added sort.seqs command. puts sequences from a fasta, name, group, quality or taxono...

[mothur.git] / sortseqscommand.h

diff --git a/sortseqscommand.h b/sortseqscommand.h
new file mode 100644 (file)
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+++ b/sortseqscommand.h
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+#ifndef Mothur_sortseqscommand_h
+#define Mothur_sortseqscommand_h
+
+
+//
+//  sortseqscommand.h
+//  Mothur
+//
+//  Created by Sarah Westcott on 2/3/12.
+//  Copyright (c) 2012 Schloss Lab. All rights reserved.
+//
+
+
+
+#include "command.hpp"
+
+class SortSeqsCommand : public Command {
+       
+public:
+       
+    SortSeqsCommand(string);   
+    SortSeqsCommand();
+    ~SortSeqsCommand(){}
+       
+    vector<string> setParameters();
+    string getCommandName()                    { return "sort.seqs";                           }
+    string getCommandCategory()                { return "Sequence Processing";         }
+    string getHelpString();    
+    string getCitation() { return "http://www.mothur.org/wiki/Sort.seqs"; }
+    string getDescription()            { return "puts sequences from a fasta, name, group, quality or taxonomy file in the same order"; }
+    
+    int execute(); 
+    void help() { m->mothurOut(getHelpString()); }     
+       
+       
+private:
+    map<string, int> names;
+    string accnosfile, fastafile, namefile, groupfile, taxfile, qualfile, outputDir;
+    bool abort, large;
+    vector<string> outputNames;
+    
+    int readFasta();
+    int readName();
+    int readGroup();
+    int readAccnos();
+    int readTax();
+    int readQual();
+    
+};
+
+#endif
+
+