X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothurout.h;h=77c5a804070eaa2dd3229375df999a5b9521dc92;hb=c7e8c2d15bd7cedcfdf18675cb0ea1a0dcd0e3c0;hp=b2c638a167d1ebf507106cc300231f0f693471b0;hpb=49d2b7459c5027557564b21e9487dadafbbbdc96;p=mothur.git

diff --git a/mothurout.h b/mothurout.h
index b2c638a..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
@@ -106,10 +106,12 @@ 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);
 		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.
 	
@@ -173,11 +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);			}	
@@ -196,6 +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();
@@ -231,12 +235,14 @@ class MothurOut {
 			processors = "1";
 			flowfile = "";
             biomfile = "";
+            counttablefile = "";
 			gui = false;
 			printedHeaders = false;
 			commandInputsConvertError = false;
             mothurCalling = false;
             debug = false;
 			sharedHeaderMode = "";
+            groupMode = "group";
 		}
 		~MothurOut();
 
@@ -245,7 +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;