X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=chimeracheckcommand.h;h=8981a14ff5e6e7813ab54123fe3fa1c8b68a0bc4;hp=6db61bd82cbfe30fd2b8c5d48e43f83b3df266b3;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=fdc1f6eaf544f695fc1511f24bddd7e6069c33ba

diff --git a/chimeracheckcommand.h b/chimeracheckcommand.h
index 6db61bd..8981a14 100644
--- a/chimeracheckcommand.h
+++ b/chimeracheckcommand.h
@@ -13,6 +13,7 @@
 #include "mothur.h"
 #include "command.hpp"
 #include "chimera.h"
+#include "chimeracheckrdp.h"
 
 
 /***********************************************************/
@@ -20,18 +21,30 @@
 class ChimeraCheckCommand : public Command {
 public:
 	ChimeraCheckCommand(string);
-	~ChimeraCheckCommand();
-	int execute();
-	void help();
+	ChimeraCheckCommand();
+	~ChimeraCheckCommand(){}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "chimera.check";		}
+	string getCommandCategory()		{ return "Sequence Processing"; }
+	
+	string getHelpString();	
+    string getOutputPattern(string);	
+	string getCitation() { return "CHIMERA_CHECK version 2.7 written by Niels Larsen (http://wdcm.nig.ac.jp/RDP/docs/chimera_doc.html) \nhttp://www.mothur.org/wiki/Chimera.check"; }
+	string getDescription()		{ return "detect chimeric sequences"; }
+	
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
+	
 	
-		
 private:
 
 	struct linePair {
-		int start;
-		int numSeqs;
-		linePair(long int i, int j) : start(i), numSeqs(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
 	vector<linePair*> lines;
 	
@@ -39,15 +52,16 @@ private:
 	int createProcesses(string, string);
 		
 	#ifdef USE_MPI
-	int driverMPI(int, int, MPI_File&, MPI_File&, vector<long>&);
+	int driverMPI(int, int, MPI_File&, MPI_File&, vector<unsigned long long>&);
 	#endif
 
-	bool abort, svg;
+	bool abort, svg, save;
 	string fastafile, templatefile, namefile, outputDir;
 	int processors, increment, ksize, numSeqs, templateSeqsLength;
 	Chimera* chimera;
-	
-	
+	vector<string> fastaFileNames;
+	vector<string> nameFileNames;
+	vector<string> outputNames;
 };
 
 /***********************************************************/