added sff.multiple command. fixed issue with windows paralellization in chimera...

[mothur.git] / consensusseqscommand.h

diff --git a/consensusseqscommand.h b/consensusseqscommand.h
index 555b62c63f263526917a388a6e03b62359cc1db3..1459b43d25bd54b525459721b5de55a5a1d6d9f6 100644 (file)
--- a/consensusseqscommand.h
+++ b/consensusseqscommand.h
@@ -1,6 +1,6 @@
 #ifndef CONSENSUSSEQSCOMMAND_H
 #define CONSENSUSSEQSCOMMAND_H
-
+//test
 /*
  *  consensusseqscommand.h
  *  Mothur
@@ -18,13 +18,19 @@ class ConsensusSeqsCommand : public Command {
 public:
        ConsensusSeqsCommand(string);
        ConsensusSeqsCommand();
-       ~ConsensusSeqsCommand();
-       vector<string> getRequiredParameters();
-       vector<string> getValidParameters();
-       vector<string> getRequiredFiles();
-       map<string, vector<string> > getOutputFiles() { return outputTypes; }
-       int execute();
-       void help();
+       ~ConsensusSeqsCommand(){}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "consensus.seqs";              }
+       string getCommandCategory()             { return "Sequence Processing"; }
+       string getOutputFileNameTag(string, string);
+       string getHelpString(); 
+       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"; }
+
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
        
 private:
        
@@ -32,16 +38,16 @@ private:
        string fastafile, listfile, namefile, label, outputDir;
        set<string> labels;
        vector<string> outputNames;
-       map<string, vector<string> > outputTypes;
        map<string, string> fastaMap;
        map<string, string> nameMap;
        map<string, string> nameFileMap;
+       int cutoff;
        
        int readFasta();
        int readNames();
        int processList(ListVector*&);
        string getConsSeq(string, ofstream&, string&, int);
-       char getBase(vector<int>);
+       char getBase(vector<int>, int);
 };
 
 #endif