X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=mothurout.h;h=5ff0810479ab3b9f0e7e91fd6c3e8f98d0845ebb;hp=33384034ae55ee7f11c72b48378fa59bfe29e16e;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=5b72d1cf3fa48730e5bb70d59cced1e43e1fe424

diff --git a/mothurout.h b/mothurout.h
index 3338403..5ff0810 100644
--- a/mothurout.h
+++ b/mothurout.h
@@ -69,17 +69,19 @@ class MothurOut {
 		vector<string> binLabelsInFile;
 		vector<string> currentBinLabels;
 		string saveNextLabel, argv, sharedHeaderMode, groupMode;
-		bool printedHeaders, commandInputsConvertError;
+		bool printedHeaders, commandInputsConvertError, changedSeqNames;
 		
 		//functions from mothur.h
 		//file operations
         bool dirCheck(string&); //completes path, appends appropriate / or \, makes sure dir is writable.
-		vector<unsigned long long> divideFile(string, int&);
+		vector<unsigned long long> divideFile(string, int&); //divides splitting unevenness by sequence
+        vector<unsigned long long> divideFilePerLine(string, int&); //divides splitting unevenness at line breaks
 		int divideFile(string, int&, vector<string>&);
 		vector<unsigned long long> setFilePosEachLine(string, int&);
 		vector<unsigned long long> setFilePosFasta(string, int&);
 		string sortFile(string, string);
 		int appendFiles(string, string);
+        int appendFilesWithoutHeaders(string, string);
 		int renameFile(string, string); //oldname, newname
 		string getFullPathName(string);
         string findProgramPath(string programName);
@@ -102,6 +104,7 @@ class MothurOut {
         set<string> readAccnos(string);
         int readAccnos(string, vector<string>&);
         map<string, int> readNames(string);
+        map<string, int> readNames(string, unsigned long int&);
         int readTax(string, map<string, string>&);
         int readNames(string, map<string, string>&, map<string, int>&);
 		int readNames(string, map<string, string>&);
@@ -120,7 +123,9 @@ class MothurOut {
 		bool checkReleaseVersion(ifstream&, string);
 		bool anyLabelsToProcess(string, set<string>&, string);
 		bool inUsersGroups(vector<string>, vector<string>);
+        bool inUsersGroups(vector<int>, vector< vector<int> >);
 		bool inUsersGroups(string, vector<string>);
+        bool inUsersGroups(int, vector<int>);
 		void getNumSeqs(ifstream&, int&);
 		int getNumSeqs(ifstream&);
 		int getNumNames(string);
@@ -139,9 +144,12 @@ class MothurOut {
 		void splitAtDash(string&, vector<string>&);
 		void splitAtChar(string&, vector<string>&, char);
         void splitAtChar(string&, string&, char);
+        vector<string> splitWhiteSpaceWithQuotes(string);
 		int removeConfidences(string&);
+        string removeQuotes(string);
         string makeList(vector<string>&);
         bool isSubset(vector<string>, vector<string>); //bigSet, subset
+        int checkName(string&);
 		
 		//math operation
 		int factorial(int num);
@@ -150,6 +158,14 @@ class MothurOut {
 		float roundDist(float, int);
 		unsigned int fromBase36(string);
 		int getRandomIndex(int); //highest
+        double getStandardDeviation(vector<int>&);
+        vector<double> getStandardDeviation(vector< vector<double> >&);
+        vector<double> getStandardDeviation(vector< vector<double> >&, vector<double>&);
+        vector<double> getAverages(vector< vector<double> >&);
+        vector< vector<seqDist> > getStandardDeviation(vector< vector< vector<seqDist> > >&);
+        vector< vector<seqDist> > getStandardDeviation(vector< vector< vector<seqDist> > >&, vector< vector<seqDist> >&);
+        vector< vector<seqDist> > getAverages(vector< vector< vector<seqDist> > >&, string);
+        vector< vector<seqDist> > getAverages(vector< vector< vector<seqDist> > >&);
 
 		int control_pressed;
 		bool executing, runParse, jumble, gui, mothurCalling, debug;
@@ -244,6 +260,7 @@ class MothurOut {
             debug = false;
 			sharedHeaderMode = "";
             groupMode = "group";
+            changedSeqNames = false;
 		}
 		~MothurOut();