Merge remote-tracking branch 'origin/master'

[mothur.git] / mothurout.h

diff --git a/mothurout.h b/mothurout.h
index b2c638a167d1ebf507106cc300231f0f693471b0..98565dc547d1e81dc03d88c9a526983727c1b124 100644 (file)
--- a/mothurout.h
+++ b/mothurout.h
@@ -106,6 +106,7 @@ class MothurOut {
         int readNames(string, map<string, string>&, map<string, int>&);
                int readNames(string, map<string, string>&);
         int readNames(string, map<string, string>&, bool);
+        int readNames(string, map<string, string>&, int);
                int readNames(string, map<string, vector<string> >&);
                int readNames(string, vector<seqPriorityNode>&, map<string, string>&);
                int mothurRemove(string);
@@ -173,6 +174,7 @@ class MothurOut {
                string getTaxonomyFile()        { return taxonomyfile;          }
                string getFlowFile()            { return flowfile;                      }
         string getBiomFile()           { return biomfile;                      }
+        string getCountTableFile()     { return counttablefile;        }
                string getProcessors()          { return processors;            }
                
                void setListFile(string f)                      { listfile = getFullPathName(f);                        }
@@ -196,6 +198,7 @@ class MothurOut {
                void setTaxonomyFile(string f)          { taxonomyfile = getFullPathName(f);            }
                void setFlowFile(string f)                      { flowfile = getFullPathName(f);                        }
         void setBiomFile(string f)                     { biomfile = getFullPathName(f);                        }
+        void setCountTableFile(string f)       { counttablefile = getFullPathName(f);          }
         void setProcessors(string p)           { processors = p; mothurOut("\nUsing " + toString(p) + " processors.\n");       }
                
                void printCurrentFiles();
@@ -231,6 +234,7 @@ class MothurOut {
                        processors = "1";
                        flowfile = "";
             biomfile = "";
+            counttablefile = "";
                        gui = false;
                        printedHeaders = false;
                        commandInputsConvertError = false;
@@ -245,7 +249,7 @@ class MothurOut {
                string releaseDate, version;
        
                string accnosfile, phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, designfile, taxonomyfile, biomfile;
-               string orderfile, treefile, sharedfile, ordergroupfile, relabundfile, fastafile, qualfile, sfffile, oligosfile, processors, flowfile;
+               string orderfile, treefile, sharedfile, ordergroupfile, relabundfile, fastafile, qualfile, sfffile, oligosfile, processors, flowfile, counttablefile;
 
                vector<string> Groups;
                vector<string> namesOfGroups;