removed read.dist, read.otu, read.tree and globaldata. added current to defaults...

[mothur.git] / mothurout.h

diff --git a/mothurout.h b/mothurout.h
index 35805320227e168d6b2862fe889374fa939a0ca9..6654455063c37b56030a89c09c8d6ee71dcdf4be 100644 (file)
--- a/mothurout.h
+++ b/mothurout.h
@@ -35,6 +35,11 @@ class MothurOut {
                void setReleaseDate(string r) { releaseDate = r; }
                string getVersion() { return version; }
                void setVersion(string r) { version = r; }
+               vector<string> Groups;
+               vector<string> Treenames;
+               map<string, string> names;
+               vector<string> namesOfGroups;
+               string saveNextLabel, argv;
                
                //functions from mothur.h
                //file operations
@@ -89,7 +94,7 @@ class MothurOut {
                unsigned int fromBase36(string);
 
                int control_pressed;
-               bool executing;
+               bool executing, runParse, jumble;
                
                //current files - if you add a new type you must edit optionParser->getParameters, get.current command and mothurOut->printCurrentFiles/clearCurrentFiles.
                string getPhylipFile()          { return phylipfile;            }
@@ -111,6 +116,7 @@ class MothurOut {
                string getOligosFile()          { return oligosfile;            }
                string getAccnosFile()          { return accnosfile;            }
                string getTaxonomyFile()        { return taxonomyfile;          }
+               string getProcessors()          { return processors;            }
                
                void setListFile(string f)                      { listfile = getFullPathName(f);                        }
                void setTreeFile(string f)                      { treefile = getFullPathName(f);                        }
@@ -131,6 +137,7 @@ class MothurOut {
                void setOligosFile(string f)            { oligosfile = getFullPathName(f);                      }
                void setAccnosFile(string f)            { accnosfile = getFullPathName(f);                      }
                void setTaxonomyFile(string f)          { taxonomyfile = getFullPathName(f);            }
+               void setProcessors(string p)            { processors = p;                                                       }
                
                void printCurrentFiles();
                void clearCurrentFiles();
@@ -160,6 +167,7 @@ class MothurOut {
                        oligosfile = "";
                        accnosfile = "";
                        taxonomyfile = "";
+                       processors = "1";
                };
                ~MothurOut();
 
@@ -168,7 +176,7 @@ 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;
+               string orderfile, treefile, sharedfile, ordergroupfile, relabundfile, fastafile, qualfile, sfffile, oligosfile, processors;
 
        
                ofstream out;