X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sffmultiplecommand.h;h=1a492a82155fe0a7314b8c2ec54a9a4b37017909;hb=250e3b11b1c9c1e1ad458ab6c7e71ac2e67e11d9;hp=ae881aa7fcacb2aab09224d204f301db0531fa35;hpb=dc383fb61b6d165a8d36e6108df8bc7129243ae6;p=mothur.git

diff --git a/sffmultiplecommand.h b/sffmultiplecommand.h
index ae881aa..1a492a8 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"; }
     
@@ -30,16 +36,29 @@ 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 inputDir;
+	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