added set.current and get.current commands and modified existing commands to update...

[mothur.git] / mothurout.h

diff --git a/mothurout.h b/mothurout.h
index 750973fde12ecffe585f354fc413612fc50f21b6..35805320227e168d6b2862fe889374fa939a0ca9 100644 (file)
--- a/mothurout.h
+++ b/mothurout.h
@@ -91,17 +91,86 @@ class MothurOut {
                int control_pressed;
                bool executing;
                
+               //current files - if you add a new type you must edit optionParser->getParameters, get.current command and mothurOut->printCurrentFiles/clearCurrentFiles.
+               string getPhylipFile()          { return phylipfile;            }
+               string getColumnFile()          { return columnfile;            }
+               string getListFile()            { return listfile;                      }
+               string getRabundFile()          { return rabundfile;            }
+               string getSabundFile()          { return sabundfile;            }
+               string getNameFile()            { return namefile;                      }       
+               string getGroupFile()           { return groupfile;                     }       
+               string getOrderFile()           { return orderfile;                     }
+               string getOrderGroupFile()      { return ordergroupfile;        }
+               string getTreeFile()            { return treefile;                      }
+               string getSharedFile()          { return sharedfile;            }
+               string getRelAbundFile()        { return relabundfile;          }
+               string getDesignFile()          { return designfile;            }
+               string getFastaFile()           { return fastafile;                     }
+               string getSFFFile()                     { return sfffile;                       }
+               string getQualFile()            { return qualfile;                      }
+               string getOligosFile()          { return oligosfile;            }
+               string getAccnosFile()          { return accnosfile;            }
+               string getTaxonomyFile()        { return taxonomyfile;          }
+               
+               void setListFile(string f)                      { listfile = getFullPathName(f);                        }
+               void setTreeFile(string f)                      { treefile = getFullPathName(f);                        }
+               void setGroupFile(string f)                     { groupfile = getFullPathName(f);                       }               
+               void setPhylipFile(string f)            { phylipfile = getFullPathName(f);                      }
+               void setColumnFile(string f)            { columnfile = getFullPathName(f);                      }
+               void setNameFile(string f)                      { namefile = getFullPathName(f);                        }       
+               void setRabundFile(string f)            { rabundfile = getFullPathName(f);                      }
+               void setSabundFile(string f)            { sabundfile = getFullPathName(f);                      }
+               void setSharedFile(string f)            { sharedfile = getFullPathName(f);                      }
+               void setRelAbundFile(string f)          { relabundfile = getFullPathName(f);            }
+               void setOrderFile(string f)                     { orderfile = getFullPathName(f);                       }
+               void setOrderGroupFile(string f)        { ordergroupfile = getFullPathName(f);          }
+               void setDesignFile(string f)            { designfile = getFullPathName(f);                      }
+               void setFastaFile(string f)                     { fastafile = getFullPathName(f);                       }
+               void setSFFFile(string f)                       { sfffile = getFullPathName(f);                         }
+               void setQualFile(string f)                      { qualfile = getFullPathName(f);                        }
+               void setOligosFile(string f)            { oligosfile = getFullPathName(f);                      }
+               void setAccnosFile(string f)            { accnosfile = getFullPathName(f);                      }
+               void setTaxonomyFile(string f)          { taxonomyfile = getFullPathName(f);            }
+               
+               void printCurrentFiles();
+               void clearCurrentFiles();
+               
        private:
                static MothurOut* _uniqueInstance;
                MothurOut( const MothurOut& ); // Disable copy constructor
                void operator=( const MothurOut& ); // Disable assignment operator
-               MothurOut() { control_pressed = false; defaultPath=""; };
+               MothurOut() { 
+                       control_pressed = false; defaultPath=""; 
+                       phylipfile = "";
+                       columnfile = "";
+                       listfile = "";
+                       rabundfile = "";
+                       sabundfile = "";
+                       namefile = "";
+                       groupfile = "";
+                       designfile = "";
+                       orderfile = "";
+                       treefile = "";
+                       sharedfile = "";
+                       ordergroupfile = "";
+                       relabundfile = "";
+                       fastafile = "";
+                       qualfile = "";
+                       sfffile = "";
+                       oligosfile = "";
+                       accnosfile = "";
+                       taxonomyfile = "";
+               };
                ~MothurOut();
 
                string logFileName;
                string defaultPath, outputDir;
                string releaseDate, version;
-               
+       
+               string accnosfile, phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, designfile, taxonomyfile;
+               string orderfile, treefile, sharedfile, ordergroupfile, relabundfile, fastafile, qualfile, sfffile, oligosfile;
+
+       
                ofstream out;
                
                int mem_usage(double&, double&);