added pca command

[mothur.git] / aligncommand.h

diff --git a/aligncommand.h b/aligncommand.h
index b5ff7825c7ae06fb8351a2ed9b398379d6abbc9a..ec0c80ff7994e533ac2a9e627936e11c296ddcd8 100644 (file)
--- a/aligncommand.h
+++ b/aligncommand.h
@@ -10,26 +10,42 @@
  *
  */
 
+#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();
-       int execute();  
-
+       int execute(); 
+       void help();    
+       
 private:
-       GlobalData* globaldata;
-       string candidateFileName, templateFileName, distanceFileName;
-       int kmerSize;
-       float match, misMatch, gapOpen, gapExtend;
-       ofstream out;
-       ifstream in;
-
+       struct linePair {
+               int start;
+               int numSeqs;
+               linePair(long int i, int j) : start(i), numSeqs(j) {}
+       };
+       vector<int> processIDS;   //processid
+       vector<linePair*> lines;
+       
+       AlignmentDB* templateDB;
+       Alignment* alignment;
+       
+       int driver(linePair*, string, string, string);
+       void createProcesses(string, string, string);
+       void appendAlignFiles(string, string); 
+       void appendReportFiles(string, string);
+       
+       string candidateFileName, templateFileName, distanceFileName, search, align;
+       float match, misMatch, gapOpen, gapExtend, threshold;
+       int processors, kmerSize;
+       
+       bool abort, flip;
 };
 
-
-
-#endif
\ No newline at end of file
+#endif