some changes while testing 1.9

[mothur.git] / filterseqscommand.h

diff --git a/filterseqscommand.h b/filterseqscommand.h
index 3c46036468401352987fb9d6cb61b48447613dab..848d08a30e29c665f028a31c9f9dd97e0a113c5d 100644 (file)
--- a/filterseqscommand.h
+++ b/filterseqscommand.h
@@ -1,61 +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 "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 num;
-               linePair(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
+#ifndef FILTERSEQSCOMMAND_H\r
+#define FILTERSEQSCOMMAND_H\r
+\r
+/*\r
+ *  filterseqscommand.h\r
+ *  Mothur\r
+ *\r
+ *  Created by Thomas Ryabin on 5/4/09.\r
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.\r
+ *\r
+ */\r
+\r
+#include "command.hpp"\r
+#include "filters.h"\r
+\r
+class Sequence;\r
+class FilterSeqsCommand : public Command {\r
+\r
+public:\r
+       FilterSeqsCommand(string);\r
+       ~FilterSeqsCommand() {};\r
+       int execute();  \r
+       void help();\r
+       \r
+private:\r
+       struct linePair {\r
+               int start;\r
+               int num;\r
+               linePair(long int i, long int j) : start(i), num(j) {}\r
+       };\r
+       vector<linePair*> lines;\r
+       vector<int> processIDS;\r
+\r
+       string vertical, filter, fasta, hard, outputDir, filterFileName;\r
+       vector<string> fastafileNames;  \r
+       int alignmentLength, processors;\r
+       vector<int> bufferSizes;\r
+       vector<string> outputNames;\r
+\r
+       char trump;\r
+       bool abort;\r
+       float soft;\r
+       int numSeqs;\r
+       \r
+       string createFilter();\r
+       int filterSequences();\r
+       int createProcessesCreateFilter(Filters&, string);\r
+       int createProcessesRunFilter(string, string);\r
+       int driverRunFilter(string, string, string, linePair*);\r
+       int driverCreateFilter(Filters& F, string filename, linePair* line);\r
+       #ifdef USE_MPI\r
+       int driverMPIRun(int, int, MPI_File&, MPI_File&, vector<long>&);\r
+       int MPICreateFilter(int, int, Filters&, MPI_File&, vector<long>&);      \r
+       #endif\r
+       int setLines(string);\r
+       \r
+       \r
+};\r
+\r
+#endif\r