working on adding count file to mgcluster

[mothur.git] / mothurout.h

diff --git a/mothurout.h b/mothurout.h
index b2c638a167d1ebf507106cc300231f0f693471b0..ac47d79f7d92b113f58dbe421fdbaad892b2b175 100644 (file)
--- a/mothurout.h
+++ b/mothurout.h
@@ -68,7 +68,7 @@ class MothurOut {
                //map<string, string> names;
                vector<string> binLabelsInFile;
                vector<string> currentBinLabels;
-               string saveNextLabel, argv, sharedHeaderMode;
+               string saveNextLabel, argv, sharedHeaderMode, groupMode;
                bool printedHeaders, commandInputsConvertError;
                
                //functions from mothur.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);
@@ -173,11 +174,12 @@ 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);                        }
                void setTreeFile(string f)                      { treefile = getFullPathName(f);                        }
-               void setGroupFile(string f)                     { groupfile = getFullPathName(f);                       }               
+               void setGroupFile(string f)                     { groupfile = getFullPathName(f);       groupMode = "group";            }               
                void setPhylipFile(string f)            { phylipfile = getFullPathName(f);                      }
                void setColumnFile(string f)            { columnfile = getFullPathName(f);                      }
                void setNameFile(string f)                      { namefile = 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);  groupMode = "count";    }
         void setProcessors(string p)           { processors = p; mothurOut("\nUsing " + toString(p) + " processors.\n");       }
                
                void printCurrentFiles();
@@ -231,12 +234,14 @@ class MothurOut {
                        processors = "1";
                        flowfile = "";
             biomfile = "";
+            counttablefile = "";
                        gui = false;
                        printedHeaders = false;
                        commandInputsConvertError = false;
             mothurCalling = false;
             debug = false;
                        sharedHeaderMode = "";
+            groupMode = "group";
                }
                ~MothurOut();
 
@@ -245,7 +250,7 @@ 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;