modified chimera commands to process multiple fasta files and added checks to pintail...

[mothur.git] / chimerapintailcommand.h

diff --git a/chimerapintailcommand.h b/chimerapintailcommand.h
index 0ddfc1c6229758991e74b0def36a778182a74da6..b0dcceb4d766e693a9d9c32819352690740c9946 100644 (file)
--- a/chimerapintailcommand.h
+++ b/chimerapintailcommand.h
@@ -44,9 +44,11 @@ private:
        #endif
 
        bool abort, filter, MPIWroteAccnos;
-       string fastafile, templatefile, consfile, quanfile, maskfile, outputDir;
+       string fastafile, templatefile, consfile, quanfile, maskfile, outputDir, inputDir;
        int processors, window, increment, numSeqs, templateSeqsLength;
        Chimera* chimera;
+       vector<string> outputNames;
+       vector<string> fastaFileNames;
        
        
 };