added pipeline commands which involved change to command factory and command class...

[mothur.git] / filterseqscommand.h

diff --git a/filterseqscommand.h b/filterseqscommand.h
index cb02732d1ede7c7a70ec5a518426bca18a0019bf..c670f37919e7da8ce3e3f3ee5d294cd4d23acd94 100644 (file)
--- a/filterseqscommand.h
+++ b/filterseqscommand.h
@@ -18,7 +18,12 @@ 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
@@ -37,6 +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