fixed get.lienage and remove.lineage bug with confidence scores that are floats....

[mothur.git] / getlineagecommand.h

diff --git a/getlineagecommand.h b/getlineagecommand.h
index 0d07ac6193f37807a25247df864f762e67369d58..5b7c43ed65808f7038b3c46cb96f3b7a32b8849a 100644 (file)
--- a/getlineagecommand.h
+++ b/getlineagecommand.h
@@ -17,7 +17,12 @@ class GetLineageCommand : public Command {
        public:
        
                GetLineageCommand(string);
+               GetLineageCommand();
                ~GetLineageCommand(){};
+               vector<string> getRequiredParameters();
+               vector<string> getValidParameters();
+               vector<string> getRequiredFiles();
+               map<string, vector<string> > getOutputFiles() { return outputTypes; }
                int execute();
                void help();    
                
@@ -26,6 +31,7 @@ class GetLineageCommand : public Command {
                vector<string> outputNames;
                string fastafile, namefile, groupfile, alignfile, listfile, taxfile, outputDir, taxons;
                bool abort, dups;
+               map<string, vector<string> > outputTypes;
                
                int readFasta();
                int readName();
@@ -34,6 +40,7 @@ class GetLineageCommand : public Command {
                int readList();
                int readTax();  
                string removeConfidences(string);
+               vector< map<string, float> > getTaxons(string);
 };
 
 #endif