added load.logfile command. changed summary.single output for subsample=t.

[mothur.git] / mothurout.h

diff --git a/mothurout.h b/mothurout.h
index 0e31f8414a3a3477c1d8ab928d79aee0ccdc9957..b2c638a167d1ebf507106cc300231f0f693471b0 100644 (file)
--- a/mothurout.h
+++ b/mothurout.h
@@ -82,6 +82,7 @@ class MothurOut {
                int appendFiles(string, string);
                int renameFile(string, string); //oldname, newname
                string getFullPathName(string);
+        string findProgramPath(string programName);
                string hasPath(string);
                string getExtension(string);
                string getPathName(string);
@@ -96,8 +97,15 @@ class MothurOut {
                string getline(istringstream&);
                void gobble(istream&);
                void gobble(istringstream&);
-               map<string, int> readNames(string);
+        vector<string> splitWhiteSpace(string& rest, char[], int);
+        vector<string> splitWhiteSpace(string);
+        set<string> readAccnos(string);
+        int readAccnos(string, vector<string>&);
+        map<string, int> readNames(string);
+        int readTax(string, map<string, string>&);
+        int readNames(string, map<string, string>&, map<string, int>&);
                int readNames(string, map<string, string>&);
+        int readNames(string, map<string, string>&, bool);
                int readNames(string, map<string, vector<string> >&);
                int readNames(string, vector<seqPriorityNode>&, map<string, string>&);
                int mothurRemove(string);
@@ -143,7 +151,7 @@ class MothurOut {
                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.
+               //current files - if you add a new type you must edit optionParser->getParameters, get.current command and mothurOut->printCurrentFiles/clearCurrentFiles/getCurrentTypes.
                string getPhylipFile()          { return phylipfile;            }
                string getColumnFile()          { return columnfile;            }
                string getListFile()            { return listfile;                      }
@@ -188,11 +196,12 @@ class MothurOut {
                void setTaxonomyFile(string f)          { taxonomyfile = getFullPathName(f);            }
                void setFlowFile(string f)                      { flowfile = getFullPathName(f);                        }
         void setBiomFile(string f)                     { biomfile = getFullPathName(f);                        }
-               void setProcessors(string p)            { processors = p;                                                       }
+        void setProcessors(string p)           { processors = p; mothurOut("\nUsing " + toString(p) + " processors.\n");       }
                
                void printCurrentFiles();
                bool hasCurrentFiles();
                void clearCurrentFiles();
+        set<string> getCurrentTypes(); 
                
        private:
                static MothurOut* _uniqueInstance;