added oligos class. added check orient parameter to trim.flows, sffinfo, fastq.info...

[mothur.git] / trimflowscommand.h

diff --git a/trimflowscommand.h b/trimflowscommand.h
index f5493eb7517db72c20048da57080a587ae675f7e..58d3ed096eac4e9b3b733adaa31d10b37a068d87 100644 (file)
--- 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