1.19.0

[mothur.git] / preclustercommand.h

diff --git a/preclustercommand.h b/preclustercommand.h
index a26fda41cba8e316fd8649604e6934a5960f22f4..d8ee57de9424e623d0455e0327e6f636ce569135 100644 (file)
--- a/preclustercommand.h
+++ b/preclustercommand.h
@@ -20,8 +20,9 @@ struct seqPNode {
        int numIdentical;
        Sequence seq;
        string names;
+       bool active;
        seqPNode() {}
-       seqPNode(int n, Sequence s, string nm) : numIdentical(n), seq(s), names(nm) {}
+       seqPNode(int n, Sequence s, string nm) : numIdentical(n), seq(s), names(nm), active(1) {}
        ~seqPNode() {}
 };
 /************************************************************/
@@ -30,25 +31,34 @@ class PreClusterCommand : public Command {
        
 public:
        PreClusterCommand(string);
-       ~PreClusterCommand();
-       int execute();  
-       void help();
+       PreClusterCommand();
+       ~PreClusterCommand(){}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "pre.cluster";                         }
+       string getCommandCategory()             { return "Sequence Processing";         }
+       string getHelpString(); 
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
        
 private:
        int diffs, length;
        bool abort;
        string fastafile, namefile, outputDir;
-       list<seqPNode> alignSeqs; //maps the number of identical seqs to a sequence
+       vector<seqPNode> alignSeqs; //maps the number of identical seqs to a sequence
        map<string, string> names; //represents the names file first column maps to second column
        map<string, int> sizes;  //this map a seq name to the number of identical seqs in the names file
        map<string, int>::iterator itSize; 
 //     map<string, bool> active; //maps sequence name to whether it has already been merged or not.
+       vector<string> outputNames;
+       map<string, vector<string> > outputTypes;
        
        int readFASTA();
        void readNameFile();
        //int readNamesFASTA();
        int calcMisMatches(string, string);
-       void printData(ofstream&, ofstream&, seqPNode); //fasta filename, names file name
+       void printData(string, string); //fasta filename, names file name
 };
 
 /************************************************************/