working on pam

[mothur.git] / mothurout.h

diff --git a/mothurout.h b/mothurout.h
index 77b1b6d4ec1efb758973d332aa8e4df00619f58b..1747b1480c732ae42f361940ff57dcbe151bbc7b 100644 (file)
--- a/mothurout.h
+++ b/mothurout.h
@@ -66,11 +66,11 @@ class MothurOut {
        
                vector<string> getAllGroups() { sort(namesOfGroups.begin(), namesOfGroups.end()); return namesOfGroups; }
                vector<string> Treenames;
-               //map<string, string> names;
-               vector<string> binLabelsInFile;
-               vector<string> currentBinLabels;
+               vector<string> sharedBinLabelsInFile;
+               vector<string> currentSharedBinLabels;
+        vector<string> listBinLabelsInFile;
                string saveNextLabel, argv, sharedHeaderMode, groupMode;
-               bool printedHeaders, commandInputsConvertError, changedSeqNames, modifyNames;
+               bool printedSharedHeaders, printedListHeaders, commandInputsConvertError, changedSeqNames, modifyNames;
                
                //functions from mothur.h
                //file operations
@@ -82,6 +82,7 @@ class MothurOut {
                vector<unsigned long long> setFilePosFasta(string, int&);
                string sortFile(string, string);
                int appendFiles(string, string);
+        int appendBinaryFiles(string, string);
         int appendFilesWithoutHeaders(string, string);
                int renameFile(string, string); //oldname, newname
                string getFullPathName(string);
@@ -93,9 +94,15 @@ class MothurOut {
                string getRootName(string);
                bool isBlank(string);
                int openOutputFile(string, ofstream&);
+        int openOutputFileBinary(string, ofstream&);
                int openOutputFileAppend(string, ofstream&);
+        int openOutputFileBinaryAppend(string, ofstream&);
                int openInputFile(string, ifstream&);
-               int openInputFile(string, ifstream&, string); //no error given 
+        int openInputFileBinary(string, ifstream&);
+        int openInputFileBinary(string, ifstream&, string);
+               int openInputFile(string, ifstream&, string); //no error given
+    
+        bool checkLocations(string&, string);  //filename, inputDir. checks for file in ./, inputdir, default and mothur's exe location.  Returns false if cant be found. If found completes name with location
                string getline(ifstream&);
                string getline(istringstream&);
                void gobble(istream&);
@@ -136,6 +143,9 @@ class MothurOut {
                bool isTrue(string);
                bool isContainingOnlyDigits(string);
                bool isNumeric1(string);
+        bool isLabelEquivalent(string, string);
+        string getSimpleLabel(string);
+        string findEdianness();
        
                
                //string manipulation
@@ -156,11 +166,14 @@ class MothurOut {
         map<string, vector<string> > parseClasses(string);
                
                //math operation
+        double max(vector<double>&); //returns largest value in vector
+        double min(vector<double>&); //returns smallest value in vector
                int factorial(int num);
                vector<vector<double> > binomial(int);
                float ceilDist(float, int);
                float roundDist(float, int);
                unsigned int fromBase36(string);
+        double median(vector<double>);
                int getRandomIndex(int); //highest
         double getStandardDeviation(vector<int>&);
         vector<double> getStandardDeviation(vector< vector<double> >&);
@@ -262,7 +275,8 @@ class MothurOut {
             counttablefile = "";
             summaryfile = "";
                        gui = false;
-                       printedHeaders = false;
+                       printedSharedHeaders = false;
+            printedListHeaders = false;
                        commandInputsConvertError = false;
             mothurCalling = false;
             debug = false;