X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=trimflowscommand.h;h=58d3ed096eac4e9b3b733adaa31d10b37a068d87;hp=f5493eb7517db72c20048da57080a587ae675f7e;hb=fefd5ee1517abd3bc38b469cb2dffc85a1571c7e;hpb=aca78ed4a47dff8672ea8fd93cef0dfbaf0f7495

diff --git a/trimflowscommand.h b/trimflowscommand.h
index f5493eb..58d3ed0 100644
--- a/trimflowscommand.h
+++ b/trimflowscommand.h
@@ -16,6 +16,7 @@
 #include "flowdata.h"
 #include "groupmap.h"
 #include "trimoligos.h"
+#include "oligos.h"
 
 class TrimFlowsCommand : public Command {
 public:
@@ -47,43 +48,29 @@ private:
 	int comboStarts;
 	vector<int> processIDS;   //processid
 	vector<linePair*> lines;
-
-	vector<unsigned long long> getFlowFileBreaks();
-	int createProcessesCreateTrim(string, string, string, string, vector<vector<string> >); 
-	int driverCreateTrim(string, string, string, string, vector<vector<string> >, linePair*);
-    string reverseOligo(string);
-    
-	vector<string> outputNames;
+    vector<string> outputNames;
 	set<string> filesToRemove;
-	
-	void getOligos(vector<vector<string> >&);		//a rewrite of what is in trimseqscommand.h
-	
-	bool allFiles;
+    bool allFiles;
 	int processors;
-	int numFPrimers, numRPrimers;
+	int numFPrimers, numRPrimers, numBarcodes;
 	int maxFlows, minFlows, minLength, maxLength, maxHomoP, tdiffs, bdiffs, pdiffs, sdiffs, ldiffs, numLinkers, numSpacers;
 	int numFlows;
 	float signal, noise;
-	bool fasta;
-	string flowOrder;	
-	
-	string flowFileName, oligoFileName, outputDir;
+	bool fasta, pairedOligos, reorient;
+	string flowOrder, flowFileName, oligoFileName, outputDir;
+    Oligos oligos;
 
-	map<string, int> barcodes;
-	map<string, int> primers;
-	vector<string> revPrimer;
-    vector<string> linker;
-    vector<string> spacer;
-
-	vector<string> primerNameVector;	//needed here?
-	vector<string> barcodeNameVector;	//needed here?
 
-	map<string, int> combos;			//needed here?
-	map<string, int> groupToIndex;		//needed here?
+	vector<unsigned long long> getFlowFileBreaks();
+	int createProcessesCreateTrim(string, string, string, string, vector<vector<string> >); 
+	int driverCreateTrim(string, string, string, string, vector<vector<string> >, linePair*);
+	int getOligos(vector<vector<string> >&);		//a rewrite of what is in trimseqscommand.h
+	
+	
 	
 };
 
-/**************************************************************************************************/
+/**************************************************************************************************
 //custom data structure for threads to use.
 // This is passed by void pointer so it can be any data type
 // that can be passed using a single void pointer (LPVOID).
@@ -133,7 +120,7 @@ struct trimFlowData {
 	}
 };
 
-/**************************************************************************************************/
+/**************************************************************************************************
 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 #else
 static DWORD WINAPI MyTrimFlowThreadFunction(LPVOID lpParam){ 
@@ -260,6 +247,6 @@ static DWORD WINAPI MyTrimFlowThreadFunction(LPVOID lpParam){
 	}
 } 
 #endif
-
+*/
 
 #endif