added count.seqs command and made some modifcations to the uchime code to allow it...

[mothur.git] / filterseqscommand.h

diff --git a/filterseqscommand.h b/filterseqscommand.h
index e068405816e3d8c0bc1e21b2fb8316f779009526..809c6eb69b427f8466cb97d60322e7a27b6d53ed 100644 (file)
--- a/filterseqscommand.h
+++ b/filterseqscommand.h
@@ -18,16 +18,25 @@ class FilterSeqsCommand : public Command {
 \r
 public:\r
        FilterSeqsCommand(string);\r
+       FilterSeqsCommand();\r
        ~FilterSeqsCommand() {};\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
+       \r
+       int execute(); \r
+       void help() { m->mothurOut(getHelpString()); }  \r
        \r
 private:\r
        struct linePair {\r
                unsigned long int start;\r
-               int num;\r
-               linePair(unsigned long int i, long int j) : start(i), num(j) {}\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
@@ -52,8 +61,6 @@ private:
        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