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 f7d59b0206c989558f0e11163d1f7abddcf9a784..8042983911c1052e100133b4284f03ddce751031 100644 (file)
--- a/aligncommand.h
+++ b/aligncommand.h
@@ -28,7 +28,7 @@ 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;
@@ -36,14 +36,15 @@ private:
        AlignmentDB* templateDB;
        Alignment* alignment;
        
-       int driver(linePair*, string, string, string);
-       void createProcesses(string, 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;
+       string candidateFileName, templateFileName, distanceFileName, search, align, outputDir;
        float match, misMatch, gapOpen, gapExtend, threshold;
        int processors, kmerSize;
+       vector<string> candidateFileNames;
        
        bool abort, flip;
 };