fixed bug with trim.seqs allfiles=t

[mothur.git] / aligncommand.h

diff --git a/aligncommand.h b/aligncommand.h
index b5ff7825c7ae06fb8351a2ed9b398379d6abbc9a..c0147512df11740241e9d4bd611a34b37a2d00b8 100644 (file)
--- a/aligncommand.h
+++ b/aligncommand.h
@@ -10,26 +10,58 @@
  *
  */
 
+#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> setParameters();
+       string getCommandName()                 { return "align.seqs";                  }
+       string getCommandCategory()             { return "Sequence Processing"; }
+       string getHelpString(); 
+       string getCitation() { return "DeSantis TZ, Jr., Hugenholtz P, Keller K, Brodie EL, Larsen N, Piceno YM, Phan R, Andersen GL (2006). NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes. Nucleic Acids Res 34: W394-9.\nSchloss PD (2009). A high-throughput DNA sequence aligner for microbial ecology studies. PLoS ONE 4: e8230.\nSchloss PD (2010). The effects of alignment quality, distance calculation method, sequence filtering, and region on the analysis of 16S rRNA gene-based studies. PLoS Comput Biol 6: e1000844.\nhttp://www.mothur.org/wiki/Align.seqs http://www.mothur.org/wiki/Align.seqs"; }
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
+       
 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;
+       
+       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, calledHelp;
 
 };
 
-
-
-#endif
\ No newline at end of file
+#endif