X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=filterseqscommand.h;h=e445023df07f7c0c6e3bcc6c4d0e95c574e6174d;hb=8742edef7a51b82834289e570d336f5a81ba1f2b;hp=5eb49d3802177bf998e8fe9d0ba1dd80c2828709;hpb=30c1fd8c45b6f0d66c17f2714dbb58b8ddccdce2;p=mothur.git

diff --git a/filterseqscommand.h b/filterseqscommand.h
index 5eb49d3..e445023 100644
--- a/filterseqscommand.h
+++ b/filterseqscommand.h
@@ -1,54 +1,68 @@
-#ifndef FILTERSEQSCOMMAND_H
-#define FILTERSEQSCOMMAND_H
-
-/*
- *  filterseqscommand.h
- *  Mothur
- *
- *  Created by Thomas Ryabin on 5/4/09.
- *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
- *
- */
-
-#include "command.hpp"
-#include "filters.h"
-#include "mpi.h"
-
-class Sequence;
-class FilterSeqsCommand : public Command {
-
-public:
-	FilterSeqsCommand(string);
-	~FilterSeqsCommand() {};
-	int execute();	
-	void help();
-	
-private:
-	struct linePair {
-		int start;
-		int numSeqs;
-		linePair(long int i, int j) : start(i), numSeqs(j) {}
-	};
-	vector<linePair*> lines;
-
-
-	string vertical, filter, fasta, hard, outputDir, filterFileName;
-	vector<string> fastafileNames;	
-	int alignmentLength, processors;
-	vector<int> bufferSizes;
-
-	char trump;
-	bool abort;
-	float soft;
-	int numSeqs;
-	
-	string createFilter();
-	int createProcessesCreateFilter(Filters&, string);
-	int driverCreateFilter(Filters&, string, linePair*);
-	int MPICreateFilter(Filters&, vector<string>&);	
-	int setLines(string);
-	int parseBuffer(string, vector<string>&);
-	
-};
-
-#endif
+#ifndef FILTERSEQSCOMMAND_H
+#define FILTERSEQSCOMMAND_H
+
+/*
+ *  filterseqscommand.h
+ *  Mothur
+ *
+ *  Created by Thomas Ryabin on 5/4/09.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+#include "command.hpp"
+#include "filters.h"
+
+class Sequence;
+class FilterSeqsCommand : public Command {
+
+public:
+	FilterSeqsCommand(string);
+	FilterSeqsCommand();
+	~FilterSeqsCommand() {};
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "filter.seqs";			}
+	string getCommandCategory()		{ return "Sequence Processing";	}
+	string getHelpString();	
+	string getCitation() { return "http://www.mothur.org/wiki/Filter.seqs"; }
+	string getDescription()		{ return "removes columns from alignments based on a criteria defined by the user"; }
+	
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
+	
+private:
+	struct linePair {
+		unsigned long int start;
+		unsigned long int end;
+		linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
+	};
+
+	vector<linePair*> lines;
+	vector<int> processIDS;
+
+	string vertical, filter, fasta, hard, outputDir, filterFileName;
+	vector<string> fastafileNames;	
+	int alignmentLength, processors;
+	vector<int> bufferSizes;
+	vector<string> outputNames;
+
+	char trump;
+	bool abort;
+	float soft;
+	int numSeqs;
+	
+	string createFilter();
+	int filterSequences();
+	int createProcessesCreateFilter(Filters&, string);
+	int createProcessesRunFilter(string, string);
+	int driverRunFilter(string, string, string, linePair*);
+	int driverCreateFilter(Filters& F, string filename, linePair* line);
+	#ifdef USE_MPI
+	int driverMPIRun(int, int, MPI_File&, MPI_File&, vector<unsigned long int>&);
+	int MPICreateFilter(int, int, Filters&, MPI_File&, vector<unsigned long int>&);	
+	#endif
+	
+};
+
+#endif