X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothurout.h;h=57d3f7647dabf43dd30f2caeefa9ae2bd09a0d30;hb=65f2be9d8f9b4cf72b4aafd800fdd11ad26435fd;hp=a1d950661d8d0f3f8084859a85110db97846cd4d;hpb=3e2465c16d187247ce3befd29811c2d5dfc15ee8;p=mothur.git

diff --git a/mothurout.h b/mothurout.h
index a1d9506..57d3f76 100644
--- 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
@@ -59,6 +64,7 @@ class MothurOut {
 		string getline(istringstream&);
 		void gobble(istream&);
 		void gobble(istringstream&);
+		map<string, int> readNames(string);
 		
 		//searchs and checks
 		bool checkReleaseVersion(ifstream&, string);
@@ -69,6 +75,7 @@ class MothurOut {
 		int getNumSeqs(ifstream&);
 		int getNumNames(string);
 		bool isTrue(string);
+		bool isContainingOnlyDigits(string);
 	
 		
 		//string manipulation
@@ -88,19 +95,92 @@ 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;		}
+		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 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 setProcessors(string p)		{ processors = p;							}
+		
+		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 = "";
+			processors = "1";
+			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;
+
+	
 		ofstream out;
 		
 		int mem_usage(double&, double&);