added otu.association command. added calcSpearman, calcKendall and calcPearson functi...

[mothur.git] / filterseqscommand.h

diff --git a/filterseqscommand.h b/filterseqscommand.h
index c670f37919e7da8ce3e3f3ee5d294cd4d23acd94..3bf36c040231c5f801281f9d553c60bed01101c8 100644 (file)
--- a/filterseqscommand.h
+++ b/filterseqscommand.h
@@ -20,18 +20,22 @@ public:
        FilterSeqsCommand(string);\r
        FilterSeqsCommand();\r
        ~FilterSeqsCommand() {};\r
-       vector<string> getRequiredParameters();\r
-       vector<string> getValidParameters();\r
-       vector<string> getRequiredFiles();\r
-       map<string, vector<string> > getOutputFiles() { return outputTypes; }\r
-       int execute();  \r
-       void help();\r
+       \r
+       vector<string> setParameters();\r
+       string getCommandName()                 { return "filter.seqs";                 }\r
+       string getCommandCategory()             { return "Sequence Processing"; }\r
+       string getHelpString(); \r
+       string getCitation() { return "http://www.mothur.org/wiki/Filter.seqs"; }\r
+       string getDescription()         { return "removes columns from alignments based on a criteria defined by the user"; }\r
+       \r
+       int execute(); \r
+       void help() { m->mothurOut(getHelpString()); }  \r
        \r
 private:\r
        struct linePair {\r
-               unsigned long int start;\r
-               unsigned long int end;\r
-               linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}\r
+               unsigned long long start;\r
+               unsigned long long end;\r
+               linePair(unsigned long long i, unsigned long long j) : start(i), end(j) {}\r
        };\r
 \r
        vector<linePair*> lines;\r
@@ -42,7 +46,6 @@ private:
        int alignmentLength, processors;\r
        vector<int> bufferSizes;\r
        vector<string> outputNames;\r
-       map<string, vector<string> > outputTypes;\r
 \r
        char trump;\r
        bool abort;\r
@@ -56,8 +59,8 @@ private:
        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<unsigned long int>&);\r
-       int MPICreateFilter(int, int, Filters&, MPI_File&, vector<unsigned long int>&); \r
+       int driverMPIRun(int, int, MPI_File&, MPI_File&, vector<unsigned long long>&);\r
+       int MPICreateFilter(int, int, Filters&, MPI_File&, vector<unsigned long long>&);        \r
        #endif\r
        \r
 };\r