X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=aligncommand.h;h=1410626a42e3a407289f18565dd0e64a3d4d3cd4;hb=af27acb766f6947c45e1eb65438d878c7ea48ef3;hp=b5ff7825c7ae06fb8351a2ed9b398379d6abbc9a;hpb=544469443afe44920bdf279aefd26d29534cabaf;p=mothur.git

diff --git a/aligncommand.h b/aligncommand.h
index b5ff782..1410626 100644
--- a/aligncommand.h
+++ b/aligncommand.h
@@ -10,26 +10,55 @@
  *
  */
 
+#include "mothur.h"
 #include "command.hpp"
-#include "globaldata.hpp"
+#include "database.hpp"
+#include "alignment.hpp"
+#include "alignmentdb.h"
 
 class AlignCommand : public Command {
 	
 public:
-	AlignCommand();	
+	AlignCommand(string);	
+	AlignCommand();
 	~AlignCommand();
-	int execute();	
-
+	vector<string> getRequiredParameters();
+	vector<string> getValidParameters();
+	vector<string> getRequiredFiles();
+	map<string, vector<string> > getOutputFiles() { return outputTypes; }
+	int execute(); 
+	void help();	
+	
 private:
-	GlobalData* globaldata;
-	string candidateFileName, templateFileName, distanceFileName;
-	int kmerSize;
-	float match, misMatch, gapOpen, gapExtend;
-	ofstream out;
-	ifstream in;
-
+	struct linePair {
+		unsigned long int start;
+		unsigned long int end;
+		linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
+	};
+	vector<int> processIDS;   //processid
+	vector<linePair*> lines;
+	bool MPIWroteAccnos;
+	map<string, vector<string> > outputTypes;
+	
+	AlignmentDB* templateDB;
+	Alignment* alignment;
+	
+	int driver(linePair*, string, string, string, string);
+	int createProcesses(string, string, string, string);
+	void appendAlignFiles(string, string); 
+	void appendReportFiles(string, string);
+	
+	#ifdef USE_MPI
+	int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long int>&);
+	#endif
+	
+	string candidateFileName, templateFileName, distanceFileName, search, align, outputDir;
+	float match, misMatch, gapOpen, gapExtend, threshold;
+	int processors, kmerSize;
+	vector<string> candidateFileNames;
+	vector<string> outputNames;
+	
+	bool abort, flip;
 };
 
-
-
-#endif
\ No newline at end of file
+#endif