changed random forest output filename

[mothur.git] / mothurout.h

diff --git a/mothurout.h b/mothurout.h
index 84f9be31f82ebc2c27aa19563fb5366519e1cba8..3cf6fa4963672b5d69acb7de389eb266b957ba24 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();
@@ -69,17 +70,19 @@ class MothurOut {
                vector<string> binLabelsInFile;
                vector<string> currentBinLabels;
                string saveNextLabel, argv, sharedHeaderMode, groupMode;
-               bool printedHeaders, commandInputsConvertError;
+               bool printedHeaders, commandInputsConvertError, changedSeqNames, modifyNames;
                
                //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);
@@ -90,7 +93,9 @@ 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 
                string getline(ifstream&);
@@ -102,7 +107,10 @@ 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>&);
+        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);
@@ -146,6 +154,8 @@ class MothurOut {
         string removeQuotes(string);
         string makeList(vector<string>&);
         bool isSubset(vector<string>, vector<string>); //bigSet, subset
+        int checkName(string&);
+        map<string, vector<string> > parseClasses(string);
                
                //math operation
                int factorial(int num);
@@ -158,11 +168,16 @@ class MothurOut {
         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);
+        vector< vector<seqDist> > getAverages(vector< vector< vector<seqDist> > >&);
 
                int control_pressed;
                bool executing, runParse, jumble, gui, mothurCalling, debug;
                
-               //current files - if you add a new type you must edit optionParser->getParameters, get.current command and mothurOut->printCurrentFiles/clearCurrentFiles/getCurrentTypes.
+               //current files - if you add a new type you must edit optionParser->getParameters, get.current and set.current commands and mothurOut->printCurrentFiles/clearCurrentFiles/getCurrentTypes. add a get and set function.
                string getPhylipFile()          { return phylipfile;            }
                string getColumnFile()          { return columnfile;            }
                string getListFile()            { return listfile;                      }
@@ -185,6 +200,7 @@ class MothurOut {
                string getFlowFile()            { return flowfile;                      }
         string getBiomFile()           { return biomfile;                      }
         string getCountTableFile()     { return counttablefile;        }
+        string getSummaryFile()     { return summaryfile;       }
                string getProcessors()          { return processors;            }
                
                void setListFile(string f)                      { listfile = getFullPathName(f);                        }
@@ -208,6 +224,7 @@ class MothurOut {
                void setTaxonomyFile(string f)          { taxonomyfile = getFullPathName(f);            }
                void setFlowFile(string f)                      { flowfile = getFullPathName(f);                        }
         void setBiomFile(string f)                     { biomfile = getFullPathName(f);                        }
+        void setSummaryFile(string f)          { summaryfile = getFullPathName(f);                     }
         void setCountTableFile(string f)       { counttablefile = getFullPathName(f);  groupMode = "count";    }
         void setProcessors(string p)           { processors = p; mothurOut("\nUsing " + toString(p) + " processors.\n");       }
                
@@ -245,6 +262,7 @@ class MothurOut {
                        flowfile = "";
             biomfile = "";
             counttablefile = "";
+            summaryfile = "";
                        gui = false;
                        printedHeaders = false;
                        commandInputsConvertError = false;
@@ -252,6 +270,8 @@ class MothurOut {
             debug = false;
                        sharedHeaderMode = "";
             groupMode = "group";
+            changedSeqNames = false;
+            modifyNames = true;
                }
                ~MothurOut();
 
@@ -260,7 +280,7 @@ class MothurOut {
                string releaseDate, version;
        
                string accnosfile, phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, designfile, taxonomyfile, biomfile;
-               string orderfile, treefile, sharedfile, ordergroupfile, relabundfile, fastafile, qualfile, sfffile, oligosfile, processors, flowfile, counttablefile;
+               string orderfile, treefile, sharedfile, ordergroupfile, relabundfile, fastafile, qualfile, sfffile, oligosfile, processors, flowfile, counttablefile, summaryfile;
 
                vector<string> Groups;
                vector<string> namesOfGroups;