forced rarefaction.single to output ending line for all groups. added subsample...

[mothur.git] / mothurout.h

diff --git a/mothurout.h b/mothurout.h
index 0659e4e3628ccb28fdfc024427fe6cebf5af5446..0e31f8414a3a3477c1d8ab928d79aee0ccdc9957 100644 (file)
--- a/mothurout.h
+++ b/mothurout.h
@@ -65,7 +65,7 @@ class MothurOut {
        
                vector<string> getAllGroups() { sort(namesOfGroups.begin(), namesOfGroups.end()); return namesOfGroups; }
                vector<string> Treenames;
-               map<string, string> names;
+               //map<string, string> names;
                vector<string> binLabelsInFile;
                vector<string> currentBinLabels;
                string saveNextLabel, argv, sharedHeaderMode;
@@ -128,7 +128,9 @@ class MothurOut {
                void splitAtDash(string&, set<string>&);
                void splitAtDash(string&, vector<string>&);
                void splitAtChar(string&, vector<string>&, char);
+        void splitAtChar(string&, string&, char);
                int removeConfidences(string&);
+        string makeList(vector<string>&);
                
                //math operation
                int factorial(int num);
@@ -139,7 +141,7 @@ class MothurOut {
                int getRandomIndex(int); //highest
 
                int control_pressed;
-               bool executing, runParse, jumble, gui, mothurCalling;
+               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.
                string getPhylipFile()          { return phylipfile;            }
@@ -162,6 +164,7 @@ class MothurOut {
                string getAccnosFile()          { return accnosfile;            }
                string getTaxonomyFile()        { return taxonomyfile;          }
                string getFlowFile()            { return flowfile;                      }
+        string getBiomFile()           { return biomfile;                      }
                string getProcessors()          { return processors;            }
                
                void setListFile(string f)                      { listfile = getFullPathName(f);                        }
@@ -184,6 +187,7 @@ class MothurOut {
                void setAccnosFile(string f)            { accnosfile = getFullPathName(f);                      }
                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 printCurrentFiles();
@@ -217,10 +221,12 @@ class MothurOut {
                        taxonomyfile = "";
                        processors = "1";
                        flowfile = "";
+            biomfile = "";
                        gui = false;
                        printedHeaders = false;
                        commandInputsConvertError = false;
             mothurCalling = false;
+            debug = false;
                        sharedHeaderMode = "";
                }
                ~MothurOut();
@@ -229,7 +235,7 @@ class MothurOut {
                string defaultPath, outputDir;
                string releaseDate, version;
        
-               string accnosfile, phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, designfile, taxonomyfile;
+               string accnosfile, phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, designfile, taxonomyfile, biomfile;
                string orderfile, treefile, sharedfile, ordergroupfile, relabundfile, fastafile, qualfile, sfffile, oligosfile, processors, flowfile;
 
                vector<string> Groups;