working on slayer bug

[mothur.git] / chimerapintailcommand.h

diff --git a/chimerapintailcommand.h b/chimerapintailcommand.h
index 93707458d3b7b7b09cd1b4eb3aa02f8f03bafa16..abaef191e2c1ba137f83aad2fb3e7ea46bc0b7de 100644 (file)
--- a/chimerapintailcommand.h
+++ b/chimerapintailcommand.h
@@ -22,17 +22,24 @@ class ChimeraPintailCommand : public Command {
 public:
 
        ChimeraPintailCommand(string);
-       ~ChimeraPintailCommand();
-       int execute();
-       void help();
+       ChimeraPintailCommand();
+       ~ChimeraPintailCommand(){}
        
+       vector<string> setParameters();
+       string getCommandName()                 { return "chimera.pintail";             }
+       string getCommandCategory()             { return "Sequence Processing"; }
+       string getHelpString(); 
+       
+       int execute(); 
+       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;
        
@@ -49,8 +56,6 @@ private:
        Chimera* chimera;
        vector<string> outputNames;
        vector<string> fastaFileNames;
-       
-       
 };
 
 /***********************************************************/