X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothurout.h;h=ffdcaf63d704d087eccf27892bf6797765955a0e;hb=4b54ce99af7db8019ea907cd7c2edf789369ada9;hp=98565dc547d1e81dc03d88c9a526983727c1b124;hpb=f06b339c5fc4b6d1b9d2a08fe16bf7670bf7aeb4;p=mothur.git

diff --git a/mothurout.h b/mothurout.h
index 98565dc..ffdcaf6 100644
--- a/mothurout.h
+++ b/mothurout.h
@@ -68,8 +68,8 @@ class MothurOut {
 		//map<string, string> names;
 		vector<string> binLabelsInFile;
 		vector<string> currentBinLabels;
-		string saveNextLabel, argv, sharedHeaderMode;
-		bool printedHeaders, commandInputsConvertError;
+		string saveNextLabel, argv, sharedHeaderMode, groupMode;
+		bool printedHeaders, commandInputsConvertError, changedSeqNames;
 		
 		//functions from mothur.h
 		//file operations
@@ -102,6 +102,7 @@ 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>&);
@@ -111,6 +112,7 @@ class MothurOut {
 		int readNames(string, vector<seqPriorityNode>&, map<string, string>&);
 		int mothurRemove(string);
 		bool mothurConvert(string, int&); //use for converting user inputs. Sets commandInputsConvertError to true if error occurs. Engines check this.
+        bool mothurConvert(string, intDist&); //use for converting user inputs. Sets commandInputsConvertError to true if error occurs. Engines check this.
 		bool mothurConvert(string, float&); //use for converting user inputs. Sets commandInputsConvertError to true if error occurs. Engines check this.
 		bool mothurConvert(string, double&); //use for converting user inputs. Sets commandInputsConvertError to true if error occurs. Engines check this.
 	
@@ -119,7 +121,9 @@ class MothurOut {
 		bool checkReleaseVersion(ifstream&, string);
 		bool anyLabelsToProcess(string, set<string>&, string);
 		bool inUsersGroups(vector<string>, vector<string>);
+        bool inUsersGroups(vector<int>, vector< vector<int> >);
 		bool inUsersGroups(string, vector<string>);
+        bool inUsersGroups(int, vector<int>);
 		void getNumSeqs(ifstream&, int&);
 		int getNumSeqs(ifstream&);
 		int getNumNames(string);
@@ -138,8 +142,12 @@ class MothurOut {
 		void splitAtDash(string&, vector<string>&);
 		void splitAtChar(string&, vector<string>&, char);
         void splitAtChar(string&, string&, char);
+        vector<string> splitWhiteSpaceWithQuotes(string);
 		int removeConfidences(string&);
+        string removeQuotes(string);
         string makeList(vector<string>&);
+        bool isSubset(vector<string>, vector<string>); //bigSet, subset
+        int checkName(string&);
 		
 		//math operation
 		int factorial(int num);
@@ -148,6 +156,14 @@ class MothurOut {
 		float roundDist(float, int);
 		unsigned int fromBase36(string);
 		int getRandomIndex(int); //highest
+        double getStandardDeviation(vector<int>&);
+        vector<double> getStandardDeviation(vector< vector<double> >&);
+        vector<double> getStandardDeviation(vector< vector<double> >&, vector<double>&);
+        vector<double> getAverages(vector< 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;
@@ -179,7 +195,7 @@ class MothurOut {
 		
 		void setListFile(string f)			{ listfile = getFullPathName(f);			}
 		void setTreeFile(string f)			{ treefile = getFullPathName(f);			}
-		void setGroupFile(string f)			{ groupfile = getFullPathName(f);			}		
+		void setGroupFile(string f)			{ groupfile = getFullPathName(f);	groupMode = "group";		}		
 		void setPhylipFile(string f)		{ phylipfile = getFullPathName(f);			}
 		void setColumnFile(string f)		{ columnfile = getFullPathName(f);			}
 		void setNameFile(string f)			{ namefile = getFullPathName(f);			}	
@@ -198,7 +214,7 @@ class MothurOut {
 		void setTaxonomyFile(string f)		{ taxonomyfile = getFullPathName(f);		}
 		void setFlowFile(string f)			{ flowfile = getFullPathName(f);			}
         void setBiomFile(string f)			{ biomfile = getFullPathName(f);			}
-        void setCountTableFile(string f)	{ counttablefile = getFullPathName(f);		}
+        void setCountTableFile(string f)	{ counttablefile = getFullPathName(f);	groupMode = "count";	}
         void setProcessors(string p)		{ processors = p; mothurOut("\nUsing " + toString(p) + " processors.\n");	}
 		
 		void printCurrentFiles();
@@ -241,6 +257,8 @@ class MothurOut {
             mothurCalling = false;
             debug = false;
 			sharedHeaderMode = "";
+            groupMode = "group";
+            changedSeqNames = false;
 		}
 		~MothurOut();