added warning about merging with something above cutoff to cluster. working on chimeras

[mothur.git] / aligncommand.h

diff --git a/aligncommand.h b/aligncommand.h
index 50e9bffb3ba26790d4b0531605d34cf99f173dbe..8042983911c1052e100133b4284f03ddce751031 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 {
        
@@ -27,24 +28,25 @@ 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) {}
        };
        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);
+       void 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;
+       vector<string> candidateFileNames;
        
-       bool abort;
+       bool abort, flip;
 };
 
 #endif