Adds sequence parser return values to calling classes

mothur · bf8bc84d996ae9f3268cea80b037b418c43d209b · mothur-westcott committed Jan 10, 2017 · Jan 10, 2017 · bf8bc84
1 parent 2ff08c3
commit bf8bc84d996ae9f3268cea80b037b418c43d209b
Unified Split

Showing with 11 additions and 8 deletions.

+5 −4 source/commands/chimerauchimecommand.cpp

+4 −3 source/commands/chimerauchimecommand.h

+2 −1 source/commands/splitgroupscommand.cpp
diff --git a/source/commands/chimerauchimecommand.cpp b/source/commands/chimerauchimecommand.cpp
@@ -1156,11 +1156,12 @@ int ChimeraUchimeCommand::driverGroups(string outputFName, string filename, stri
 			int start = time(NULL);	 if (m->control_pressed) {  outCountList.close(); m->mothurRemove(countlist); return 0; }
             
 			int error;
-            if (hasCount) { error = cparser->getSeqs(groups[i], filename, "/ab=", "/", true); if ((error == 1) || m->control_pressed) {  return 0; } }
-            else { error = sparser->getSeqs(groups[i], filename, "/ab=", "/", true); if ((error == 1) || m->control_pressed) {  return 0; } }
-			
-			int numSeqs = driver((outputFName + groups[i]), filename, (accnos+groups[i]), (alns+ groups[i]), numChimeras);
+            long long numSeqs = 0;
+            if (hasCount) { error = cparser->getSeqs(groups[i], filename, "/ab=", "/", numSeqs, true); if ((error == 1) || m->control_pressed) {  return 0; } }
+            else { error = sparser->getSeqs(groups[i], filename, "/ab=", "/", numSeqs, true); if ((error == 1) || m->control_pressed) {  return 0; } }
 			totalSeqs += numSeqs;
+            
+			driver((outputFName + groups[i]), filename, (accnos+groups[i]), (alns+ groups[i]), numChimeras);
 			
 			if (m->control_pressed) { return 0; }
 			
diff --git a/source/commands/chimerauchimecommand.h b/source/commands/chimerauchimecommand.h
@@ -188,13 +188,14 @@ static DWORD WINAPI MyUchimeThreadFunction(LPVOID lpParam){
 			
             
 			int error;
+            long long numSeqs = 0;
             if (pDataArray->hasCount) { 
-                error = cparser->getSeqs(pDataArray->groups[i], pDataArray->filename, "/ab=", "/", true); if ((error == 1) || pDataArray->m->control_pressed) {  delete cparser; return 0; }
+                error = cparser->getSeqs(pDataArray->groups[i], pDataArray->filename, "/ab=", "/", numSeqs, true); if ((error == 1) || pDataArray->m->control_pressed) {  delete cparser; return 0; }
             }else {
-               error = parser->getSeqs(pDataArray->groups[i], pDataArray->filename, "/ab=", "/", true); if ((error == 1) || pDataArray->m->control_pressed) {  delete parser; return 0; }
+               error = parser->getSeqs(pDataArray->groups[i], pDataArray->filename, "/ab=", "/", numSeqs, true); if ((error == 1) || pDataArray->m->control_pressed) {  delete parser; return 0; }
             }
 			
-			//int numSeqs = driver((outputFName + groups[i]), filename, (accnos+ groups[i]), (alns+ groups[i]), numChimeras);
+			//driver((outputFName + groups[i]), filename, (accnos+ groups[i]), (alns+ groups[i]), numChimeras);
 			////////////////////////////////////////////////////////////////////////////////////////////////////////////////
 			
 			//to allow for spaces in the path
diff --git a/source/commands/splitgroupscommand.cpp b/source/commands/splitgroupscommand.cpp
@@ -294,7 +294,8 @@ int SplitGroupCommand::runNameGroup(){
             variables["[filename]"] = namefileRoot;
 			string newName = getOutputFileName("name",variables);
 			
-			parser->getSeqs(Groups[i], newFasta, "/ab=", "/", false);
+            long long numSeqs = 0;
+			parser->getSeqs(Groups[i], newFasta, "/ab=", "/", numSeqs, false);
 			outputNames.push_back(newFasta); outputTypes["fasta"].push_back(newFasta);
 			if (m->control_pressed) { delete parser; for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]);	} return 0; }