X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothurout.h;h=77c5a804070eaa2dd3229375df999a5b9521dc92;hb=529ec122f7cac4af987e121d150b878d7c7a0d5d;hp=968ff97221ab7e277dfba48efc01682648998f0f;hpb=957d67f7d8bbadfd2930de061e89fd9b149270fd;p=mothur.git

diff --git a/mothurout.h b/mothurout.h
index 968ff97..77c5a80 100644
--- 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
@@ -111,6 +111,7 @@ class MothurOut {
 		int readNames(string, vector<seqPriorityNode>&, map<string, string>&);
 		int mothurRemove(string);
 		bool mothurConvert(string, int&); //use for converting user inputs. Sets commandInputsConvertError to true if error occurs. Engines check this.
+        bool mothurConvert(string, intDist&); //use for converting user inputs. Sets commandInputsConvertError to true if error occurs. Engines check this.
 		bool mothurConvert(string, float&); //use for converting user inputs. Sets commandInputsConvertError to true if error occurs. Engines check this.
 		bool mothurConvert(string, double&); //use for converting user inputs. Sets commandInputsConvertError to true if error occurs. Engines check this.
 	
@@ -174,11 +175,12 @@ 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);			}	
@@ -197,6 +199,7 @@ 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();
@@ -232,12 +235,14 @@ class MothurOut {
 			processors = "1";
 			flowfile = "";
             biomfile = "";
+            counttablefile = "";
 			gui = false;
 			printedHeaders = false;
 			commandInputsConvertError = false;
             mothurCalling = false;
             debug = false;
 			sharedHeaderMode = "";
+            groupMode = "group";
 		}
 		~MothurOut();
 
@@ -246,7 +251,7 @@ 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;