added method parameter to get.oturep. options method=abundance or distance. default...

[mothur.git] / mothurout.h

diff --git a/mothurout.h b/mothurout.h
index 5ff0810479ab3b9f0e7e91fd6c3e8f98d0845ebb..4a46e051b67bb08caee8c4d97f3947c366d01926 100644 (file)
--- a/mothurout.h
+++ b/mothurout.h
@@ -170,7 +170,7 @@ class MothurOut {
                int control_pressed;
                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/getCurrentTypes.
+               //current files - if you add a new type you must edit optionParser->getParameters, get.current and set.current commands and mothurOut->printCurrentFiles/clearCurrentFiles/getCurrentTypes. add a get and set function.
                string getPhylipFile()          { return phylipfile;            }
                string getColumnFile()          { return columnfile;            }
                string getListFile()            { return listfile;                      }
@@ -193,6 +193,7 @@ class MothurOut {
                string getFlowFile()            { return flowfile;                      }
         string getBiomFile()           { return biomfile;                      }
         string getCountTableFile()     { return counttablefile;        }
+        string getSummaryFile()     { return summaryfile;       }
                string getProcessors()          { return processors;            }
                
                void setListFile(string f)                      { listfile = getFullPathName(f);                        }
@@ -216,6 +217,7 @@ class MothurOut {
                void setTaxonomyFile(string f)          { taxonomyfile = getFullPathName(f);            }
                void setFlowFile(string f)                      { flowfile = getFullPathName(f);                        }
         void setBiomFile(string f)                     { biomfile = getFullPathName(f);                        }
+        void setSummaryFile(string f)          { summaryfile = getFullPathName(f);                     }
         void setCountTableFile(string f)       { counttablefile = getFullPathName(f);  groupMode = "count";    }
         void setProcessors(string p)           { processors = p; mothurOut("\nUsing " + toString(p) + " processors.\n");       }
                
@@ -253,6 +255,7 @@ class MothurOut {
                        flowfile = "";
             biomfile = "";
             counttablefile = "";
+            summaryfile = "";
                        gui = false;
                        printedHeaders = false;
                        commandInputsConvertError = false;
@@ -269,7 +272,7 @@ class MothurOut {
                string releaseDate, version;
        
                string accnosfile, phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, designfile, taxonomyfile, biomfile;
-               string orderfile, treefile, sharedfile, ordergroupfile, relabundfile, fastafile, qualfile, sfffile, oligosfile, processors, flowfile, counttablefile;
+               string orderfile, treefile, sharedfile, ordergroupfile, relabundfile, fastafile, qualfile, sfffile, oligosfile, processors, flowfile, counttablefile, summaryfile;
 
                vector<string> Groups;
                vector<string> namesOfGroups;