added namefile to align.check and added seqs from namefile to optimizing piece of...

[mothur.git] / secondarystructurecommand.h

diff --git a/secondarystructurecommand.h b/secondarystructurecommand.h
index c1cc057cd190cd4570b57d9bcc9f622a8f6bf0f4..0b654a4e02bdf42cdf5ebfc9ee419bdbd71eec2f 100644 (file)
--- a/secondarystructurecommand.h
+++ b/secondarystructurecommand.h
@@ -44,11 +44,12 @@ class AlignCheckCommand : public Command {
                
        private:
                vector<int> structMap;
-               string mapfile, fastafile, outputDir;
+               string mapfile, fastafile, outputDir, namefile;
                bool abort;
                int seqLength, haderror;
                vector<string> outputNames;
                map<string, vector<string> > outputTypes;
+               map<string, int> nameMap;
                
                void readMap();
                statData getStats(string sequence);