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

[mothur.git] / getlineagecommand.h

diff --git a/getlineagecommand.h b/getlineagecommand.h
index a6770614b6dfffac32f4e57ce65f451a0046085e..68f974f21461933b8feed0657bc07f86c17b4e20 100644 (file)
--- a/getlineagecommand.h
+++ b/getlineagecommand.h
@@ -23,7 +23,9 @@ class GetLineageCommand : public Command {
                vector<string> setParameters();
                string getCommandName()                 { return "get.lineage";                         }
                string getCommandCategory()             { return "Phylotype Analysis";          }
-               string getHelpString(); 
+               
+       string getHelpString(); 
+    string getOutputPattern(string);   
                string getCitation() { return "http://www.mothur.org/wiki/Get.lineage"; }
                string getDescription()         { return "gets sequences from a list, fasta, name, group, alignreport or taxonomy file from a given taxonomy or set of taxonomies"; }
 
@@ -35,11 +37,12 @@ class GetLineageCommand : public Command {
        private:
                set<string> names;
                vector<string> outputNames, listOfTaxons;
-               string fastafile, namefile, groupfile, alignfile, listfile, taxfile, outputDir, taxons;
+               string fastafile, namefile, groupfile, alignfile, countfile, listfile, taxfile, outputDir, taxons;
                bool abort, dups;
                
                int readFasta();
                int readName();
+        int readCount();
                int readGroup();
                int readAlign();
                int readList();