X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=filterseqscommand.h;h=2ec152bb557eb27970c3660136b1b879f658949d;hb=bbdb72971ea4cd171abe34985af89f97bc2a31d3;hp=9e703ceeb62c2d610776c7f245980de651ab28a1;hpb=3117b1c3109121dff476997d3c5db5b47a77729b;p=mothur.git

diff --git a/filterseqscommand.h b/filterseqscommand.h
index 9e703ce..2ec152b 100644
--- a/filterseqscommand.h
+++ b/filterseqscommand.h
@@ -1,48 +1,60 @@
-#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 "mothur.h"
-#include "globaldata.hpp"
-#include "readfasta.h"
-#include "readnexus.h"
-#include "readclustal.h"
-#include "readseqsphylip.h"
-
-using namespace std;
-
-class FilterSeqsCommand : public Command {
-
-public:
-	FilterSeqsCommand() {};
-	~FilterSeqsCommand() {};
-	int execute();	
-	
-private:
-	void doTrump();
-	void doSoft();
-	void doFilter();
-	
-	GlobalData* globaldata;
-	string filename, trump, filter;
-	
-	ReadFasta* readFasta;
-	ReadNexus* readNexus;
-	ReadClustal* readClustal;
-	ReadPhylip* readPhylip;
-	
-	vector<bool> columnsToRemove;
-	SequenceDB* db;
-	double soft;
-};
-
-#endif
\ No newline at end of file
+#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() {};
+	int execute();	
+	void help();
+	
+private:
+	struct linePair {
+		unsigned long int start;
+		int num;
+		linePair(unsigned long int i, long int j) : start(i), num(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<long>&);
+	int MPICreateFilter(int, int, Filters&, MPI_File&, vector<long>&);	
+	#endif
+	int setLines(string);
+	
+	
+};
+
+#endif