changes for chimera slayer

[mothur.git] / mothurout.h

diff --git a/mothurout.h b/mothurout.h
index f20d5c197df59b06c3f5069709aa4e036436a768..f6f505dce6409db716561b061a2e66eda3efae5a 100644 (file)
--- a/mothurout.h
+++ b/mothurout.h
@@ -65,6 +65,7 @@ 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);
@@ -95,7 +96,7 @@ class MothurOut {
                unsigned int fromBase36(string);
 
                int control_pressed;
-               bool executing, runParse, jumble;
+               bool executing, runParse, jumble, gui;
                
                //current files - if you add a new type you must edit optionParser->getParameters, get.current command and mothurOut->printCurrentFiles/clearCurrentFiles.
                string getPhylipFile()          { return phylipfile;            }
@@ -117,6 +118,7 @@ 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);                        }
@@ -138,9 +140,11 @@ 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();
+               bool hasCurrentFiles();
                void clearCurrentFiles();
                
        private:
@@ -169,6 +173,8 @@ class MothurOut {
                        accnosfile = "";
                        taxonomyfile = "";
                        processors = "1";
+                       flowfile = "";
+                       gui = false;
                };
                ~MothurOut();
 
@@ -177,7 +183,7 @@ 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;