adding mothurout.h and .cpp to repo

[mothur.git] / aligncommand.h

diff --git a/aligncommand.h b/aligncommand.h
index 62bf3dc100297c2c3f089257329a750e2301f598..f0496a54a9070b31dcb699a0deefc7cb51fc8a50 100644 (file)
--- a/aligncommand.h
+++ b/aligncommand.h
@@ -14,6 +14,7 @@
 #include "command.hpp"
 #include "database.hpp"
 #include "alignment.hpp"
+#include "alignmentdb.h"
 
 class AlignCommand : public Command {
        
@@ -22,29 +23,30 @@ public:
        ~AlignCommand();
        int execute(); 
        void help();    
-
+       
 private:
        struct linePair {
                int start;
                int numSeqs;
-               linePair(int i, int j) : start(i), numSeqs(j) {}
+               linePair(long int i, int j) : start(i), numSeqs(j) {}
        };
-       map<int, int> processIDS;   //end line, processid
+       vector<int> processIDS;   //processid
        vector<linePair*> lines;
-
-       Database* templateDB;
+       
+       AlignmentDB* templateDB;
        Alignment* alignment;
-
-       int driver(linePair*, string, string);
-       void createProcesses(string, string);
+       
+       int driver(linePair*, string, string, string, string);
+       int createProcesses(string, string, string, string);
        void appendAlignFiles(string, string); 
        void appendReportFiles(string, string);
        
-       string candidateFileName, templateFileName, distanceFileName, search, align;
-       float match, misMatch, gapOpen, gapExtend;
+       string candidateFileName, templateFileName, distanceFileName, search, align, outputDir;
+       float match, misMatch, gapOpen, gapExtend, threshold;
        int processors, kmerSize;
-
-       bool abort;
+       vector<string> candidateFileNames;
+       
+       bool abort, flip;
 };
 
 #endif