added template=self capability to chimers.slayer, worked on corr.axes and added accno...

[mothur.git] / mothurout.h

diff --git a/mothurout.h b/mothurout.h
index ac1ec3fd402af357cc956a816df8de6dc27f9e29..a1d950661d8d0f3f8084859a85110db97846cd4d 100644 (file)
--- a/mothurout.h
+++ b/mothurout.h
@@ -2,7 +2,7 @@
 #define MOTHUROUT_H
 
 /*
- *  m->mothurOut.h
+ *  mothurOut.h
  *  Mothur
  *
  *  Created by westcott on 2/25/10.
@@ -12,6 +12,7 @@
 
 #include "mothur.h"
 
+
 /***********************************************/
 
 class MothurOut {
@@ -24,18 +25,85 @@ class MothurOut {
                void mothurOutEndLine();
                void mothurOutJustToLog(string);
                void errorOut(exception&, string, string);
-               int control_pressed;
+               void closeLog();
+               string getDefaultPath() { return defaultPath; }
+               void setDefaultPath(string);
+               string getOutputDir() { return outputDir; }
+               void setOutputDir(string);
+               
+               string getReleaseDate() { return releaseDate; }
+               void setReleaseDate(string r) { releaseDate = r; }
+               string getVersion() { return version; }
+               void setVersion(string r) { version = r; }
+               
+               //functions from mothur.h
+               //file operations
+               vector<unsigned long int> divideFile(string, int&);
+               vector<unsigned long int> setFilePosEachLine(string, int&);
+               vector<unsigned long int> setFilePosFasta(string, int&);
+               string sortFile(string, string);
+               void appendFiles(string, string);
+               int renameFile(string, string); //oldname, newname
+               string getFullPathName(string);
+               string hasPath(string);
+               string getExtension(string);
+               string getPathName(string);
+               string getSimpleName(string);
+               string getRootName(string);
+               bool isBlank(string);
+               int openOutputFile(string, ofstream&);
+               int openOutputFileAppend(string, ofstream&);
+               int openInputFile(string, ifstream&);
+               int openInputFile(string, ifstream&, string); //no error given 
+               string getline(ifstream&);
+               string getline(istringstream&);
+               void gobble(istream&);
+               void gobble(istringstream&);
+               
+               //searchs and checks
+               bool checkReleaseVersion(ifstream&, string);
+               bool anyLabelsToProcess(string, set<string>&, string);
+               bool inUsersGroups(vector<string>, vector<string>);
+               bool inUsersGroups(string, vector<string>);
+               void getNumSeqs(ifstream&, int&);
+               int getNumSeqs(ifstream&);
+               int getNumNames(string);
+               bool isTrue(string);
+       
                
+               //string manipulation
+               void splitAtEquals(string&, string&);
+               void splitAtComma(string&, string&);    
+               void splitAtComma(string&, vector<string>&);
+               void splitAtDash(string&, set<int>&);
+               void splitAtDash(string&, set<string>&);
+               void splitAtDash(string&, vector<string>&);
+               void splitAtChar(string&, vector<string>&, char);
+               
+               //math operation
+               int factorial(int num);
+               vector<vector<double> > binomial(int);
+               float ceilDist(float, int);
+               float roundDist(float, int);
+               unsigned int fromBase36(string);
 
+               int control_pressed;
+               bool executing;
+               
        private:
                static MothurOut* _uniqueInstance;
                MothurOut( const MothurOut& ); // Disable copy constructor
                void operator=( const MothurOut& ); // Disable assignment operator
-               MothurOut() {};
+               MothurOut() { control_pressed = false; defaultPath=""; };
                ~MothurOut();
 
                string logFileName;
+               string defaultPath, outputDir;
+               string releaseDate, version;
+               
                ofstream out;
+               
+               int mem_usage(double&, double&);
 
 };
 /***********************************************/