added count file to get.sabund and get.rabund commands. fixed bug in windows paralell...

[mothur.git] / pairwiseseqscommand.h

diff --git a/pairwiseseqscommand.h b/pairwiseseqscommand.h
index 06dbad975bc6f6b3035024f1260108e65470db64..defccb5227104798667b49c879617bf9d1811200 100644 (file)
--- a/pairwiseseqscommand.h
+++ b/pairwiseseqscommand.h
@@ -95,7 +95,7 @@ struct pairwiseData {
     SequenceDB alignDB;
        
        pairwiseData(){}
-       pairwiseData(string ofn, string al, string sq, string di, bool co, string op, SequenceDB DB, MothurOut* mout, unsigned long long st, unsigned long long en, float ma, float misMa, float gapO, float gapE, int thr, int tid) {
+       pairwiseData(string ofn, string al, string sq, string di, bool co, string op, SequenceDB DB, MothurOut* mout, unsigned long long st, unsigned long long en, float ma, float misMa, float gapO, float gapE, int thr, float cu, int tid) {
                outputFileName = ofn;
                m = mout;
                start = st;
@@ -112,6 +112,7 @@ struct pairwiseData {
         alignDB = DB;
                count = 0;
         output = op;
+        cutoff = cu;
                threadID = tid;
        }
 };
@@ -225,8 +226,6 @@ static DWORD WINAPI MyPairwiseThreadFunction(LPVOID lpParam){
                ofstream outFile((pDataArray->outputFileName).c_str(), ios::trunc);
                outFile.setf(ios::fixed, ios::showpoint);
                outFile << setprecision(4);
-               
-        pDataArray->count = pDataArray->end;
         
         int startTime = time(NULL);
         
@@ -259,7 +258,9 @@ static DWORD WINAPI MyPairwiseThreadFunction(LPVOID lpParam){
         
         if((pDataArray->output == "lt") && pDataArray->start == 0){    outFile << pDataArray->alignDB.getNumSeqs() << endl;    }
                
+        pDataArray->count = 0;
                for(int i=pDataArray->start;i<pDataArray->end;i++){
+            pDataArray->count++;
             
                        if(pDataArray->output == "lt")  {       
                                string name = pDataArray->alignDB.get(i).getName();