added adjustDots function to pcr.seqs, keeps sequences aligned in case where primers...

[mothur.git] / removelineagecommand.h

diff --git a/removelineagecommand.h b/removelineagecommand.h
index a5caec8e4c3e0f04ec7744489c3f27c0a495e38d..f644972c2672aa19509059c78d631ef0618eba28 100644 (file)
--- a/removelineagecommand.h
+++ b/removelineagecommand.h
@@ -23,8 +23,9 @@ class RemoveLineageCommand : public Command {
                vector<string> setParameters();
                string getCommandName()                 { return "remove.lineage";                      }
                string getCommandCategory()             { return "Phylotype Analysis";          }
-               string getOutputFileNameTag(string, string);
+               
        string getHelpString(); 
+    string getOutputPattern(string);   
                string getCitation() { return "http://www.mothur.org/wiki/Remove.lineage"; }
                string getDescription()         { return "removes sequences from a list, fasta, name, group, alignreport or taxonomy file from a given taxonomy or set of taxonomies"; }
 
@@ -34,12 +35,13 @@ class RemoveLineageCommand : public Command {
        private:
                set<string> names;
                vector<string> outputNames, listOfTaxons;
-               string fastafile, namefile, groupfile, alignfile, listfile, taxfile, outputDir, taxons;
+               string fastafile, namefile, groupfile, alignfile, listfile, countfile, taxfile, outputDir, taxons;
                bool abort, dups;
                
                int readFasta();
                int readName();
                int readGroup();
+        int readCount();
                int readAlign();
                int readList();
                int readTax();