<= change for anova and homova. finished chimera.uchime dereplicate=t issue.

[mothur.git] / getseqscommand.h

diff --git a/getseqscommand.h b/getseqscommand.h
index c71b5f2804a71190c6919f0dc80bf80d32f15508..42070e53a57cf05c6d5674e022c602636fa374bf 100644 (file)
--- a/getseqscommand.h
+++ b/getseqscommand.h
@@ -23,8 +23,9 @@ class GetSeqsCommand : public Command {
                vector<string> setParameters();
                string getCommandName()                 { return "get.seqs";                            }
                string getCommandCategory()             { return "Sequence Processing";         }
-               string getOutputFileNameTag(string, string);
+               
        string getHelpString(); 
+    string getOutputPattern(string);   
                string getCitation() { return "http://www.mothur.org/wiki/Get.seqs"; }
                string getDescription()         { return "gets sequences from a list, fasta, name, group, alignreport, quality or taxonomy file"; }
 
@@ -35,7 +36,7 @@ class GetSeqsCommand : public Command {
        private:
                set<string> names;
                vector<string> outputNames;
-               string accnosfile, accnosfile2, fastafile, namefile, groupfile, alignfile, listfile, taxfile, qualfile, outputDir;
+               string accnosfile, accnosfile2, fastafile, namefile, countfile, groupfile, alignfile, listfile, taxfile, qualfile, outputDir;
                bool abort, dups;
     
         //for debug
@@ -44,6 +45,7 @@ class GetSeqsCommand : public Command {
                int readFasta();
                int readName();
                int readGroup();
+        int readCount();
                int readAlign();
                int readList();
                int readTax();