X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=summaryqualcommand.h;h=b9edc5148ca5f7a834433815204b40f9ea317db4;hb=541bab1dac00688b4c3a8c4a95ab464412663c50;hp=1ec3cf1891893227d07d256cecd15f742ee9d127;hpb=0718c426add1df69adcc24444ef45550fb262ca7;p=mothur.git

diff --git a/summaryqualcommand.h b/summaryqualcommand.h
index 1ec3cf1..b9edc51 100644
--- a/summaryqualcommand.h
+++ b/summaryqualcommand.h
@@ -25,7 +25,9 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "summary.qual";			}
 	string getCommandCategory()		{ return "Sequence Processing";		}
+	
 	string getHelpString();	
+    string getOutputPattern(string);	
 	string getCitation() { return "http://www.mothur.org/wiki/Summary.qual"; }
 	string getDescription()		{ return "summarize the quality of a set of sequences"; }
 	
@@ -34,7 +36,7 @@ public:
 	
 private:
 	bool abort;
-	string qualfile, outputDir, namefile;
+	string qualfile, outputDir, namefile, countfile;
 	vector<string> outputNames;
 	map<string, int> nameMap;
 	int processors;
@@ -58,33 +60,31 @@ private:
 // This is passed by void pointer so it can be any data type
 // that can be passed using a single void pointer (LPVOID).
 struct seqSumQualData {
-	vector<int>* position;
-	vector<int>* averageQ;
-	vector< vector<int> >* scores; 
-	string filename, namefile; 
+	vector<int> position;
+	vector<int> averageQ;
+	vector< vector<int> > scores; 
+	string filename; 
 	unsigned long long start;
 	unsigned long long end;
-	int count;
+	int count, numSeqs;
 	MothurOut* m;
+    bool hasNameMap;
 	map<string, int> nameMap;
 	
 	~seqSumQualData(){}
-	seqSumQualData(vector<int>* p, vector<int>* a, vector< vector<int> >* s, string f, MothurOut* mout, unsigned long long st, unsigned long long en, string n, map<string, int> nam) {
-		position = p;
-		averageQ = a;
-		scores = s;
+	seqSumQualData(string f, MothurOut* mout, unsigned long long st, unsigned long long en, bool n, map<string, int> nam) {
 		filename = f;
 		m = mout;
 		start = st;
 		end = en;
-		namefile = n;
+		hasNameMap = n;
 		nameMap = nam;
 		count = 0;
 	}
 };
 
 /**************************************************************************************************/
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 #else
 static DWORD WINAPI MySeqSumQualThreadFunction(LPVOID lpParam){ 
 	seqSumQualData* pDataArray;
@@ -101,7 +101,8 @@ static DWORD WINAPI MySeqSumQualThreadFunction(LPVOID lpParam){
 			in.seekg(pDataArray->start-1); pDataArray->m->gobble(in); 
 		}
 		
-		int count = 0;
+		pDataArray->count = 0;
+        pDataArray->numSeqs = 0;
 		for(int i = 0; i < pDataArray->end; i++){ //end is the number of sequences to process
 				
 			if (pDataArray->m->control_pressed) { in.close(); pDataArray->count = 1; return 1; }
@@ -111,7 +112,7 @@ static DWORD WINAPI MySeqSumQualThreadFunction(LPVOID lpParam){
 			if (current.getName() != "") {
 			
 				int num = 1;
-				if (pDataArray->namefile != "") {
+				if (pDataArray->hasNameMap) {
 					//make sure this sequence is in the namefile, else error 
 					map<string, int>::iterator it = pDataArray->nameMap.find(current.getName());
 					
@@ -122,27 +123,27 @@ static DWORD WINAPI MySeqSumQualThreadFunction(LPVOID lpParam){
 				vector<int> thisScores = current.getQualityScores();
 				
 				//resize to num of positions setting number of seqs with that size to 1
-				if (pDataArray->position->size() < thisScores.size()) { pDataArray->position->resize(thisScores.size(), 0); }
-				if (pDataArray->averageQ->size() < thisScores.size()) { pDataArray->averageQ->resize(thisScores.size(), 0); }
-				if (pDataArray->scores->size() < thisScores.size()) { 
-					pDataArray->scores->resize(thisScores.size()); 
-					for (int i = 0; i < pDataArray->scores->size(); i++) { pDataArray->scores->at(i).resize(41, 0); }
+				if (pDataArray->position.size() < thisScores.size()) { pDataArray->position.resize(thisScores.size(), 0); }
+				if (pDataArray->averageQ.size() < thisScores.size()) { pDataArray->averageQ.resize(thisScores.size(), 0); }
+				if (pDataArray->scores.size() < thisScores.size()) { 
+					pDataArray->scores.resize(thisScores.size()); 
+					for (int i = 0; i < pDataArray->scores.size(); i++) { pDataArray->scores.at(i).resize(41, 0); }
 				}
 				
 				//increase counts of number of seqs with this position
 				//average is really the total, we will average in execute
 				for (int i = 0; i < thisScores.size(); i++) { 
-					pDataArray->position->at(i) += num; 
-					pDataArray->averageQ->at(i) += (thisScores[i] * num); //weighting for namesfile
+					pDataArray->position.at(i) += num; 
+					pDataArray->averageQ.at(i) += (thisScores[i] * num); //weighting for namesfile
 					if (thisScores[i] > 40) { pDataArray->m->mothurOut("[ERROR]: " + current.getName() + " has a quality scores of " + toString(thisScores[i]) + ", expecting values to be less than 40."); pDataArray->m->mothurOutEndLine(); pDataArray->m->control_pressed = true; }
-					else { pDataArray->scores->at(i)[thisScores[i]] += num; }  
+					else { pDataArray->scores.at(i)[thisScores[i]] += num; }  
 				}
 				
-				count += num;
+				pDataArray->numSeqs += num;
+                pDataArray->count++;
 			}
 		}
 		
-		pDataArray->count = count;
 		in.close();
 		
 		return 0;