added checks to make sure windows processes completed their tasks.

[mothur.git] / pairwiseseqscommand.h

diff --git a/pairwiseseqscommand.h b/pairwiseseqscommand.h
index 33fcfca0b6d0207ed1f282a36061893805745203..06dbad975bc6f6b3035024f1260108e65470db64 100644 (file)
--- a/pairwiseseqscommand.h
+++ b/pairwiseseqscommand.h
@@ -128,7 +128,7 @@ static DWORD WINAPI MyPairwiseSquareThreadFunction(LPVOID lpParam){
                outFile.setf(ios::fixed, ios::showpoint);
                outFile << setprecision(4);
                
-               pDataArray->count = pDataArray->end;
+               pDataArray->count = 0;
         
         int startTime = time(NULL);
         
@@ -162,6 +162,7 @@ static DWORD WINAPI MyPairwiseSquareThreadFunction(LPVOID lpParam){
         if(pDataArray->start == 0){    outFile << pDataArray->alignDB.getNumSeqs() << endl;    }
                
                for(int i=pDataArray->start;i<pDataArray->end;i++){
+            pDataArray->count++;
             
                        string name = pDataArray->alignDB.get(i).getName();
                        //pad with spaces to make compatible
@@ -201,7 +202,7 @@ static DWORD WINAPI MyPairwiseSquareThreadFunction(LPVOID lpParam){
                        }
                        
                }
-               pDataArray->m->mothurOut(toString(pDataArray->end-1) + "\t" + toString(time(NULL) - startTime)); pDataArray->m->mothurOutEndLine();
+               pDataArray->m->mothurOut(toString(pDataArray->count) + "\t" + toString(time(NULL) - startTime)); pDataArray->m->mothurOutEndLine();
                
                outFile.close();
         delete alignment;