added name option to read.tree for use in unifrac and parimony commands

[mothur.git] / aligncommand.h

diff --git a/aligncommand.h b/aligncommand.h
index a3ec827c80e1dfa229bf228eb45df61499aef265..8042983911c1052e100133b4284f03ddce751031 100644 (file)
--- a/aligncommand.h
+++ b/aligncommand.h
@@ -10,10 +10,11 @@
  *
  */
 
+#include "mothur.h"
 #include "command.hpp"
-#include "globaldata.hpp"
-
-
+#include "database.hpp"
+#include "alignment.hpp"
+#include "alignmentdb.h"
 
 class AlignCommand : public Command {
        
@@ -22,23 +23,30 @@ public:
        ~AlignCommand();
        int execute(); 
        void help();    
-
+       
 private:
-       GlobalData* globaldata;
-       OptionParser* parser;
-       map<string, string> parameters;
-       map<string, string>::iterator it;
-       bool abort;
-       string candidateFileName, templateFileName, distanceFileName, search, align;
-       int kmerSize;
-       float match, misMatch, gapOpen, gapExtend;
-       ofstream out;
-       ifstream in;
-       int ableToOpen;
+       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, string);
+       void createProcesses(string, string, string, string);
+       void appendAlignFiles(string, string); 
+       void appendReportFiles(string, string);
+       
+       string candidateFileName, templateFileName, distanceFileName, search, align, outputDir;
+       float match, misMatch, gapOpen, gapExtend, threshold;
+       int processors, kmerSize;
+       vector<string> candidateFileNames;
+       
+       bool abort, flip;
 };
 
-
-
-#endif
\ No newline at end of file
+#endif