X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothurout.h;h=d2a36b351902f3bc25d7c2132fb2c20f15421b23;hb=8dd3c225255d7084e3aff8740aa4f1f1cabb367a;hp=57d3f7647dabf43dd30f2caeefa9ae2bd09a0d30;hpb=65f2be9d8f9b4cf72b4aafd800fdd11ad26435fd;p=mothur.git

diff --git a/mothurout.h b/mothurout.h
index 57d3f76..d2a36b3 100644
--- a/mothurout.h
+++ b/mothurout.h
@@ -12,7 +12,6 @@
 
 #include "mothur.h"
 
-
 /***********************************************/
 
 class MothurOut {
@@ -21,8 +20,10 @@ 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();
@@ -35,19 +36,33 @@ class MothurOut {
 		void setReleaseDate(string r) { releaseDate = r; }
 		string getVersion() { return version; }
 		void setVersion(string r) { version = r; }
-		vector<string> Groups;
+	
+		void addGroup(string g) { Groups.push_back(g); }
+		void setGroups(vector<string>& g) { sort(g.begin(), g.end()); Groups = g; }
+		void clearGroups() { Groups.clear(); }
+	    int getNumGroups() { return Groups.size(); }
+		vector<string> getGroups() { sort(Groups.begin(), Groups.end()); return Groups; }
+		void addAllGroup(string g) { namesOfGroups.push_back(g); }
+		void setAllGroups(vector<string>& g) { sort(g.begin(), g.end()); namesOfGroups = g; }
+		void clearAllGroups() { namesOfGroups.clear(); }
+		int getNumAllGroups() { return namesOfGroups.size(); }
+	
+		vector<string> getAllGroups() { sort(namesOfGroups.begin(), namesOfGroups.end()); return namesOfGroups; }
 		vector<string> Treenames;
 		map<string, string> names;
-		vector<string> namesOfGroups;
-		string saveNextLabel, argv;
+		vector<string> binLabelsInFile;
+		vector<string> currentBinLabels;
+		string saveNextLabel, argv, sharedHeaderMode;
+		bool printedHeaders, commandInputsConvertError;
 		
 		//functions from mothur.h
 		//file operations
-		vector<unsigned long int> divideFile(string, int&);
-		vector<unsigned long int> setFilePosEachLine(string, int&);
-		vector<unsigned long int> setFilePosFasta(string, int&);
+		vector<unsigned long long> divideFile(string, int&);
+		int divideFile(string, int&, vector<string>&);
+		vector<unsigned long long> setFilePosEachLine(string, int&);
+		vector<unsigned long long> setFilePosFasta(string, int&);
 		string sortFile(string, string);
-		void appendFiles(string, string);
+		int appendFiles(string, string);
 		int renameFile(string, string); //oldname, newname
 		string getFullPathName(string);
 		string hasPath(string);
@@ -65,6 +80,14 @@ class MothurOut {
 		void gobble(istream&);
 		void gobble(istringstream&);
 		map<string, int> readNames(string);
+		int readNames(string, map<string, string>&);
+		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, 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.
+	
 		
 		//searchs and checks
 		bool checkReleaseVersion(ifstream&, string);
@@ -74,8 +97,10 @@ class MothurOut {
 		void getNumSeqs(ifstream&, int&);
 		int getNumSeqs(ifstream&);
 		int getNumNames(string);
+		int getNumChar(string, char);
 		bool isTrue(string);
 		bool isContainingOnlyDigits(string);
+		bool isNumeric1(string);
 	
 		
 		//string manipulation
@@ -86,6 +111,7 @@ class MothurOut {
 		void splitAtDash(string&, set<string>&);
 		void splitAtDash(string&, vector<string>&);
 		void splitAtChar(string&, vector<string>&, char);
+		int removeConfidences(string&);
 		
 		//math operation
 		int factorial(int num);
@@ -93,6 +119,7 @@ class MothurOut {
 		float ceilDist(float, int);
 		float roundDist(float, int);
 		unsigned int fromBase36(string);
+		int getRandomIndex(int); //highest
 
 		int control_pressed;
 		bool executing, runParse, jumble, gui;
@@ -117,6 +144,7 @@ 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 +166,11 @@ 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:
@@ -169,8 +199,12 @@ class MothurOut {
 			accnosfile = "";
 			taxonomyfile = "";
 			processors = "1";
+			flowfile = "";
 			gui = false;
-		};
+			printedHeaders = false;
+			commandInputsConvertError = false;
+			sharedHeaderMode = "";
+		}
 		~MothurOut();
 
 		string logFileName;
@@ -178,9 +212,10 @@ 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;
 
-	
+		vector<string> Groups;
+		vector<string> namesOfGroups;
 		ofstream out;
 		
 		int mem_usage(double&, double&);