added countable class to read and store count file. added count parameter to make...

[mothur.git] / mothurout.h

diff --git a/mothurout.h b/mothurout.h
index cc8bfb6b101b13b0ebe45a2eb2f5472600d6e0fc..ac47d79f7d92b113f58dbe421fdbaad892b2b175 100644 (file)
--- a/mothurout.h
+++ b/mothurout.h
@@ -68,7 +68,7 @@ class MothurOut {
                //map<string, string> names;
                vector<string> binLabelsInFile;
                vector<string> currentBinLabels;
-               string saveNextLabel, argv, sharedHeaderMode;
+               string saveNextLabel, argv, sharedHeaderMode, groupMode;
                bool printedHeaders, commandInputsConvertError;
                
                //functions from mothur.h
@@ -97,8 +97,16 @@ 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, string>&, int);
                int readNames(string, map<string, vector<string> >&);
                int readNames(string, vector<seqPriorityNode>&, map<string, string>&);
                int mothurRemove(string);
@@ -144,7 +152,7 @@ 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;                      }
@@ -166,11 +174,12 @@ class MothurOut {
                string getTaxonomyFile()        { return taxonomyfile;          }
                string getFlowFile()            { return flowfile;                      }
         string getBiomFile()           { return biomfile;                      }
+        string getCountTableFile()     { return counttablefile;        }
                string getProcessors()          { return processors;            }
                
                void setListFile(string f)                      { listfile = getFullPathName(f);                        }
                void setTreeFile(string f)                      { treefile = getFullPathName(f);                        }
-               void setGroupFile(string f)                     { groupfile = getFullPathName(f);                       }               
+               void setGroupFile(string f)                     { groupfile = getFullPathName(f);       groupMode = "group";            }               
                void setPhylipFile(string f)            { phylipfile = getFullPathName(f);                      }
                void setColumnFile(string f)            { columnfile = getFullPathName(f);                      }
                void setNameFile(string f)                      { namefile = getFullPathName(f);                        }       
@@ -189,11 +198,13 @@ 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 setCountTableFile(string f)       { counttablefile = getFullPathName(f);  groupMode = "count";    }
+        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;
@@ -223,12 +234,14 @@ class MothurOut {
                        processors = "1";
                        flowfile = "";
             biomfile = "";
+            counttablefile = "";
                        gui = false;
                        printedHeaders = false;
                        commandInputsConvertError = false;
             mothurCalling = false;
             debug = false;
                        sharedHeaderMode = "";
+            groupMode = "group";
                }
                ~MothurOut();
 
@@ -237,7 +250,7 @@ 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;
+               string orderfile, treefile, sharedfile, ordergroupfile, relabundfile, fastafile, qualfile, sfffile, oligosfile, processors, flowfile, counttablefile;
 
                vector<string> Groups;
                vector<string> namesOfGroups;