X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=mothurout.h;h=3cf6fa4963672b5d69acb7de389eb266b957ba24;hp=be657f4df4b72eefdf9c0494201815be4eea968f;hb=615301e57c25e241356a9c2380648d117709458d;hpb=c85db0a4be3a1f8037a71a23ca73f9762184e28a

diff --git a/mothurout.h b/mothurout.h
index be657f4..3cf6fa4 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();
@@ -69,7 +70,7 @@ class MothurOut {
 		vector<string> binLabelsInFile;
 		vector<string> currentBinLabels;
 		string saveNextLabel, argv, sharedHeaderMode, groupMode;
-		bool printedHeaders, commandInputsConvertError, changedSeqNames;
+		bool printedHeaders, commandInputsConvertError, changedSeqNames, modifyNames;
 		
 		//functions from mothur.h
 		//file operations
@@ -81,6 +82,7 @@ class MothurOut {
 		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);
@@ -91,7 +93,9 @@ class MothurOut {
 		string getRootName(string);
 		bool isBlank(string);
 		int openOutputFile(string, ofstream&);
+        int openOutputFileBinary(string, ofstream&);
 		int openOutputFileAppend(string, ofstream&);
+        int openOutputFileBinaryAppend(string, ofstream&);
 		int openInputFile(string, ifstream&);
 		int openInputFile(string, ifstream&, string); //no error given 
 		string getline(ifstream&);
@@ -105,6 +109,8 @@ class MothurOut {
         map<string, int> readNames(string);
         map<string, int> readNames(string, unsigned long int&);
         int readTax(string, map<string, string>&);
+        vector<consTax> readConsTax(string);
+        int readConsTax(string, map<string, consTax2>&);
         int readNames(string, map<string, string>&, map<string, int>&);
 		int readNames(string, map<string, string>&);
         int readNames(string, map<string, string>&, bool);
@@ -149,6 +155,7 @@ class MothurOut {
         string makeList(vector<string>&);
         bool isSubset(vector<string>, vector<string>); //bigSet, subset
         int checkName(string&);
+        map<string, vector<string> > parseClasses(string);
 		
 		//math operation
 		int factorial(int num);
@@ -161,6 +168,7 @@ 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);
@@ -169,7 +177,7 @@ class MothurOut {
 		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;			}
@@ -192,6 +200,7 @@ 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);			}
@@ -215,6 +224,7 @@ 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");	}
 		
@@ -252,6 +262,7 @@ class MothurOut {
 			flowfile = "";
             biomfile = "";
             counttablefile = "";
+            summaryfile = "";
 			gui = false;
 			printedHeaders = false;
 			commandInputsConvertError = false;
@@ -260,6 +271,7 @@ class MothurOut {
 			sharedHeaderMode = "";
             groupMode = "group";
             changedSeqNames = false;
+            modifyNames = true;
 		}
 		~MothurOut();
 
@@ -268,7 +280,7 @@ 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;