added zap method to classify.seqs and changed bayesian method name to wang.

[mothur.git] / mothurout.h

diff --git a/mothurout.h b/mothurout.h
index 98565dc547d1e81dc03d88c9a526983727c1b124..53d4250c771cdbdac15c715c44d97fabf0a92c1a 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
@@ -111,6 +111,7 @@ class MothurOut {
                int readNames(string, vector<seqPriorityNode>&, map<string, string>&);
                int mothurRemove(string);
                bool mothurConvert(string, int&); //use for converting user inputs. Sets commandInputsConvertError to true if error occurs. Engines check this.
+        bool mothurConvert(string, intDist&); //use for converting user inputs. Sets commandInputsConvertError to true if error occurs. Engines check this.
                bool mothurConvert(string, float&); //use for converting user inputs. Sets commandInputsConvertError to true if error occurs. Engines check this.
                bool mothurConvert(string, double&); //use for converting user inputs. Sets commandInputsConvertError to true if error occurs. Engines check this.
        
@@ -139,7 +140,9 @@ class MothurOut {
                void splitAtChar(string&, vector<string>&, char);
         void splitAtChar(string&, string&, char);
                int removeConfidences(string&);
+        string removeQuotes(string);
         string makeList(vector<string>&);
+        bool isSubset(vector<string>, vector<string>); //bigSet, subset
                
                //math operation
                int factorial(int num);
@@ -148,6 +151,7 @@ class MothurOut {
                float roundDist(float, int);
                unsigned int fromBase36(string);
                int getRandomIndex(int); //highest
+        double getStandardDeviation(vector<int>&);
 
                int control_pressed;
                bool executing, runParse, jumble, gui, mothurCalling, debug;
@@ -179,7 +183,7 @@ class MothurOut {
                
                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);                        }       
@@ -198,7 +202,7 @@ class MothurOut {
                void setTaxonomyFile(string f)          { taxonomyfile = getFullPathName(f);            }
                void setFlowFile(string f)                      { flowfile = getFullPathName(f);                        }
         void setBiomFile(string f)                     { biomfile = getFullPathName(f);                        }
-        void setCountTableFile(string f)       { counttablefile = getFullPathName(f);          }
+        void setCountTableFile(string f)       { counttablefile = getFullPathName(f);  groupMode = "count";    }
         void setProcessors(string p)           { processors = p; mothurOut("\nUsing " + toString(p) + " processors.\n");       }
                
                void printCurrentFiles();
@@ -241,6 +245,7 @@ class MothurOut {
             mothurCalling = false;
             debug = false;
                        sharedHeaderMode = "";
+            groupMode = "group";
                }
                ~MothurOut();