added chimera.uchime

[mothur.git] / mothurout.h

diff --git a/mothurout.h b/mothurout.h
index 8138f28e46115b8d527270a80d904e68ebbc322a..8ac84007de59225ccffb9642a4d0dd023818e40a 100644 (file)
--- a/mothurout.h
+++ b/mothurout.h
@@ -44,6 +44,7 @@ class MothurOut {
                //functions from mothur.h
                //file operations
                vector<unsigned long int> divideFile(string, int&);
+               int divideFile(string, int&, vector<string>&);
                vector<unsigned long int> setFilePosEachLine(string, int&);
                vector<unsigned long int> setFilePosFasta(string, int&);
                string sortFile(string, string);
@@ -65,6 +66,7 @@ class MothurOut {
                void gobble(istream&);
                void gobble(istringstream&);
                map<string, int> readNames(string);
+               int readNames(string, vector<seqPriorityNode>&, map<string, string>&);
                
                //searchs and checks
                bool checkReleaseVersion(ifstream&, string);
@@ -117,6 +119,7 @@ class MothurOut {
                string getOligosFile()          { return oligosfile;            }
                string getAccnosFile()          { return accnosfile;            }
                string getTaxonomyFile()        { return taxonomyfile;          }
+               string getFlowFile()            { return flowfile;                      }
                string getProcessors()          { return processors;            }
                
                void setListFile(string f)                      { listfile = getFullPathName(f);                        }
@@ -138,6 +141,7 @@ class MothurOut {
                void setOligosFile(string f)            { oligosfile = getFullPathName(f);                      }
                void setAccnosFile(string f)            { accnosfile = getFullPathName(f);                      }
                void setTaxonomyFile(string f)          { taxonomyfile = getFullPathName(f);            }
+               void setFlowFile(string f)                      { flowfile = getFullPathName(f);                        }
                void setProcessors(string p)            { processors = p;                                                       }
                
                void printCurrentFiles();
@@ -170,6 +174,7 @@ class MothurOut {
                        accnosfile = "";
                        taxonomyfile = "";
                        processors = "1";
+                       flowfile = "";
                        gui = false;
                };
                ~MothurOut();
@@ -179,7 +184,7 @@ class MothurOut {
                string releaseDate, version;
        
                string accnosfile, phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, designfile, taxonomyfile;
-               string orderfile, treefile, sharedfile, ordergroupfile, relabundfile, fastafile, qualfile, sfffile, oligosfile, processors;
+               string orderfile, treefile, sharedfile, ordergroupfile, relabundfile, fastafile, qualfile, sfffile, oligosfile, processors, flowfile;
 
        
                ofstream out;