changes while testing

[mothur.git] / chimeraperseuscommand.h

diff --git a/chimeraperseuscommand.h b/chimeraperseuscommand.h
index 664200fd85e486ddca190acea16228aeaf76ddc6..b6d4fc9323f659abe52cd70a1e3598a84d9db936 100644 (file)
--- a/chimeraperseuscommand.h
+++ b/chimeraperseuscommand.h
@@ -130,7 +130,7 @@ static DWORD WINAPI MyPerseusThreadFunction(LPVOID lpParam){
         SequenceCountParser* cparser;
                if (pDataArray->hasCount) {
             CountTable* ct = new CountTable();
-            ct->readTable(pDataArray->namefile);
+            ct->readTable(pDataArray->namefile, true);
             cparser = new SequenceCountParser(pDataArray->fastafile, *ct);
             delete ct;
         }else {
@@ -343,10 +343,10 @@ static DWORD WINAPI MyPerseusThreadFunction(LPVOID lpParam){
                                        chimeraFile << j << '\t' << sequences[j].seqName << "\t0\t0\tNull\t0\t0\t0\tNull\tNull\t0.0\t0.0\t0.0\t0\t0\t0\t0.0\t0.0\tgood" << endl;
                                }
                                //report progress
-                               if((j+1) % 100 == 0){   pDataArray->m->mothurOut("Processing sequence: " + toString(j+1) + "\n");               }
+                               if((j+1) % 100 == 0){   pDataArray->m->mothurOutJustToScreen("Processing sequence: " + toString(j+1) + "\n");           }
                        }
                        
-                       if((numSeqs) % 100 != 0){       pDataArray->m->mothurOut("Processing sequence: " + toString(numSeqs) + "\n");           }
+                       if((numSeqs) % 100 != 0){       pDataArray->m->mothurOutJustToScreen("Processing sequence: " + toString(numSeqs) + "\n");               }
                        
                        chimeraFile.close();
                        accnosFile.close();
@@ -362,11 +362,11 @@ static DWORD WINAPI MyPerseusThreadFunction(LPVOID lpParam){
                     if (pDataArray->hasCount) {
                         while (!in.eof()) {
                             in >> name; pDataArray->m->gobble(in);
-                            outCountList << name << '\t' << groups[u] << endl;
+                            outCountList << name << '\t' << pDataArray->groups[u] << endl;
                         }
                         in.close();
                     }else {
-                        map<string, string> thisnamemap = parser->getNameMap(groups[u]);
+                        map<string, string> thisnamemap = parser->getNameMap(pDataArray->groups[u]);
                         map<string, string>::iterator itN;
                         ofstream out;
                         pDataArray->m->openOutputFile(accnosFileName+".temp", out);