added sff.multiple command. fixed issue with windows paralellization in chimera...

[mothur.git] / sffmultiplecommand.h

diff --git a/sffmultiplecommand.h b/sffmultiplecommand.h
index ecf33b7b87b04890479ef41ce2cc09dd6048e658..4ab2c972557500c059b48ef38f712483f5731231 100644 (file)
--- 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 {
        
@@ -37,21 +42,21 @@ 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