X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimerapintailcommand.h;h=fa195e7253e870f2a38b8e72ca90a1a6875e4652;hb=a0f1fca79d2ddfa7ad36b4485039c68b5704fe8d;hp=d2b2e03a3196d61cf7036ff879f1a18bec741ae6;hpb=8bc3e5b38c2317a1715f53be22fa96455868c281;p=mothur.git

diff --git a/chimerapintailcommand.h b/chimerapintailcommand.h
index d2b2e03..fa195e7 100644
--- a/chimerapintailcommand.h
+++ b/chimerapintailcommand.h
@@ -13,7 +13,7 @@
 #include "mothur.h"
 #include "command.hpp"
 #include "chimera.h"
-
+#include "referencedb.h"
 
 /***********************************************************/
 
@@ -23,20 +23,26 @@ public:
 
 	ChimeraPintailCommand(string);
 	ChimeraPintailCommand();
-	~ChimeraPintailCommand();
-	vector<string> getRequiredParameters();
-	vector<string> getValidParameters();
-	vector<string> getRequiredFiles();
-	map<string, vector<string> > getOutputFiles() { return outputTypes; }
-	int execute();
-	void help();
+	~ChimeraPintailCommand(){}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "chimera.pintail";		}
+	string getCommandCategory()		{ return "Sequence Processing"; }
 	
+	string getHelpString();	
+    string getOutputPattern(string);	
+	string getCitation() { return "Ashelford KE, Chuzhanova NA, Fry JC, Jones AJ, Weightman AJ (2005). At least 1 in 20 16S rRNA sequence records currently held in public repositories is estimated to contain substantial anomalies. Appl Environ Microbiol 71: 7724-36. \nAshelford KE, Chuzhanova NA, Fry JC, Jones AJ, Weightman AJ (2006). New screening software shows that most recent large 16S rRNA gene clone libraries contain chimeras. Appl Environ Microbiol 72: 5734-41. \nhttp://www.mothur.org/wiki/Chimera.pintail"; }
+	string getDescription()		{ return "detect chimeric sequences"; }
+	
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }		
 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) {}
 	};
 
 	vector<int> processIDS;   //processid
@@ -46,18 +52,15 @@ private:
 	int createProcesses(string, string, string);
 	
 	#ifdef USE_MPI
-	int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long int>&);
+	int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long long>&);
 	#endif
 
-	bool abort, filter;
+	bool abort, filter, save;
 	string fastafile, templatefile, consfile, quanfile, maskfile, outputDir, inputDir;
 	int processors, window, increment, numSeqs, templateSeqsLength;
 	Chimera* chimera;
 	vector<string> outputNames;
-	map<string, vector<string> > outputTypes;
 	vector<string> fastaFileNames;
-	
-	
 };
 
 /***********************************************************/