X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=seqsummarycommand.h;h=79e8be96974141da315d1038a51096695212ad5c;hb=5b72d1cf3fa48730e5bb70d59cced1e43e1fe424;hp=32947cac88b546e386e7e9960715364e384db3b3;hpb=ae57e166b2ed7b475ec3f466106bd76fabadd063;p=mothur.git

diff --git a/seqsummarycommand.h b/seqsummarycommand.h
index 32947ca..79e8be9 100644
--- a/seqsummarycommand.h
+++ b/seqsummarycommand.h
@@ -25,6 +25,7 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "summary.seqs";			}
 	string getCommandCategory()		{ return "Sequence Processing";		}
+	string getOutputFileNameTag(string, string);
 	string getHelpString();	
 	string getCitation() { return "http://www.mothur.org/wiki/Summary.seqs"; }
 	string getDescription()		{ return "summarize the quality of sequences in an unaligned or aligned fasta file"; }
@@ -61,12 +62,12 @@ private:
 //custom data structure for threads to use.
 // This is passed by void pointer so it can be any data type
 // that can be passed using a single void pointer (LPVOID).
-typedef struct seqSumData {
-	vector<int>* startPosition;
-	vector<int>* endPosition;
-	vector<int>* seqLength; 
-	vector<int>* ambigBases; 
-	vector<int>* longHomoPolymer; 
+struct seqSumData {
+	vector<int> startPosition;
+	vector<int> endPosition;
+	vector<int> seqLength; 
+	vector<int> ambigBases; 
+	vector<int> longHomoPolymer; 
 	string filename; 
 	string sumFile; 
 	unsigned long long start;
@@ -78,12 +79,7 @@ typedef struct seqSumData {
 	
 	
 	seqSumData(){}
-	seqSumData(vector<int>* s, vector<int>* e, vector<int>* l, vector<int>* a, vector<int>* h, string f, string sf, MothurOut* mout, unsigned long long st, unsigned long long en, string na, map<string, int> nam) {
-		startPosition = s;
-		endPosition = e;
-		seqLength = l;
-		ambigBases = a;
-		longHomoPolymer = h;
+	seqSumData(string f, string sf, MothurOut* mout, unsigned long long st, unsigned long long en, string na, map<string, int> nam) {
 		filename = f;
 		sumFile = sf;
 		m = mout;
@@ -96,7 +92,7 @@ typedef struct seqSumData {
 };
 
 /**************************************************************************************************/
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 #else
 static DWORD WINAPI MySeqSumThreadFunction(LPVOID lpParam){ 
 	seqSumData* pDataArray;
@@ -137,11 +133,11 @@ static DWORD WINAPI MySeqSumThreadFunction(LPVOID lpParam){
 				
 				//for each sequence this sequence represents
 				for (int i = 0; i < num; i++) {
-					pDataArray->startPosition->push_back(current.getStartPos());
-					pDataArray->endPosition->push_back(current.getEndPos());
-					pDataArray->seqLength->push_back(current.getNumBases());
-					pDataArray->ambigBases->push_back(current.getAmbigBases());
-					pDataArray->longHomoPolymer->push_back(current.getLongHomoPolymer());
+					pDataArray->startPosition.push_back(current.getStartPos());
+					pDataArray->endPosition.push_back(current.getEndPos());
+					pDataArray->seqLength.push_back(current.getNumBases());
+					pDataArray->ambigBases.push_back(current.getAmbigBases());
+					pDataArray->longHomoPolymer.push_back(current.getLongHomoPolymer());
 				}
 				
 				outSummary << current.getName() << '\t';