X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=mothurout.h;h=fb5b432f549de88a1fa519bc83541649a0882389;hb=f06fdb807822f8e06db003ed809c87250905cfc8;hp=35805320227e168d6b2862fe889374fa939a0ca9;hpb=348de0f8b17d84ede77081dcf67bd6ef43496677;p=mothur.git

diff --git a/mothurout.h b/mothurout.h
index 3580532..fb5b432 100644
--- a/mothurout.h
+++ b/mothurout.h
@@ -21,8 +21,10 @@ class MothurOut {
 		static MothurOut* getInstance();
 		void setFileName(string);
 		
-		void mothurOut(string);
-		void mothurOutEndLine();
+		void mothurOut(string); //writes to cout and the logfile
+		void mothurOutEndLine(); //writes to cout and the logfile
+		void mothurOut(string, ofstream&); //writes to the ofstream, cout and the logfile
+		void mothurOutEndLine(ofstream&); //writes to the ofstream, cout and the logfile
 		void mothurOutJustToLog(string);
 		void errorOut(exception&, string, string);
 		void closeLog();
@@ -35,10 +37,16 @@ class MothurOut {
 		void setReleaseDate(string r) { releaseDate = r; }
 		string getVersion() { return version; }
 		void setVersion(string r) { version = r; }
+		vector<string> Groups;
+		vector<string> Treenames;
+		map<string, string> names;
+		vector<string> namesOfGroups;
+		string saveNextLabel, argv;
 		
 		//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);
@@ -60,6 +68,8 @@ 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);
@@ -70,6 +80,7 @@ class MothurOut {
 		int getNumSeqs(ifstream&);
 		int getNumNames(string);
 		bool isTrue(string);
+		bool isContainingOnlyDigits(string);
 	
 		
 		//string manipulation
@@ -89,7 +100,7 @@ class MothurOut {
 		unsigned int fromBase36(string);
 
 		int control_pressed;
-		bool executing;
+		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;		}
@@ -111,6 +122,8 @@ 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);			}
 		void setTreeFile(string f)			{ treefile = getFullPathName(f);			}
@@ -131,8 +144,11 @@ 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:
@@ -160,6 +176,9 @@ class MothurOut {
 			oligosfile = "";
 			accnosfile = "";
 			taxonomyfile = "";
+			processors = "1";
+			flowfile = "";
+			gui = false;
 		};
 		~MothurOut();
 
@@ -168,7 +187,7 @@ 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;
+		string orderfile, treefile, sharedfile, ordergroupfile, relabundfile, fastafile, qualfile, sfffile, oligosfile, processors, flowfile;
 
 	
 		ofstream out;