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 c670f37919e7da8ce3e3f3ee5d294cd4d23acd94..809c6eb69b427f8466cb97d60322e7a27b6d53ed 100644 (file)
--- a/filterseqscommand.h
+++ b/filterseqscommand.h
@@ -20,12 +20,15 @@ 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
+       \r
+       int execute(); \r
+       void help() { m->mothurOut(getHelpString()); }  \r
        \r
 private:\r
        struct linePair {\r
@@ -42,7 +45,6 @@ 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