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

[mothur.git] / clusterfragmentscommand.h

diff --git a/clusterfragmentscommand.h b/clusterfragmentscommand.h
deleted file mode 100644 (file)
index c7ea7e0..0000000
--- a/clusterfragmentscommand.h
+++ /dev/null
@@ -1,67 +0,0 @@
-#ifndef CLUSTERFRAGMENTSCOMMAND_H
-#define CLUSTERFRAGMENTSCOMMAND_H
-
-/*
- *  clusterfragmentscommand.h
- *  Mothur
- *
- *  Created by westcott on 9/23/10.
- *  Copyright 2010 Schloss Lab. All rights reserved.
- *
- */
-
-
-#include "command.hpp"
-#include "sequence.hpp"
-
-/************************************************************/
-struct seqRNode {
-       int numIdentical;
-       int length;
-       Sequence seq;
-       string names;
-       bool active;
-       seqRNode() {}
-       seqRNode(int n, Sequence s, string nm, int l) : numIdentical(n), seq(s), names(nm), active(1), length(l) {}
-       ~seqRNode() {}
-};
-/************************************************************/
-
-class ClusterFragmentsCommand : public Command {
-       
-public:
-       ClusterFragmentsCommand(string);
-       ClusterFragmentsCommand();
-       ~ClusterFragmentsCommand() {}
-       
-       vector<string> setParameters();
-       string getCommandName()                 { return "cluster.fragments";           }
-       string getCommandCategory()             { return "Sequence Processing";         }
-       string getHelpString(); 
-       string getCitation() { return "http://www.mothur.org/wiki/Cluster.fragments"; }
-       string getDescription()         { return "creates a namesfile with sequences that are a fragment of a larger sequence"; }
-       
-       int execute(); 
-       void help() { m->mothurOut(getHelpString()); }  
-       
-private:
-       bool abort;
-       string fastafile, namefile, outputDir;
-       int diffs, percent;
-       vector<seqRNode> alignSeqs; 
-       map<string, string> names; //represents the names file first column maps to second column
-       map<string, int> sizes;  //this map a seq name to the number of identical seqs in the names file
-       map<string, int>::iterator itSize; 
-       vector<string> outputNames;
-       
-       int readFASTA();
-       void readNameFile();
-       void printData(string, string); //fasta filename, names file name
-       bool isFragment(string, string);
-       
-};
-
-/************************************************************/
-
-#endif
-