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 d62c50f55d253b7e3fd15790e2a6d4b21cb35b8f..68f974f21461933b8feed0657bc07f86c17b4e20 100644 (file)
--- a/getlineagecommand.h
+++ b/getlineagecommand.h
@@ -23,8 +23,12 @@ 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"; }
+
        
                int execute(); 
                void help() { m->mothurOut(getHelpString()); }  
@@ -32,17 +36,17 @@ class GetLineageCommand : public Command {
        
        private:
                set<string> names;
-               vector<string> outputNames;
-               string fastafile, namefile, groupfile, alignfile, listfile, taxfile, outputDir, taxons;
+               vector<string> outputNames, listOfTaxons;
+               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();
                int readTax();  
-               string removeConfidences(string);
                vector< map<string, float> > getTaxons(string);
 };