added list.labels command. started work on make.contigs command. fixed fastq.info...

[mothur.git] / listotulabelscommand.h

diff --git a/listotulabelscommand.h b/listotulabelscommand.h
new file mode 100644 (file)
index 0000000..ea41539
--- /dev/null
+++ b/listotulabelscommand.h
@@ -0,0 +1,54 @@
+#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