added get.dists and remove.dists commands. fixed bug in trim.seqs windows paralelliza...

[mothur.git] / getdistscommand.h

diff --git a/getdistscommand.h b/getdistscommand.h
new file mode 100644 (file)
index 0000000..8767067
--- /dev/null
+++ b/getdistscommand.h
@@ -0,0 +1,48 @@
+//
+//  getdistscommand.h
+//  Mothur
+//
+//  Created by Sarah Westcott on 1/28/13.
+//  Copyright (c) 2013 Schloss Lab. All rights reserved.
+//
+
+#ifndef Mothur_getdistscommand_h
+#define Mothur_getdistscommand_h
+
+#include "command.hpp"
+
+class GetDistsCommand : public Command {
+       
+public:
+       
+       GetDistsCommand(string);        
+       GetDistsCommand();
+       ~GetDistsCommand(){}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "get.dists";                           }
+       string getCommandCategory()             { return "General";                 }
+       
+       string getHelpString(); 
+    string getOutputPattern(string);   
+       string getCitation() { return "http://www.mothur.org/wiki/Get.dists"; }
+       string getDescription()         { return "gets distances from a phylip or column file related to groups or sequences listed in an accnos file"; }
+    
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
+       
+       
+private:
+       set<string> names;
+       string accnosfile, phylipfile, columnfile, outputDir;
+       bool abort;
+       vector<string> outputNames;
+       
+       int readPhylip();
+       int readColumn();
+       
+};
+
+
+#endif