added current as option is lists of file names, processors now outputted with current...

[mothur.git] / mothurout.h

diff --git a/mothurout.h b/mothurout.h
index 9921a40dccec386ad1266e9954ed72686f7be130..f6f505dce6409db716561b061a2e66eda3efae5a 100644 (file)
--- a/mothurout.h
+++ b/mothurout.h
@@ -12,6 +12,7 @@
 
 #include "mothur.h"
 
+
 /***********************************************/
 
 class MothurOut {
@@ -34,6 +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
@@ -58,6 +64,8 @@ class MothurOut {
                string getline(istringstream&);
                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);
@@ -68,6 +76,7 @@ class MothurOut {
                int getNumSeqs(ifstream&);
                int getNumNames(string);
                bool isTrue(string);
+               bool isContainingOnlyDigits(string);
        
                
                //string manipulation
@@ -84,22 +93,99 @@ class MothurOut {
                vector<vector<double> > binomial(int);
                float ceilDist(float, int);
                float roundDist(float, int);
+               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;            }
+               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;          }
+               string getFlowFile()            { return flowfile;                      }
+               string getProcessors()          { return processors;            }
+               
+               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 setFlowFile(string f)                      { flowfile = getFullPathName(f);                        }
+               void setProcessors(string p)            { processors = p;                                                       }
+               
+               void printCurrentFiles();
+               bool hasCurrentFiles();
+               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 = "";
+                       processors = "1";
+                       flowfile = "";
+                       gui = false;
+               };
                ~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, processors, flowfile;
+
+       
                ofstream out;
                
                int mem_usage(double&, double&);