X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=seqerrorcommand.h;h=aac17b6979910ebc733be840eb37ec720ecc1105;hp=590c554b25ec761a42ecc9593d3b6376b725f15e;hb=050a3ff02473a3d4c0980964e1a9ebe52e55d6b8;hpb=65b6a38d00b3a72021611211e7c25392022c69ed

diff --git a/seqerrorcommand.h b/seqerrorcommand.h
index 590c554..aac17b6 100644
--- a/seqerrorcommand.h
+++ b/seqerrorcommand.h
@@ -10,47 +10,25 @@
  *
  */
 
-#include "mothur.h"
 #include "command.hpp"
 #include "sequence.hpp"
 #include "referencedb.h"
+#include "counttable.h"
 
-struct Compare {
-	int AA, AT, AG, AC,	TA, TT, TG, TC,	GA, GT, GG, GC,	CA, CT, CG, CC,	NA, NT, NG, NC, Ai, Ti, Gi, Ci, Ni, dA, dT, dG, dC;
-	string refName, queryName, sequence;
-	double errorRate;
-	int weight, matches, mismatches, total;
-	
-	Compare(){
-		AA=0; AT=0; AG=0; AC=0;
-		TA=0; TT=0; TG=0; TC=0;
-		GA=0; GT=0; GG=0; GC=0;
-		CA=0; CT=0; CG=0; CC=0;
-		NA=0; NT=0; NG=0; NC=0;
-		Ai=0; Ti=0; Gi=0; Ci=0; Ni=0;
-		dA=0; dT=0; dG=0; dC=0;
-		refName = "";
-		queryName = "";
-		weight = 1;
-		matches = 0;
-		mismatches = 0;
-		total = 0;
-		errorRate = 1.0000;
-		sequence = "";
-	}
-};
 
 class SeqErrorCommand : public Command {
 public:
 	SeqErrorCommand(string);
 	SeqErrorCommand();
-	~SeqErrorCommand() {}
+	~SeqErrorCommand(){}
 	
 	vector<string> setParameters();
 	string getCommandName()			{ return "seq.error";				}
 	string getCommandCategory()		{ return "Sequence Processing";		}
+	
 	string getHelpString();	
-	string getCitation() { return "http://www.mothur.org/wiki/Seq.error"; }
+    string getOutputPattern(string);	
+	string getCitation() { return "Schloss PD, Gevers D, Westcott SL (2011).  Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies.  PLoS ONE.  6:e27310.\nhttp://www.mothur.org/wiki/Seq.error"; }
 	string getDescription()		{ return "seq.error"; }
 
 	
@@ -62,11 +40,38 @@ private:
 	ReferenceDB* rdb;
 	
 	struct linePair {
-		unsigned long int start;
-		unsigned long int end;
-		linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
+		unsigned long long start;
+		unsigned long long end;
+		linePair(unsigned long long i, unsigned long long j) : start(i), end(j) {}
+        ~linePair(){}
 	};
 	
+    struct Compare {
+        int AA, AT, AG, AC,	TA, TT, TG, TC,	GA, GT, GG, GC,	CA, CT, CG, CC,	NA, NT, NG, NC, Ai, Ti, Gi, Ci, Ni, dA, dT, dG, dC;
+        string refName, queryName, sequence;
+        double errorRate;
+        int weight, matches, mismatches, total;
+        
+        Compare(){
+            AA=0; AT=0; AG=0; AC=0;
+            TA=0; TT=0; TG=0; TC=0;
+            GA=0; GT=0; GG=0; GC=0;
+            CA=0; CT=0; CG=0; CC=0;
+            NA=0; NT=0; NG=0; NC=0;
+            Ai=0; Ti=0; Gi=0; Ci=0; Ni=0;
+            dA=0; dT=0; dG=0; dC=0;
+            refName = "";
+            queryName = "";
+            weight = 1;
+            matches = 0;
+            mismatches = 0;
+            total = 0;
+            errorRate = 1.0000;
+            sequence = "";
+        }
+        ~Compare(){};
+    };
+
 	vector<int> processIDS;   //processid
 	vector<linePair> lines;
 	vector<linePair> qLines;
@@ -74,7 +79,7 @@ private:
 
 	void getReferences();
 	map<string,int> getWeights();
-	Compare getErrors(Sequence, Sequence);
+	int getErrors(Sequence, Sequence, Compare&);
 	void printErrorHeader(ofstream&);
 	void printErrorData(Compare, int, ofstream&, ofstream&);
 	void printSubMatrix();
@@ -82,13 +87,13 @@ private:
 	void printErrorQuality(map<char, vector<int> >);
 	void printQualityFR(vector<vector<int> >, vector<vector<int> >);
 	
-	int setLines(string, string, string, vector<unsigned long int>&, vector<unsigned long int>&, vector<unsigned long int>&);
+	int setLines(string, string, string, vector<unsigned long long>&, vector<unsigned long long>&, vector<unsigned long long>&);
 	int driver(string, string, string, string, string, string, linePair, linePair, linePair);
 	int createProcesses(string, string, string, string, string, string);
 
-	string queryFileName, referenceFileName, qualFileName, reportFileName, namesFileName, outputDir;
+	string queryFileName, referenceFileName, qualFileName, reportFileName, namesFileName, outputDir, countfile;
 	double threshold;
-	bool ignoreChimeras, save;
+	bool ignoreChimeras, save, aligned;
 	int numRefs, processors;
 	int maxLength, totalBases, totalMatches;
 	//ofstream errorSummaryFile, errorSeqFile;