added uchime_src folder. added biom parameter to make.shared. added biom as a current...

[mothur.git] / mothurout.h

diff --git a/mothurout.h b/mothurout.h
index 2a6ba2de6316eb24ff281d703f8e27d4c94a45a3..9ce698be4e1963e6af9abee67673ded3e1743fde 100644 (file)
--- a/mothurout.h
+++ b/mothurout.h
@@ -128,6 +128,7 @@ class MothurOut {
                void splitAtDash(string&, set<string>&);
                void splitAtDash(string&, vector<string>&);
                void splitAtChar(string&, vector<string>&, char);
+        void splitAtChar(string&, string&, char);
                int removeConfidences(string&);
                
                //math operation
@@ -162,6 +163,7 @@ class MothurOut {
                string getAccnosFile()          { return accnosfile;            }
                string getTaxonomyFile()        { return taxonomyfile;          }
                string getFlowFile()            { return flowfile;                      }
+        string getBiomFile()           { return biomfile;                      }
                string getProcessors()          { return processors;            }
                
                void setListFile(string f)                      { listfile = getFullPathName(f);                        }
@@ -184,6 +186,7 @@ class MothurOut {
                void setAccnosFile(string f)            { accnosfile = getFullPathName(f);                      }
                void setTaxonomyFile(string f)          { taxonomyfile = getFullPathName(f);            }
                void setFlowFile(string f)                      { flowfile = getFullPathName(f);                        }
+        void setBiomFile(string f)                     { biomfile = getFullPathName(f);                        }
                void setProcessors(string p)            { processors = p;                                                       }
                
                void printCurrentFiles();
@@ -217,6 +220,7 @@ class MothurOut {
                        taxonomyfile = "";
                        processors = "1";
                        flowfile = "";
+            biomfile = "";
                        gui = false;
                        printedHeaders = false;
                        commandInputsConvertError = false;
@@ -229,7 +233,7 @@ class MothurOut {
                string defaultPath, outputDir;
                string releaseDate, version;
        
-               string accnosfile, phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, designfile, taxonomyfile;
+               string accnosfile, phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, designfile, taxonomyfile, biomfile;
                string orderfile, treefile, sharedfile, ordergroupfile, relabundfile, fastafile, qualfile, sfffile, oligosfile, processors, flowfile;
 
                vector<string> Groups;