sffinfo bug with flow grams right index when clipQualRight=0

[mothur.git] / mothurout.h

diff --git a/mothurout.h b/mothurout.h
index 53d4250c771cdbdac15c715c44d97fabf0a92c1a..5ff0810479ab3b9f0e7e91fd6c3e8f98d0845ebb 100644 (file)
--- 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);
@@ -139,10 +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);
@@ -152,6 +159,13 @@ class MothurOut {
                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;
@@ -246,6 +260,7 @@ class MothurOut {
             debug = false;
                        sharedHeaderMode = "";
             groupMode = "group";
+            changedSeqNames = false;
                }
                ~MothurOut();