moved mothur's source into a folder to make grabbing just the source easier on github

[mothur.git] / secondarystructurecommand.h

diff --git a/secondarystructurecommand.h b/secondarystructurecommand.h
deleted file mode 100644 (file)
index 4e7bdea..0000000
--- a/secondarystructurecommand.h
+++ /dev/null
@@ -1,64 +0,0 @@
-#ifndef SECONDARYSTRUCTURECHECKERCOMMAND_H
-#define SECONDARYSTRUCTURECHECKERCOMMAND_H
-
-/*
- *  secondarystructurecommand.h
- *  Mothur
- *
- *  Created by westcott on 9/18/09.
- *  Copyright 2009 Schloss Lab. All rights reserved.
- *
- */
- 
-#include "command.hpp"
-
-/**************************************************************************************************/
-
-struct statData {
-       int pound;
-       int tilde;
-       int dash;
-       int plus;
-       int equal;
-       int loop;
-       int total;
-       statData() : pound(0), loop(0), tilde(0), dash(0), plus(0), equal(0), total(0) {};      
-};
-
-/**************************************************************************************************/
-
-
-class AlignCheckCommand : public Command {
-       
-       public:
-       
-               AlignCheckCommand(string);      
-               AlignCheckCommand();
-               ~AlignCheckCommand(){}
-       
-               vector<string> setParameters();
-               string getCommandName()                 { return "align.check";                         }
-               string getCommandCategory()             { return "Sequence Processing";         }
-               string getHelpString(); 
-               string getCitation() { return "http://www.mothur.org/wiki/Align.check"; }
-               string getDescription()         { return "calculate the number of potentially misaligned bases in a 16S rRNA gene sequence alignment"; }
-
-       
-               int execute(); 
-               void help() { m->mothurOut(getHelpString()); }  
-       
-       private:
-               vector<int> structMap;
-               string mapfile, fastafile, outputDir, namefile;
-               bool abort;
-               int seqLength, haderror;
-               vector<string> outputNames;
-               map<string, int> nameMap;
-               
-               void readMap();
-               statData getStats(string sequence);
-};
-
-/**************************************************************************************************/
-#endif
-