added get.otulabels and remove.otulabels commands per user request

[mothur.git] / getotulabelscommand.h

diff --git a/getotulabelscommand.h b/getotulabelscommand.h
new file mode 100644 (file)
index 0000000..bad0f55
--- /dev/null
+++ b/getotulabelscommand.h
@@ -0,0 +1,53 @@
+#ifndef Mothur_getotulabelscommand_h
+#define Mothur_getotulabelscommand_h
+
+//
+//  getotulabelscommand.h
+//  Mothur
+//
+//  Created by Sarah Westcott on 5/21/12.
+//  Copyright (c) 2012 Schloss Lab. All rights reserved.
+//
+
+
+#include "command.hpp"
+
+/**************************************************************************************************/
+
+class GetOtuLabelsCommand : public Command {
+public:
+    GetOtuLabelsCommand(string);
+    GetOtuLabelsCommand();
+    ~GetOtuLabelsCommand(){}
+    
+    vector<string> setParameters();
+    string getCommandName()                    { return "get.otulabels";          }
+    string getCommandCategory()                { return "OTU-Based Approaches";        } 
+    string getHelpString();    
+    string getCitation() { return "http://www.mothur.org/wiki/Get.otulabels"; }
+    string getDescription()            { return "Can be used with output from classify.otu, otu.association, or corr.axes to select specific otus."; }
+    
+    int execute(); 
+    void help() { m->mothurOut(getHelpString()); }     
+    
+private:
+    bool abort;
+    string outputDir, accnosfile, constaxonomyfile, otucorrfile, corraxesfile;
+    vector<string> outputNames;
+    set<string> labels;
+    
+    int readClassifyOtu();
+    int readOtuAssociation();
+    int readCorrAxes();
+    int readAccnos();
+    
+};
+
+/**************************************************************************************************/
+
+
+
+
+
+
+#endif