added oligos class. added check orient parameter to trim.flows, sffinfo, fastq.info...

[mothur.git] / consensusseqscommand.h

diff --git a/consensusseqscommand.h b/consensusseqscommand.h
index e0c97150bfb0bc3e5baafcea911c4ba1c6c60dcb..165d420f820d89c3015737e62cbda2226fbb07fc 100644 (file)
--- a/consensusseqscommand.h
+++ b/consensusseqscommand.h
@@ -24,8 +24,9 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "consensus.seqs";              }
        string getCommandCategory()             { return "Sequence Processing"; }
-       string getOutputFileNameTag(string, string);
+       
        string getHelpString(); 
+    string getOutputPattern(string);   
        string getCitation() { return "http://www.mothur.org/wiki/Consensus.seqs"; }
        string getDescription()         { return "create a consensus sequence for each OTU or for a fasta file"; }
 
@@ -43,7 +44,8 @@ private:
        map<string, string> fastaMap;
        map<string, string> nameMap;
        map<string, int> nameFileMap;
-       int cutoff, seqLength;
+       int seqLength;
+    float cutoff;
        
        int readFasta();
        int readNames();