fixed sub.sample groups bug

[mothur.git] / mothurout.h

diff --git a/mothurout.h b/mothurout.h
index 35805320227e168d6b2862fe889374fa939a0ca9..57d3f7647dabf43dd30f2caeefa9ae2bd09a0d30 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
@@ -70,6 +75,7 @@ class MothurOut {
                int getNumSeqs(ifstream&);
                int getNumNames(string);
                bool isTrue(string);
+               bool isContainingOnlyDigits(string);
        
                
                //string manipulation
@@ -89,7 +95,7 @@ class MothurOut {
                unsigned int fromBase36(string);
 
                int control_pressed;
-               bool executing;
+               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;            }
@@ -111,6 +117,7 @@ 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 +138,7 @@ 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 +168,8 @@ class MothurOut {
                        oligosfile = "";
                        accnosfile = "";
                        taxonomyfile = "";
+                       processors = "1";
+                       gui = false;
                };
                ~MothurOut();
 
@@ -168,7 +178,7 @@ 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;