added MPI code, broke up chimera.seqs into 5 separated commands, added parse.sff...

[mothur.git] / aligncommand.h

diff --git a/aligncommand.h b/aligncommand.h
index f0496a54a9070b31dcb699a0deefc7cb51fc8a50..b100287269f16781839c884bd83121c620e279ba 100644 (file)
--- a/aligncommand.h
+++ b/aligncommand.h
@@ -32,6 +32,7 @@ private:
        };
        vector<int> processIDS;   //processid
        vector<linePair*> lines;
+       bool MPIWroteAccnos;
        
        AlignmentDB* templateDB;
        Alignment* alignment;
@@ -41,6 +42,10 @@ private:
        void appendAlignFiles(string, string); 
        void appendReportFiles(string, string);
        
+       #ifdef USE_MPI
+       int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, MPI_File&, vector<long>&);
+       #endif
+       
        string candidateFileName, templateFileName, distanceFileName, search, align, outputDir;
        float match, misMatch, gapOpen, gapExtend, threshold;
        int processors, kmerSize;