X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=summaryqualcommand.h;h=b9edc5148ca5f7a834433815204b40f9ea317db4;hp=bbd103c1d14f7b40badd9654152aec0fd2b47a10;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=91a27e0483827c06c21c4fe89558923bbfe86573

diff --git a/summaryqualcommand.h b/summaryqualcommand.h
index bbd103c..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;
@@ -61,20 +63,21 @@ struct seqSumQualData {
 	vector<int> position;
 	vector<int> averageQ;
 	vector< vector<int> > scores; 
-	string filename, namefile; 
+	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(string f, MothurOut* mout, unsigned long long st, unsigned long long en, string n, map<string, int> nam) {
+	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;
 	}
@@ -98,7 +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; }
@@ -108,7 +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());
 					
@@ -135,11 +139,11 @@ static DWORD WINAPI MySeqSumQualThreadFunction(LPVOID lpParam){
 					else { pDataArray->scores.at(i)[thisScores[i]] += num; }  
 				}
 				
-				count += num;
+				pDataArray->numSeqs += num;
+                pDataArray->count++;
 			}
 		}
 		
-		pDataArray->count = count;
 		in.close();
 		
 		return 0;