X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=listotulabelscommand.h;fp=listotulabelscommand.h;h=ea41539adb021cdc56fd6175f7845f2ae70363e4;hb=4c302368ef34f0d897afefc7853edf86fb45b9f3;hp=0000000000000000000000000000000000000000;hpb=4522aebe2246c5f47875d5c8cc505f1b615bfc7e;p=mothur.git

diff --git a/listotulabelscommand.h b/listotulabelscommand.h
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+++ b/listotulabelscommand.h
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+#ifndef Mothur_listotucommand_h
+#define Mothur_listotucommand_h
+
+//
+//  listotucommand.h
+//  Mothur
+//
+//  Created by Sarah Westcott on 5/15/12.
+//  Copyright (c) 2012 Schloss Lab. All rights reserved.
+//
+
+
+#include "command.hpp"
+#include "sharedrabundvector.h"
+
+/**************************************************************************************************/
+
+class ListOtuLabelsCommand : public Command {
+public:
+    ListOtuLabelsCommand(string);
+    ListOtuLabelsCommand();
+    ~ListOtuLabelsCommand(){}
+    
+    vector<string> setParameters();
+    string getCommandName()			{ return "list.otulabels";          }
+    string getCommandCategory()		{ return "OTU-Based Approaches";	} 
+    //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/List.otulabels"; }
+    string getDescription()		{ return "lists otu labels from shared or relabund file. 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, allLines;
+    string outputDir, sharedfile, relabundfile, label, inputFileName, format;
+    vector<string> outputNames;
+    vector<string> Groups;
+    set<string> labels;
+    
+    int createList(vector<SharedRAbundFloatVector*>&);
+    int createList(vector<SharedRAbundVector*>&);
+
+};
+
+/**************************************************************************************************/
+
+
+
+
+
+
+#endif