X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=mothurout.h;h=f99eac1917cbe2ce5a1ce278c66d27d1df71737e;hp=84f9be31f82ebc2c27aa19563fb5366519e1cba8;hb=df7e3ff9f68ef157b0328a2d353c3258c5d45d89;hpb=20071b183e619c122bf9f63b4bb42722507c4e4a

diff --git a/mothurout.h b/mothurout.h
index 84f9be3..f99eac1 100644
--- a/mothurout.h
+++ b/mothurout.h
@@ -40,6 +40,7 @@ class MothurOut {
 		void mothurOutEndLine(); //writes to cout and the logfile
 		void mothurOut(string, ofstream&); //writes to the ofstream, cout and the logfile
 		void mothurOutEndLine(ofstream&); //writes to the ofstream, cout and the logfile
+        void mothurOutJustToScreen(string); //writes to cout
 		void mothurOutJustToLog(string);
 		void errorOut(exception&, string, string);
 		void closeLog();
@@ -69,17 +70,19 @@ class MothurOut {
 		vector<string> binLabelsInFile;
 		vector<string> currentBinLabels;
 		string saveNextLabel, argv, sharedHeaderMode, groupMode;
-		bool printedHeaders, commandInputsConvertError;
+		bool printedHeaders, commandInputsConvertError, changedSeqNames, modifyNames;
 		
 		//functions from mothur.h
 		//file operations
         bool dirCheck(string&); //completes path, appends appropriate / or \, makes sure dir is writable.
-		vector<unsigned long long> divideFile(string, int&);
+		vector<unsigned long long> divideFile(string, int&); //divides splitting unevenness by sequence
+        vector<unsigned long long> divideFilePerLine(string, int&); //divides splitting unevenness at line breaks
 		int divideFile(string, int&, vector<string>&);
 		vector<unsigned long long> setFilePosEachLine(string, int&);
 		vector<unsigned long long> setFilePosFasta(string, int&);
 		string sortFile(string, string);
 		int appendFiles(string, string);
+        int appendFilesWithoutHeaders(string, string);
 		int renameFile(string, string); //oldname, newname
 		string getFullPathName(string);
         string findProgramPath(string programName);
@@ -102,6 +105,7 @@ class MothurOut {
         set<string> readAccnos(string);
         int readAccnos(string, vector<string>&);
         map<string, int> readNames(string);
+        map<string, int> readNames(string, unsigned long int&);
         int readTax(string, map<string, string>&);
         int readNames(string, map<string, string>&, map<string, int>&);
 		int readNames(string, map<string, string>&);
@@ -146,6 +150,7 @@ class MothurOut {
         string removeQuotes(string);
         string makeList(vector<string>&);
         bool isSubset(vector<string>, vector<string>); //bigSet, subset
+        int checkName(string&);
 		
 		//math operation
 		int factorial(int num);
@@ -158,11 +163,16 @@ class MothurOut {
         vector<double> getStandardDeviation(vector< vector<double> >&);
         vector<double> getStandardDeviation(vector< vector<double> >&, vector<double>&);
         vector<double> getAverages(vector< vector<double> >&);
+        double getAverage(vector<double>);
+        vector< vector<seqDist> > getStandardDeviation(vector< vector< vector<seqDist> > >&);
+        vector< vector<seqDist> > getStandardDeviation(vector< vector< vector<seqDist> > >&, vector< vector<seqDist> >&);
+        vector< vector<seqDist> > getAverages(vector< vector< vector<seqDist> > >&, string);
+        vector< vector<seqDist> > getAverages(vector< vector< vector<seqDist> > >&);
 
 		int control_pressed;
 		bool executing, runParse, jumble, gui, mothurCalling, debug;
 		
-		//current files - if you add a new type you must edit optionParser->getParameters, get.current command and mothurOut->printCurrentFiles/clearCurrentFiles/getCurrentTypes.
+		//current files - if you add a new type you must edit optionParser->getParameters, get.current and set.current commands and mothurOut->printCurrentFiles/clearCurrentFiles/getCurrentTypes. add a get and set function.
 		string getPhylipFile()		{ return phylipfile;		}
 		string getColumnFile()		{ return columnfile;		}
 		string getListFile()		{ return listfile;			}
@@ -185,6 +195,7 @@ class MothurOut {
 		string getFlowFile()		{ return flowfile;			}
         string getBiomFile()		{ return biomfile;			}
         string getCountTableFile()	{ return counttablefile;	}
+        string getSummaryFile()     { return summaryfile;       }
 		string getProcessors()		{ return processors;		}
 		
 		void setListFile(string f)			{ listfile = getFullPathName(f);			}
@@ -208,6 +219,7 @@ class MothurOut {
 		void setTaxonomyFile(string f)		{ taxonomyfile = getFullPathName(f);		}
 		void setFlowFile(string f)			{ flowfile = getFullPathName(f);			}
         void setBiomFile(string f)			{ biomfile = getFullPathName(f);			}
+        void setSummaryFile(string f)		{ summaryfile = getFullPathName(f);			}
         void setCountTableFile(string f)	{ counttablefile = getFullPathName(f);	groupMode = "count";	}
         void setProcessors(string p)		{ processors = p; mothurOut("\nUsing " + toString(p) + " processors.\n");	}
 		
@@ -245,6 +257,7 @@ class MothurOut {
 			flowfile = "";
             biomfile = "";
             counttablefile = "";
+            summaryfile = "";
 			gui = false;
 			printedHeaders = false;
 			commandInputsConvertError = false;
@@ -252,6 +265,8 @@ class MothurOut {
             debug = false;
 			sharedHeaderMode = "";
             groupMode = "group";
+            changedSeqNames = false;
+            modifyNames = true;
 		}
 		~MothurOut();
 
@@ -260,7 +275,7 @@ class MothurOut {
 		string releaseDate, version;
 	
 		string accnosfile, phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, designfile, taxonomyfile, biomfile;
-		string orderfile, treefile, sharedfile, ordergroupfile, relabundfile, fastafile, qualfile, sfffile, oligosfile, processors, flowfile, counttablefile;
+		string orderfile, treefile, sharedfile, ordergroupfile, relabundfile, fastafile, qualfile, sfffile, oligosfile, processors, flowfile, counttablefile, summaryfile;
 
 		vector<string> Groups;
 		vector<string> namesOfGroups;