X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=seqsummarycommand.h;h=552f4a08bee284bf914e6a50cd51176864b8b1d8;hp=32947cac88b546e386e7e9960715364e384db3b3;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=ae57e166b2ed7b475ec3f466106bd76fabadd063

diff --git a/seqsummarycommand.h b/seqsummarycommand.h
index 32947ca..552f4a0 100644
--- a/seqsummarycommand.h
+++ b/seqsummarycommand.h
@@ -25,7 +25,9 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "summary.seqs";			}
 	string getCommandCategory()		{ return "Sequence Processing";		}
+	
 	string getHelpString();	
+    string getOutputPattern(string);	
 	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"; }
 	
@@ -33,7 +35,7 @@ public:
 	void help() { m->mothurOut(getHelpString()); }		
 private:
 	bool abort;
-	string fastafile, outputDir, namefile;
+	string fastafile, outputDir, namefile, countfile;
 	int processors;
 	vector<string> outputNames;
 	map<string, int> nameMap;
@@ -61,42 +63,37 @@ 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;
 	unsigned long long end;
 	int count;
 	MothurOut* m;
-	string namefile;
+	bool hasNameMap;
 	map<string, int> nameMap;
 	
 	
 	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, bool na, map<string, int> nam) {
 		filename = f;
 		sumFile = sf;
 		m = mout;
 		start = st;
 		end = en;
-		namefile = na;
+		hasNameMap = na;
 		nameMap = nam;
 		count = 0;
 	}
 };
 
 /**************************************************************************************************/
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 #else
 static DWORD WINAPI MySeqSumThreadFunction(LPVOID lpParam){ 
 	seqSumData* pDataArray;
@@ -117,9 +114,10 @@ static DWORD WINAPI MySeqSumThreadFunction(LPVOID lpParam){
 			in.seekg(pDataArray->start-1); pDataArray->m->gobble(in); 
 		}
 		
-		pDataArray->count = pDataArray->end;
 		for(int i = 0; i < pDataArray->end; i++){ //end is the number of sequences to process
 			
+            pDataArray->count++;
+            
 			if (pDataArray->m->control_pressed) { in.close(); outSummary.close(); pDataArray->count = 1; return 1; }
 			
 			Sequence current(in); pDataArray->m->gobble(in); 
@@ -127,21 +125,21 @@ static DWORD WINAPI MySeqSumThreadFunction(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());
 					
-					if (it == pDataArray->nameMap.end()) { pDataArray->m->mothurOut("[ERROR]: " + current.getName() + " is not in your namefile, please correct."); pDataArray->m->mothurOutEndLine(); pDataArray->m->control_pressed = true; }
+					if (it == pDataArray->nameMap.end()) { pDataArray->m->mothurOut("[ERROR]: " + current.getName() + " is not in your name or count file, please correct."); pDataArray->m->mothurOutEndLine(); pDataArray->m->control_pressed = true; }
 					else { num = it->second; }
 				}
 				
 				//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';