X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=clusterfragmentscommand.h;h=ee25fb30da91c4ab338b0b173bcf05a6f1689c81;hp=842485e15c1c9679cf6cd8b1cb16f987454a27c5;hb=df7e3ff9f68ef157b0328a2d353c3258c5d45d89;hpb=8bc3e5b38c2317a1715f53be22fa96455868c281

diff --git a/clusterfragmentscommand.h b/clusterfragmentscommand.h
index 842485e..ee25fb3 100644
--- a/clusterfragmentscommand.h
+++ b/clusterfragmentscommand.h
@@ -13,6 +13,7 @@
 
 #include "command.hpp"
 #include "sequence.hpp"
+#include "counttable.h"
 
 /************************************************************/
 struct seqRNode {
@@ -32,27 +33,35 @@ class ClusterFragmentsCommand : public Command {
 public:
 	ClusterFragmentsCommand(string);
 	ClusterFragmentsCommand();
-	~ClusterFragmentsCommand();
-	vector<string> getRequiredParameters();
-	vector<string> getValidParameters();
-	vector<string> getRequiredFiles();
-	map<string, vector<string> > getOutputFiles() { return outputTypes; }
-	int execute();	
-	void help();
+	~ClusterFragmentsCommand() {}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "cluster.fragments";		}
+	string getCommandCategory()		{ return "Sequence Processing";		}
+	
+	string getHelpString();	
+    string getOutputPattern(string);	
+	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:
+    CountTable ct;
 	bool abort;
-	string fastafile, namefile, outputDir;
+	string fastafile, namefile, countfile, 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;
-	map<string, vector<string> > outputTypes;
 	
 	int readFASTA();
 	void readNameFile();
 	void printData(string, string); //fasta filename, names file name
+	bool isFragment(string, string);
 	
 };