X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=pcrseqscommand.h;h=9fc40419411ff2535f01eb150699b30227225a3b;hb=98ca1e6ab30ab49e4a78bb6012d34c9c2db22702;hp=03092bca2a70da8428e77f5599e6ab200c2b8960;hpb=91a27e0483827c06c21c4fe89558923bbfe86573;p=mothur.git

diff --git a/pcrseqscommand.h b/pcrseqscommand.h
index 03092bc..9fc4041 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);	
@@ -315,11 +319,11 @@ static DWORD WINAPI MyPcrThreadFunction(LPVOID lpParam){
                         pDataArray->m->mothurOut("[ERROR]: seqs are not the same length as ecoli seq. When using ecoli option your sequences must be aligned and the same length as the ecoli sequence.\n"); pDataArray->m->control_pressed = true; break; 
                     }else {
                         if (pDataArray->keepdots)   { 
-                            currSeq.filterToPos(start); 
-                            currSeq.filterFromPos(end);
+                            currSeq.filterToPos(pDataArray->start); 
+                            currSeq.filterFromPos(pDataArray->end);
                         }else {
-                            string seqString = currSeq.getAligned().substr(0, end);
-                            seqString = seqString.substr(start);
+                            string seqString = currSeq.getAligned().substr(0, pDataArray->end);
+                            seqString = seqString.substr(pDataArray->start);
                             currSeq.setAligned(seqString); 
                         }
                     }
@@ -331,17 +335,17 @@ static DWORD WINAPI MyPcrThreadFunction(LPVOID lpParam){
                         if (pDataArray->end != -1) {
                             if (pDataArray->end > currSeq.getAligned().length()) {  pDataArray->m->mothurOut("[ERROR]: end is longer than your sequence length, aborting.\n"); pDataArray->m->control_pressed = true; break; }
                             else {
-                                if (pDataArray->keepdots)   { currSeq.filterFromPos(end); }
+                                if (pDataArray->keepdots)   { currSeq.filterFromPos(pDataArray->end); }
                                 else {
-                                    string seqString = currSeq.getAligned().substr(0, end);
+                                    string seqString = currSeq.getAligned().substr(0, pDataArray->end);
                                     currSeq.setAligned(seqString); 
                                 }
                             }
                         }
                         if (pDataArray->start != -1) { 
-                            if (pDataArray->keepdots)   {  currSeq.filterToPos(start);  }
+                            if (pDataArray->keepdots)   {  currSeq.filterToPos(pDataArray->start);  }
                             else {
-                                string seqString = currSeq.getAligned().substr(start);
+                                string seqString = currSeq.getAligned().substr(pDataArray->start);
                                 currSeq.setAligned(seqString); 
                             }
                         }