bug fixes

[mothur.git] / filterseqscommand.h

diff --git a/filterseqscommand.h b/filterseqscommand.h
index 848d08a30e29c665f028a31c9f9dd97e0a113c5d..c670f37919e7da8ce3e3f3ee5d294cd4d23acd94 100644 (file)
--- a/filterseqscommand.h
+++ b/filterseqscommand.h
@@ -18,16 +18,22 @@ class FilterSeqsCommand : public Command {
 \r
 public:\r
        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
 private:\r
        struct linePair {\r
-               int start;\r
-               int num;\r
-               linePair(long int i, long int j) : start(i), num(j) {}\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
        };\r
+\r
        vector<linePair*> lines;\r
        vector<int> processIDS;\r
 \r
@@ -36,6 +42,7 @@ 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
@@ -49,11 +56,9 @@ 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<long>&);\r
-       int MPICreateFilter(int, int, Filters&, MPI_File&, vector<long>&);      \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
        #endif\r
-       int setLines(string);\r
-       \r
        \r
 };\r
 \r