added set.dir command and modified commands to redirect input and output, removed...

[mothur.git] / aligncommand.h

diff --git a/aligncommand.h b/aligncommand.h
index 0a2e7ba618291f99044cfd187f3e616b40a936cd..8042983911c1052e100133b4284f03ddce751031 100644 (file)
--- a/aligncommand.h
+++ b/aligncommand.h
@@ -41,7 +41,7 @@ private:
        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;