X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=summaryqualcommand.h;h=49583b059f5380ce049ac759dd94d8d25b1c7193;hb=4b54ce99af7db8019ea907cd7c2edf789369ada9;hp=31390b4296ff7659fdfb2946d3f37ff33b2877b7;hpb=49d2b7459c5027557564b21e9487dadafbbbdc96;p=mothur.git

diff --git a/summaryqualcommand.h b/summaryqualcommand.h
index 31390b4..49583b0 100644
--- a/summaryqualcommand.h
+++ b/summaryqualcommand.h
@@ -25,8 +25,9 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "summary.qual";			}
 	string getCommandCategory()		{ return "Sequence Processing";		}
-	string getOutputFileNameTag(string, string);
+	
 	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"; }
 	
@@ -35,7 +36,7 @@ public:
 	
 private:
 	bool abort;
-	string qualfile, outputDir, namefile;
+	string qualfile, outputDir, namefile, countfile;
 	vector<string> outputNames;
 	map<string, int> nameMap;
 	int processors;
@@ -62,20 +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;
 	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;
 	}
@@ -109,7 +111,7 @@ 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());