X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothurout.h;h=968ff97221ab7e277dfba48efc01682648998f0f;hb=957d67f7d8bbadfd2930de061e89fd9b149270fd;hp=0659e4e3628ccb28fdfc024427fe6cebf5af5446;hpb=eb4bb52af987ff4df7354d95d60cd763aec537e1;p=mothur.git

diff --git a/mothurout.h b/mothurout.h
index 0659e4e..968ff97 100644
--- a/mothurout.h
+++ b/mothurout.h
@@ -65,7 +65,7 @@ class MothurOut {
 	
 		vector<string> getAllGroups() { sort(namesOfGroups.begin(), namesOfGroups.end()); return namesOfGroups; }
 		vector<string> Treenames;
-		map<string, string> names;
+		//map<string, string> names;
 		vector<string> binLabelsInFile;
 		vector<string> currentBinLabels;
 		string saveNextLabel, argv, sharedHeaderMode;
@@ -82,6 +82,7 @@ class MothurOut {
 		int appendFiles(string, string);
 		int renameFile(string, string); //oldname, newname
 		string getFullPathName(string);
+        string findProgramPath(string programName);
 		string hasPath(string);
 		string getExtension(string);
 		string getPathName(string);
@@ -96,8 +97,16 @@ class MothurOut {
 		string getline(istringstream&);
 		void gobble(istream&);
 		void gobble(istringstream&);
-		map<string, int> readNames(string);
+        vector<string> splitWhiteSpace(string& rest, char[], int);
+        vector<string> splitWhiteSpace(string);
+        set<string> readAccnos(string);
+        int readAccnos(string, vector<string>&);
+        map<string, int> readNames(string);
+        int readTax(string, map<string, string>&);
+        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);
@@ -128,7 +137,9 @@ class MothurOut {
 		void splitAtDash(string&, set<string>&);
 		void splitAtDash(string&, vector<string>&);
 		void splitAtChar(string&, vector<string>&, char);
+        void splitAtChar(string&, string&, char);
 		int removeConfidences(string&);
+        string makeList(vector<string>&);
 		
 		//math operation
 		int factorial(int num);
@@ -139,9 +150,9 @@ class MothurOut {
 		int getRandomIndex(int); //highest
 
 		int control_pressed;
-		bool executing, runParse, jumble, gui, mothurCalling;
+		bool executing, runParse, jumble, gui, mothurCalling, debug;
 		
-		//current files - if you add a new type you must edit optionParser->getParameters, get.current command and mothurOut->printCurrentFiles/clearCurrentFiles.
+		//current files - if you add a new type you must edit optionParser->getParameters, get.current command and mothurOut->printCurrentFiles/clearCurrentFiles/getCurrentTypes.
 		string getPhylipFile()		{ return phylipfile;		}
 		string getColumnFile()		{ return columnfile;		}
 		string getListFile()		{ return listfile;			}
@@ -162,6 +173,7 @@ class MothurOut {
 		string getAccnosFile()		{ return accnosfile;		}
 		string getTaxonomyFile()	{ return taxonomyfile;		}
 		string getFlowFile()		{ return flowfile;			}
+        string getBiomFile()		{ return biomfile;			}
 		string getProcessors()		{ return processors;		}
 		
 		void setListFile(string f)			{ listfile = getFullPathName(f);			}
@@ -184,11 +196,13 @@ class MothurOut {
 		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 setBiomFile(string f)			{ biomfile = getFullPathName(f);			}
+        void setProcessors(string p)		{ processors = p; mothurOut("\nUsing " + toString(p) + " processors.\n");	}
 		
 		void printCurrentFiles();
 		bool hasCurrentFiles();
 		void clearCurrentFiles();
+        set<string> getCurrentTypes(); 
 		
 	private:
 		static MothurOut* _uniqueInstance;
@@ -217,10 +231,12 @@ class MothurOut {
 			taxonomyfile = "";
 			processors = "1";
 			flowfile = "";
+            biomfile = "";
 			gui = false;
 			printedHeaders = false;
 			commandInputsConvertError = false;
             mothurCalling = false;
+            debug = false;
 			sharedHeaderMode = "";
 		}
 		~MothurOut();
@@ -229,7 +245,7 @@ class MothurOut {
 		string defaultPath, outputDir;
 		string releaseDate, version;
 	
-		string accnosfile, phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, designfile, taxonomyfile;
+		string accnosfile, phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, designfile, taxonomyfile, biomfile;
 		string orderfile, treefile, sharedfile, ordergroupfile, relabundfile, fastafile, qualfile, sfffile, oligosfile, processors, flowfile;
 
 		vector<string> Groups;