X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=filterseqscommand.h;h=3bf36c040231c5f801281f9d553c60bed01101c8;hb=2bb9267aa4b4ecdf8488b06605cc9f3f36fa4332;hp=924c36627fec65abd777c5ae530bf154583e954f;hpb=ab750bdf95b4eb92186e4ce333edbd77396cda23;p=mothur.git

diff --git a/filterseqscommand.h b/filterseqscommand.h
index 924c366..3bf36c0 100644
--- a/filterseqscommand.h
+++ b/filterseqscommand.h
@@ -1,46 +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 "globaldata.hpp"
-#include "readfasta.h"
-#include "readnexus.h"
-#include "readclustal.h"
-#include "readseqsphylip.h"
-
-
-class FilterSeqsCommand : public Command {
-
-public:
-	FilterSeqsCommand();
-	~FilterSeqsCommand() {};
-	int execute();	
-	
-private:
-	void doHard();
-	void doTrump(Sequence);
-	void doSoft(Sequence);
-	void doVertical(Sequence);
-	string filter;	
-	int alignmentLength;
-
-	char trump;
-	bool vertical;
-	
-	GlobalData* globaldata;	
-//	ReadSeqs* readSeqs;
-//	SequenceDB* db;
-	
-
-};
-
-#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 long start;
+		unsigned long long end;
+		linePair(unsigned long long i, unsigned long long 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 long>&);
+	int MPICreateFilter(int, int, Filters&, MPI_File&, vector<unsigned long long>&);	
+	#endif
+	
+};
+
+#endif