X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothurout.h;h=12de987e231247a4fb195aef20054bd94dacd375;hb=d6c0a11d1cecfac18b323285e7ffadb7f58e848f;hp=fb5b432f549de88a1fa519bc83541649a0882389;hpb=f06fdb807822f8e06db003ed809c87250905cfc8;p=mothur.git

diff --git a/mothurout.h b/mothurout.h
index fb5b432..12de987 100644
--- a/mothurout.h
+++ b/mothurout.h
@@ -12,7 +12,22 @@
 
 #include "mothur.h"
 
-
+/***********************************************/
+struct logger {
+    
+    logger() {}
+    ~logger() {}
+    
+    template< class T >
+    logger& operator <<( const T& o ) {
+        cout << o; return *this;
+    }
+    
+    logger& operator<<(ostream& (*m)(ostream&) ) {
+        cout << m; return *this;
+    }
+    
+}; 
 /***********************************************/
 
 class MothurOut {
@@ -37,20 +52,33 @@ 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 long> divideFile(string, int&);
 		int divideFile(string, int&, vector<string>&);
-		vector<unsigned long int> setFilePosEachLine(string, int&);
-		vector<unsigned long int> setFilePosFasta(string, int&);
+		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);
@@ -69,7 +97,13 @@ class MothurOut {
 		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);
@@ -79,8 +113,10 @@ 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
@@ -91,6 +127,7 @@ 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);
@@ -98,6 +135,7 @@ 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;
@@ -179,7 +217,10 @@ class MothurOut {
 			processors = "1";
 			flowfile = "";
 			gui = false;
-		};
+			printedHeaders = false;
+			commandInputsConvertError = false;
+			sharedHeaderMode = "";
+		}
 		~MothurOut();
 
 		string logFileName;
@@ -189,7 +230,8 @@ class MothurOut {
 		string accnosfile, phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, designfile, taxonomyfile;
 		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&);