added citation function to commands

[mothur.git] / classifyseqscommand.h

diff --git a/classifyseqscommand.h b/classifyseqscommand.h
index 03e6826d1276b4efbdf12b5fce0aeb4cdea8fb08..b813d40223a383dfb1e5c8734ded39f4e0b0e2a5 100644 (file)
--- a/classifyseqscommand.h
+++ b/classifyseqscommand.h
@@ -12,7 +12,6 @@
 
 #include "mothur.h"
 #include "command.hpp"
-//#include "alignment.hpp"
 #include "classify.h"
 
 //KNN and Bayesian methods modeled from algorithms in
@@ -29,21 +28,34 @@ class ClassifySeqsCommand : public Command {
        
 public:
        ClassifySeqsCommand(string);
+       ClassifySeqsCommand();
        ~ClassifySeqsCommand();
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "classify.seqs";               }
+       string getCommandCategory()             { return "Phylotype Analysis";  }
+       string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Classify.seqs"; }
+
+       
        int execute(); 
-       void help();    
+       void help() { m->mothurOut(getHelpString()); }  
+       
+       
        
 private:
        struct linePair {
                unsigned long int start;
-               int numSeqs;
-               linePair(unsigned long int i, int j) : start(i), numSeqs(j) {}
+               unsigned long int end;
+               linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
        };
+
        vector<int> processIDS;   //processid
        vector<linePair*> lines;
        vector<string> fastaFileNames;
        vector<string> namefileNames;
        vector<string> groupfileNames;
+       vector<string> outputNames;
        map<string, vector<string> > nameMap;
        map<string,  vector<string> >::iterator itNames;
        
@@ -56,7 +68,7 @@ private:
        
        int driver(linePair*, string, string, string);
        void appendTaxFiles(string, string);
-       void createProcesses(string, string, string); 
+       int createProcesses(string, string, string); 
        string addUnclassifieds(string, int);
        
        int MPIReadNamesFile(string);