added sparseDistanceMatrix class. Modified cluster commands to use the new sparse...

[mothur.git] / getlineagecommand.h

diff --git a/getlineagecommand.h b/getlineagecommand.h
index 6375b9483fb335bafde123f3e99e4620c2614234..0ab042bac365b64840e32212a6705f62d46d5ff1 100644 (file)
--- a/getlineagecommand.h
+++ b/getlineagecommand.h
@@ -23,7 +23,11 @@ class GetLineageCommand : public Command {
                vector<string> setParameters();
                string getCommandName()                 { return "get.lineage";                         }
                string getCommandCategory()             { return "Phylotype Analysis";          }
-               string getHelpString(); 
+               string getOutputFileNameTag(string, string);
+       string getHelpString(); 
+               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()); }  
@@ -31,7 +35,7 @@ class GetLineageCommand : public Command {
        
        private:
                set<string> names;
-               vector<string> outputNames;
+               vector<string> outputNames, listOfTaxons;
                string fastafile, namefile, groupfile, alignfile, listfile, taxfile, outputDir, taxons;
                bool abort, dups;
                
@@ -41,7 +45,6 @@ class GetLineageCommand : public Command {
                int readAlign();
                int readList();
                int readTax();  
-               string removeConfidences(string);
                vector< map<string, float> > getTaxons(string);
 };