X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothurout.h;h=7b71fcfbd48c823db529f0bc8d1a54f78422543d;hb=1c898913f53fe4c6574102896b967d9347d1b42a;hp=f20d5c197df59b06c3f5069709aa4e036436a768;hpb=10c8178dc5e3f96ef8e92a986f1eddd13e622173;p=mothur.git

diff --git a/mothurout.h b/mothurout.h
index f20d5c1..7b71fcf 100644
--- a/mothurout.h
+++ b/mothurout.h
@@ -44,6 +44,7 @@ class MothurOut {
 		//functions from mothur.h
 		//file operations
 		vector<unsigned long int> divideFile(string, int&);
+		int divideFile(string, int&, vector<string>&);
 		vector<unsigned long int> setFilePosEachLine(string, int&);
 		vector<unsigned long int> setFilePosFasta(string, int&);
 		string sortFile(string, string);
@@ -65,6 +66,8 @@ class MothurOut {
 		void gobble(istream&);
 		void gobble(istringstream&);
 		map<string, int> readNames(string);
+		int readNames(string, map<string, string>&);
+		int readNames(string, vector<seqPriorityNode>&, map<string, string>&);
 		
 		//searchs and checks
 		bool checkReleaseVersion(ifstream&, string);
@@ -95,7 +98,7 @@ class MothurOut {
 		unsigned int fromBase36(string);
 
 		int control_pressed;
-		bool executing, runParse, jumble;
+		bool executing, runParse, jumble, gui;
 		
 		//current files - if you add a new type you must edit optionParser->getParameters, get.current command and mothurOut->printCurrentFiles/clearCurrentFiles.
 		string getPhylipFile()		{ return phylipfile;		}
@@ -117,6 +120,7 @@ class MothurOut {
 		string getOligosFile()		{ return oligosfile;		}
 		string getAccnosFile()		{ return accnosfile;		}
 		string getTaxonomyFile()	{ return taxonomyfile;		}
+		string getFlowFile()		{ return flowfile;			}
 		string getProcessors()		{ return processors;		}
 		
 		void setListFile(string f)			{ listfile = getFullPathName(f);			}
@@ -138,9 +142,11 @@ class MothurOut {
 		void setOligosFile(string f)		{ oligosfile = getFullPathName(f);			}
 		void setAccnosFile(string f)		{ accnosfile = getFullPathName(f);			}
 		void setTaxonomyFile(string f)		{ taxonomyfile = getFullPathName(f);		}
+		void setFlowFile(string f)			{ flowfile = getFullPathName(f);			}
 		void setProcessors(string p)		{ processors = p;							}
 		
 		void printCurrentFiles();
+		bool hasCurrentFiles();
 		void clearCurrentFiles();
 		
 	private:
@@ -169,6 +175,8 @@ class MothurOut {
 			accnosfile = "";
 			taxonomyfile = "";
 			processors = "1";
+			flowfile = "";
+			gui = false;
 		};
 		~MothurOut();
 
@@ -177,7 +185,7 @@ class MothurOut {
 		string releaseDate, version;
 	
 		string accnosfile, phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, designfile, taxonomyfile;
-		string orderfile, treefile, sharedfile, ordergroupfile, relabundfile, fastafile, qualfile, sfffile, oligosfile, processors;
+		string orderfile, treefile, sharedfile, ordergroupfile, relabundfile, fastafile, qualfile, sfffile, oligosfile, processors, flowfile;
 
 	
 		ofstream out;