working on pam

[mothur.git] / mothurout.h

diff --git a/mothurout.h b/mothurout.h
index 4a46e051b67bb08caee8c4d97f3947c366d01926..1747b1480c732ae42f361940ff57dcbe151bbc7b 100644 (file)
--- a/mothurout.h
+++ b/mothurout.h
@@ -40,6 +40,7 @@ class MothurOut {
                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 mothurOutJustToScreen(string); //writes to cout
                void mothurOutJustToLog(string);
                void errorOut(exception&, string, string);
                void closeLog();
@@ -65,11 +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;
+               bool printedSharedHeaders, printedListHeaders, commandInputsConvertError, changedSeqNames, modifyNames;
                
                //functions from mothur.h
                //file operations
@@ -81,6 +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);
@@ -92,9 +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&);
@@ -106,6 +114,8 @@ class MothurOut {
         map<string, int> readNames(string);
         map<string, int> readNames(string, unsigned long int&);
         int readTax(string, map<string, string>&);
+        vector<consTax> readConsTax(string);
+        int readConsTax(string, map<string, consTax2>&);
         int readNames(string, map<string, string>&, map<string, int>&);
                int readNames(string, map<string, string>&);
         int readNames(string, map<string, string>&, bool);
@@ -133,6 +143,9 @@ class MothurOut {
                bool isTrue(string);
                bool isContainingOnlyDigits(string);
                bool isNumeric1(string);
+        bool isLabelEquivalent(string, string);
+        string getSimpleLabel(string);
+        string findEdianness();
        
                
                //string manipulation
@@ -150,18 +163,23 @@ class MothurOut {
         string makeList(vector<string>&);
         bool isSubset(vector<string>, vector<string>); //bigSet, subset
         int checkName(string&);
+        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> >&);
         vector<double> getStandardDeviation(vector< vector<double> >&, vector<double>&);
         vector<double> getAverages(vector< vector<double> >&);
+        double getAverage(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);
@@ -257,13 +275,15 @@ class MothurOut {
             counttablefile = "";
             summaryfile = "";
                        gui = false;
-                       printedHeaders = false;
+                       printedSharedHeaders = false;
+            printedListHeaders = false;
                        commandInputsConvertError = false;
             mothurCalling = false;
             debug = false;
                        sharedHeaderMode = "";
             groupMode = "group";
             changedSeqNames = false;
+            modifyNames = true;
                }
                ~MothurOut();