, minDelta;
 	vector<string> outputNames;
-	bool abort, trim;
-	int maxFlows, minFlows, minLength, maxLength, maxHomoP, tdiffs, bdiffs, pdiffs, sdiffs, ldiffs, numLinkers, numSpacers;
-	int numFlows, numFPrimers, numRPrimers, processors;
-	float signal, noise;
+	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, 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