a few minor things - pds

[mothur.git] / aligncommand.h

diff --git a/aligncommand.h b/aligncommand.h
index 62bf3dc100297c2c3f089257329a750e2301f598..50e9bffb3ba26790d4b0531605d34cf99f173dbe 100644 (file)
--- a/aligncommand.h
+++ b/aligncommand.h
@@ -22,19 +22,19 @@ public:
        ~AlignCommand();
        int execute(); 
        void help();    
-
+       
 private:
        struct linePair {
                int start;
                int numSeqs;
                linePair(int i, int j) : start(i), numSeqs(j) {}
        };
-       map<int, int> processIDS;   //end line, processid
+       vector<int> processIDS;   //processid
        vector<linePair*> lines;
-
+       
        Database* templateDB;
        Alignment* alignment;
-
+       
        int driver(linePair*, string, string);
        void createProcesses(string, string);
        void appendAlignFiles(string, string); 
@@ -43,7 +43,7 @@ private:
        string candidateFileName, templateFileName, distanceFileName, search, align;
        float match, misMatch, gapOpen, gapExtend;
        int processors, kmerSize;
-
+       
        bool abort;
 };