X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=pcrseqscommand.h;h=c6f7ff9c7f6670073a7080496f80eac1cdfb2a72;hb=1f0e54b53b714781f3f2fee7d01177fade98a625;hp=45ce6f3f153e6020f00c859b1928cc1d74ea2a55;hpb=bb8d942036365d2a66330944269f17841ed2388a;p=mothur.git

diff --git a/pcrseqscommand.h b/pcrseqscommand.h
index 45ce6f3..c6f7ff9 100644
--- a/pcrseqscommand.h
+++ b/pcrseqscommand.h
@@ -15,6 +15,7 @@
 #include "trimoligos.h"
 #include "alignment.hpp"
 #include "needlemanoverlap.hpp"
+#include "counttable.h"
 
 class PcrSeqsCommand : public Command {
 public:
@@ -25,7 +26,9 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "pcr.seqs";	}
 	string getCommandCategory()		{ return "Sequence Processing";		}
+	
 	string getHelpString();	
+    string getOutputPattern(string);	
 	string getCitation() { return "http://www.mothur.org/wiki/Pcr.seqs"; }
 	string getDescription()		{ return "pcr.seqs"; }
     
@@ -44,8 +47,8 @@ private:
     vector<linePair> lines;
 	bool getOligos(vector<vector<string> >&, vector<vector<string> >&, vector<vector<string> >&);
     bool abort, keepprimer, keepdots;
-	string fastafile, oligosfile, taxfile, groupfile, namefile, ecolifile, outputDir, nomatch;
-	int start, end, pdiffs, processors, length;
+	string fastafile, oligosfile, taxfile, groupfile, namefile, countfile, ecolifile, outputDir, nomatch;
+	int start, end, processors, length;
 	
     vector<string> revPrimer, outputNames;
 	vector<string> primers;
@@ -54,6 +57,7 @@ private:
     int readName(set<string>&);
     int readGroup(set<string>);
     int readTax(set<string>);
+    int readCount(set<string>);
     bool readOligos();
     bool readEcoli();
 	int driverPcr(string, string, string, set<string>&, linePair);	
@@ -128,9 +132,9 @@ static DWORD WINAPI MyPcrThreadFunction(LPVOID lpParam){
 		}
         
         set<int> lengths;
-		pDataArray->count = pDataArray->fend;
+		
 		for(int i = 0; i < pDataArray->fend; i++){ //end is the number of sequences to process
-            
+            pDataArray->count++;
 			if (pDataArray->m->control_pressed) {  break; }
 			
 			Sequence currSeq(inFASTA); pDataArray->m->gobble(inFASTA);