added debug flag to mothurOut. added debug parameter to set.dir. added debug code...

[mothur.git] / newcommandtemplate.h

diff --git a/newcommandtemplate.h b/newcommandtemplate.h
new file mode 100644 (file)
index 0000000..5fd36b1
--- /dev/null
+++ b/newcommandtemplate.h
@@ -0,0 +1,57 @@
+#ifndef Mothur_newcommandtemplate_h
+#define Mothur_newcommandtemplate_h
+
+//
+//  newcommandtemplate.h
+//  Mothur
+//
+//  Created by westcott on 5/3/12.
+//  Copyright (c) 2012 Schloss Lab. All rights reserved.
+//
+
+
+//*********Be sure to change ifdef and define to a unique name.**************//
+
+/* This class is designed to provide a template for creating new commands. 
+ It includes code snippets to make creating the command classes virtually pure
+ functions easier. It includes sample parameter declaration and parameter checking,
+ as well as reference to other classes you may find helpful.
+ It also includes the code needed to read a sharedfile. It is a work in progress so 
+ please add things you may find helpful to yourself or other developers trying to 
+ add commands to mothur.
+ 
+*/
+
+#include "command.hpp"
+
+/**************************************************************************************************/
+
+class NewCommand : public Command {
+public:
+    NewCommand(string);
+    NewCommand();
+    ~NewCommand(){}
+    
+    vector<string> setParameters();
+    string getCommandName()                    { return "newCommandNameToBeSeenByUser";                        }
+    string getCommandCategory()                { return "commandCategory";             } 
+    //commmand category choices: Sequence Processing, OTU-Based Approaches, Hypothesis Testing, Phylotype Analysis, General, Clustering and Hidden
+    string getHelpString();    
+    string getCitation() { return "http://www.mothur.org/wiki/newCommandNameToBeSeenByUser"; }
+    string getDescription()            { return "brief description"; }
+    
+    int execute(); 
+    void help() { m->mothurOut(getHelpString()); }     
+    
+private:
+    bool abort;
+    string outputDir;
+    vector<string> outputNames;
+};
+
+/**************************************************************************************************/
+
+
+
+
+#endif