added namefile to align.check and added seqs from namefile to optimizing piece of...

[mothur.git] / mothurout.h

diff --git a/mothurout.h b/mothurout.h
index 2244eeef21b571ed94bcd8a12820e76416e5b7b8..750973fde12ecffe585f354fc413612fc50f21b6 100644 (file)
--- a/mothurout.h
+++ b/mothurout.h
@@ -12,6 +12,7 @@
 
 #include "mothur.h"
 
+
 /***********************************************/
 
 class MothurOut {
@@ -27,6 +28,8 @@ class MothurOut {
                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; }
@@ -56,6 +59,7 @@ class MothurOut {
                string getline(istringstream&);
                void gobble(istream&);
                void gobble(istringstream&);
+               map<string, int> readNames(string);
                
                //searchs and checks
                bool checkReleaseVersion(ifstream&, string);
@@ -82,11 +86,11 @@ class MothurOut {
                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
@@ -95,7 +99,7 @@ class MothurOut {
                ~MothurOut();
 
                string logFileName;
-               string defaultPath;
+               string defaultPath, outputDir;
                string releaseDate, version;
                
                ofstream out;