added count file to trim.seqs, get.groups, get.lineage, get.seqs, heatmap.sim, list...

[mothur.git] / mothurout.h

diff --git a/mothurout.h b/mothurout.h
index 98565dc547d1e81dc03d88c9a526983727c1b124..33384034ae55ee7f11c72b48378fa59bfe29e16e 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.
        
@@ -140,6 +141,7 @@ class MothurOut {
         void splitAtChar(string&, string&, char);
                int removeConfidences(string&);
         string makeList(vector<string>&);
+        bool isSubset(vector<string>, vector<string>); //bigSet, subset
                
                //math operation
                int factorial(int num);
@@ -179,7 +181,7 @@ 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 +200,7 @@ 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 +243,7 @@ class MothurOut {
             mothurCalling = false;
             debug = false;
                        sharedHeaderMode = "";
+            groupMode = "group";
                }
                ~MothurOut();