added make.lookup command.

[mothur.git] / makelookupcommand.h

diff --git a/makelookupcommand.h b/makelookupcommand.h
new file mode 100644 (file)
index 0000000..743e756
--- /dev/null
+++ b/makelookupcommand.h
@@ -0,0 +1,51 @@
+//
+//  makelookupcommand.h
+//  Mothur
+//
+//  Created by SarahsWork on 5/14/13.
+//  Copyright (c) 2013 Schloss Lab. All rights reserved.
+//
+
+#ifndef Mothur_makelookupcommand_h
+#define Mothur_makelookupcommand_h
+
+#include "command.hpp"
+#include "sequence.hpp"
+
+/**************************************************************************************************/
+
+class MakeLookupCommand : public Command {
+public:
+    MakeLookupCommand(string);
+    MakeLookupCommand();
+    ~MakeLookupCommand(){}
+    
+    vector<string> setParameters();
+    string getCommandName()                    { return "make.lookup";                 }
+    string getCommandCategory()                { return "Sequence Processing";         }
+    
+    string getOutputPattern(string);
+       string getHelpString();
+    string getCitation() { return "http://www.mothur.org/wiki/Make.lookup"; }
+    string getDescription()            { return "create custom lookup files for use with shhh.flows"; }
+    
+    int execute();
+    void help() { m->mothurOut(getHelpString()); }
+    
+private:
+    bool abort;
+    string outputDir, flowFileName, errorFileName, flowOrder, refFastaFileName, barcodeSequence, keySequence;
+    vector<string> outputNames;
+    int thresholdCount;
+    
+    vector<double> convertSeqToFlow(string sequence, string order);
+    int alignFlowGrams(vector<double>& flowgram, vector<double>& refFlow, double gapOpening, vector<vector<double> > penaltyMatrix, string flowOrder);
+    int regress(vector<double>& data, int N);
+};
+
+/**************************************************************************************************/
+
+
+
+
+#endif