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 5b7c43ed65808f7038b3c46cb96f3b7a32b8849a..68f974f21461933b8feed0657bc07f86c17b4e20 100644 (file)
--- a/getlineagecommand.h
+++ b/getlineagecommand.h
@@ -18,28 +18,35 @@ class GetLineageCommand : public Command {
        
                GetLineageCommand(string);
                GetLineageCommand();
-               ~GetLineageCommand(){};
-               vector<string> getRequiredParameters();
-               vector<string> getValidParameters();
-               vector<string> getRequiredFiles();
-               map<string, vector<string> > getOutputFiles() { return outputTypes; }
-               int execute();
-               void help();    
+               ~GetLineageCommand(){}
+       
+               vector<string> setParameters();
+               string getCommandName()                 { return "get.lineage";                         }
+               string getCommandCategory()             { return "Phylotype Analysis";          }
                
+       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()); }  
+       
+       
        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;
-               map<string, vector<string> > outputTypes;
                
                int readFasta();
                int readName();
+        int readCount();
                int readGroup();
                int readAlign();
                int readList();
                int readTax();  
-               string removeConfidences(string);
                vector< map<string, float> > getTaxons(string);
 };