added mothurOutJustToScreen function and changed all counter outputs to use it.

diff --git a/aligncommand.cpp b/aligncommand.cpp
index fc98c10924138a3aa168dabbc609f64bfb89f3e4..f9c0436c62874864279e533a3258d72bf2f6cf2d 100644 (file)
--- a/aligncommand.cpp
+++ b/aligncommand.cpp
@@ -644,11 +644,11 @@ int AlignCommand::driver(linePair* filePos, string alignFName, string reportFNam
                        #endif
                        
                        //report progress
-                       if((count) % 100 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine();           }
+                       if((count) % 100 == 0){ m->mothurOutJustToScreen(toString(count) + "\n");               }
                        
                }
                //report progress
-               if((count) % 100 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine();           }
+               if((count) % 100 != 0){ m->mothurOutJustToScreen(toString(count) + "\n");               }
                
                delete alignment;
                alignmentFile.close();

diff --git a/aligncommand.h b/aligncommand.h
index e5e9601781fdff5e35125b49de6ba452e180f9a2..4e1b8d39f81dc067c60575d1938a21fd1de8dee0 100644 (file)
--- a/aligncommand.h
+++ b/aligncommand.h
@@ -245,11 +245,11 @@ static DWORD WINAPI MyAlignThreadFunction(LPVOID lpParam){
                        delete candidateSeq;
                        
                        //report progress
-                       if((pDataArray->count) % 100 == 0){     pDataArray->m->mothurOut(toString(pDataArray->count)); pDataArray->m->mothurOutEndLine();               }
+                       if((pDataArray->count) % 100 == 0){     pDataArray->m->mothurOutJustToScreen(toString(pDataArray->count)+"\n");         }
                        
                }
                //report progress
-               if((pDataArray->count) % 100 != 0){     pDataArray->m->mothurOut(toString(pDataArray->count)); pDataArray->m->mothurOutEndLine();               }
+               if((pDataArray->count) % 100 != 0){     pDataArray->m->mothurOutJustToScreen(toString(pDataArray->count)+"\n");         }
                
                delete alignment;
                delete templateDB;

diff --git a/chimeraccodecommand.cpp b/chimeraccodecommand.cpp
index 7adf82814ee5447edef7e203bbb046ad61c51b07..627f3a950f69bec32971b65b96d7eba89942558a 100644 (file)
--- a/chimeraccodecommand.cpp
+++ b/chimeraccodecommand.cpp
@@ -548,10 +548,10 @@ int ChimeraCcodeCommand::driver(linePair* filePos, string outputFName, string fi
                        #endif
                        
                        //report progress
-                       if((count) % 100 == 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
+                       if((count) % 100 == 0){ m->mothurOutJustToScreen("Processing sequence: " + toString(count) + "\n");             }
                }
                //report progress
-               if((count) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
+               if((count) % 100 != 0){ m->mothurOutJustToScreen("Processing sequence: " + toString(count) + "\n");     }
                
                out.close();
                out2.close();

diff --git a/chimeracheckcommand.cpp b/chimeracheckcommand.cpp
index 6caa606dc10ee387cd2eb829d264a7d17f0ee670..31a36f73c6d0339d775dd6a1a4efa8e523c0f14f 100644 (file)
--- a/chimeracheckcommand.cpp
+++ b/chimeracheckcommand.cpp
@@ -547,11 +547,10 @@ int ChimeraCheckCommand::driver(linePair* filePos, string outputFName, string fi
                        #endif
                        
                        //report progress
-                       if((count) % 100 == 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
-            count++;
+                       if((count) % 100 == 0){ m->mothurOutJustToScreen("Processing sequence: " + toString(count) + "\n");             }
                }
                //report progress
-               if((count) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
+               if((count) % 100 != 0){ m->mothurOutJustToScreen("Processing sequence: " + toString(count) + "\n");     }
                
                out.close();
                inFASTA.close();
@@ -599,10 +598,10 @@ int ChimeraCheckCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File
                        delete candidateSeq;
                        
                        //report progress
-                       if((i+1) % 100 == 0){  cout << "Processing sequence: " << (i+1) << endl;        m->mothurOutJustToLog("Processing sequence: " + toString(i+1) + "\n");          }
+                       if((i+1) % 100 == 0){  cout << "Processing sequence: " << (i+1) << endl;                }
                }
                //report progress
-               if(num % 100 != 0){             cout << "Processing sequence: " << num << endl; m->mothurOutJustToLog("Processing sequence: " + toString(num) + "\n");  }
+               if(num % 100 != 0){             cout << "Processing sequence: " << num << endl;         }
                
                return 0;
        }

diff --git a/chimeraperseuscommand.cpp b/chimeraperseuscommand.cpp
index f7dc597cf8ca514712bf06f29f2010982d6c03c9..fd94fcab7e289590da462eef7f03fc7069ab551f 100644 (file)
--- a/chimeraperseuscommand.cpp
+++ b/chimeraperseuscommand.cpp
@@ -1046,10 +1046,10 @@ int ChimeraPerseusCommand::driver(string chimeraFileName, vector<seqData>& seque
                        }
        
                        //report progress
-                       if((i+1) % 100 == 0){   m->mothurOut("Processing sequence: " + toString(i+1) + "\n");           }
+                       if((i+1) % 100 == 0){   m->mothurOutJustToScreen("Processing sequence: " + toString(i+1) + "\n");               }
                }
                
-               if((numSeqs) % 100 != 0){       m->mothurOut("Processing sequence: " + toString(numSeqs) + "\n");               }
+               if((numSeqs) % 100 != 0){       m->mothurOutJustToScreen("Processing sequence: " + toString(numSeqs) + "\n");           }
                
                chimeraFile.close();
                accnosFile.close();

diff --git a/chimeraperseuscommand.h b/chimeraperseuscommand.h
index 4fa4cfff55e9582ffd699d5a66409717df8fbd36..99a66f8838e4ccbbe10fe72ef66135be7dfda869 100644 (file)
--- a/chimeraperseuscommand.h
+++ b/chimeraperseuscommand.h
@@ -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();

diff --git a/chimerapintailcommand.cpp b/chimerapintailcommand.cpp
index d2b73998da9e0319880a8baf5948ed15a6132ae6..9d492afe950713cefd4d1fad7fcd72a6da74640c 100644 (file)
--- a/chimerapintailcommand.cpp
+++ b/chimerapintailcommand.cpp
@@ -636,10 +636,10 @@ int ChimeraPintailCommand::driver(linePair* filePos, string outputFName, string
                        #endif
                        
                        //report progress
-                       if((count) % 100 == 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
+                       if((count) % 100 == 0){ m->mothurOutJustToScreen("Processing sequence: " + toString(count) + "\n");             }
                }
                //report progress
-               if((count) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
+               if((count) % 100 != 0){ m->mothurOutJustToScreen("Processing sequence: " + toString(count) + "\n");             }
                
                out.close();
                out2.close();
@@ -695,10 +695,10 @@ int ChimeraPintailCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_Fi
                        delete candidateSeq;
                        
                        //report progress
-                       if((i+1) % 100 == 0){  cout << "Processing sequence: " << (i+1) << endl;        m->mothurOutJustToLog("Processing sequence: " + toString(i+1) + "\n");          }
+                       if((i+1) % 100 == 0){  cout << "Processing sequence: " << (i+1) << endl;                        }
                }
                //report progress
-               if(num % 100 != 0){             cout << "Processing sequence: " << num << endl; m->mothurOutJustToLog("Processing sequence: " + toString(num) + "\n");  }
+               if(num % 100 != 0){             cout << "Processing sequence: " << num << endl;         }
                
                                
                return 0;

diff --git a/chimeraslayercommand.cpp b/chimeraslayercommand.cpp
index d16843c8d612fac2bde8c03db8e45ce68e869412..e7003c4d88bfe40266dffcf0770e3037cb39f38f 100644 (file)
--- a/chimeraslayercommand.cpp
+++ b/chimeraslayercommand.cpp
@@ -1823,10 +1823,10 @@ int ChimeraSlayerCommand::driver(linePair filePos, string outputFName, string fi
                        
                        delete candidateSeq;
                        //report progress
-                       if((count) % 100 == 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
+                       if((count) % 100 == 0){ m->mothurOutJustToScreen("Processing sequence: " + toString(count) + "\n");             }
                }
                //report progress
-               if((count) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
+               if((count) % 100 != 0){ m->mothurOutJustToScreen("Processing sequence: " + toString(count)+ "\n");              }
                
                int numNoParents = chimera->getNumNoParents();
                if (numNoParents == count) { m->mothurOut("[WARNING]: megablast returned 0 potential parents for all your sequences. This could be due to formatdb.exe not being setup properly, please check formatdb.log for errors."); m->mothurOutEndLine(); } 
@@ -1973,10 +1973,10 @@ int ChimeraSlayerCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_Fil
                        delete candidateSeq;
                        
                        //report progress
-                       if((i+1) % 100 == 0){  cout << "Processing sequence: " << (i+1) << endl;        m->mothurOutJustToLog("Processing sequence: " + toString(i+1) + "\n");          }
+                       if((i+1) % 100 == 0){  cout << "Processing sequence: " << (i+1) << endl;                }
                }
                //report progress
-               if(num % 100 != 0){             cout << "Processing sequence: " << num << endl; m->mothurOutJustToLog("Processing sequence: " + toString(num) + "\n");  }
+               if(num % 100 != 0){             cout << "Processing sequence: " << num << endl;         }
                
                int numNoParents = chimera->getNumNoParents();
                if (numNoParents == num) { cout << "[WARNING]: megablast returned 0 potential parents for all your sequences. This could be due to formatdb.exe not being setup properly, please check formatdb.log for errors." << endl; }

diff --git a/chimeraslayercommand.h b/chimeraslayercommand.h
index 68e03b8f881930fd919fc36b2283cc4024d3a2b0..e8afc61a5b32e5379d8c02a47a9a965eb3d1606d 100644 (file)
--- a/chimeraslayercommand.h
+++ b/chimeraslayercommand.h
@@ -327,10 +327,10 @@ static DWORD WINAPI MySlayerThreadFunction(LPVOID lpParam){
                        
                        delete candidateSeq;
                        //report progress
-                       if((pDataArray->count) % 100 == 0){     pDataArray->m->mothurOut("Processing sequence: " + toString(pDataArray->count)); pDataArray->m->mothurOutEndLine();             }
+                       if((pDataArray->count) % 100 == 0){     pDataArray->m->mothurOutJustToScreen("Processing sequence: " + toString(pDataArray->count) +"\n");      }
                }
                //report progress
-               if((pDataArray->count) % 100 != 0){     pDataArray->m->mothurOut("Processing sequence: " + toString(pDataArray->count)); pDataArray->m->mothurOutEndLine();             }
+               if((pDataArray->count) % 100 != 0){     pDataArray->m->mothurOutJustToScreen("Processing sequence: " + toString(pDataArray->count)+"\n");               }
                
                pDataArray->numNoParents = chimera->getNumNoParents();
                if (pDataArray->numNoParents == pDataArray->count) {    pDataArray->m->mothurOut("[WARNING]: megablast returned 0 potential parents for all your sequences. This could be due to formatdb.exe not being setup properly, please check formatdb.log for errors.\n"); }
@@ -506,10 +506,10 @@ static DWORD WINAPI MySlayerGroupThreadFunction(LPVOID lpParam){
                                if (inFASTA.eof()) { break; }
                                
                                //report progress
-                               if((numSeqs) % 100 == 0){       pDataArray->m->mothurOut("Processing sequence: " + toString(numSeqs)); pDataArray->m->mothurOutEndLine();               }
+                               if((numSeqs) % 100 == 0){       pDataArray->m->mothurOutJustToScreen("Processing sequence: " + toString(numSeqs)+"\n"); pDataArray->m->mothurOutEndLine();              }
                        }
                        //report progress
-                       if((numSeqs) % 100 != 0){       pDataArray->m->mothurOut("Processing sequence: " + toString(numSeqs)); pDataArray->m->mothurOutEndLine();               }
+                       if((numSeqs) % 100 != 0){       pDataArray->m->mothurOutJustToScreen("Processing sequence: " + toString(numSeqs)+"\n");                 }
                        
                        pDataArray->numNoParents = chimera->getNumNoParents();
                        if (pDataArray->numNoParents == numSeqs) {      pDataArray->m->mothurOut("[WARNING]: megablast returned 0 potential parents for all your sequences. This could be due to formatdb.exe not being setup properly, please check formatdb.log for errors.\n"); }

diff --git a/classifyseqscommand.cpp b/classifyseqscommand.cpp
index 8b6a77b4936b0095741747cb255e143a1cd78e64..edbd4c466bfa500bcaa72b1f8266f3dd40185ae9 100644 (file)
--- a/classifyseqscommand.cpp
+++ b/classifyseqscommand.cpp
@@ -1151,11 +1151,11 @@ int ClassifySeqsCommand::driver(linePair* filePos, string taxFName, string tempT
                        #endif
                        
                        //report progress
-                       if((count) % 100 == 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
+                       if((count) % 100 == 0){ m->mothurOutJustToScreen("Processing sequence: " + toString(count) +"\n");              }
                        
                }
                //report progress
-               if((count) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
+               if((count) % 100 != 0){ m->mothurOutJustToScreen("Processing sequence: " + toString(count)+"\n");               }
                        
                inFASTA.close();
                outTax.close();

diff --git a/classifyseqscommand.h b/classifyseqscommand.h
index f8a820dcf6347aa39432d461c78f6f8613ae6acf..59d9ee275800195255961639d77fb6c57d97f417 100644 (file)
--- a/classifyseqscommand.h
+++ b/classifyseqscommand.h
@@ -211,11 +211,11 @@ static DWORD WINAPI MyClassThreadFunction(LPVOID lpParam){
                        }
                        delete candidateSeq;
                        //report progress
-                       if((pDataArray->count) % 100 == 0){     pDataArray->m->mothurOut("Processing sequence: " + toString(pDataArray->count)); pDataArray->m->mothurOutEndLine();             }
+                       if((pDataArray->count) % 100 == 0){     pDataArray->m->mothurOutJustToScreen("Processing sequence: " + toString(pDataArray->count)+"\n");       }
                        
                }
                //report progress
-               if((pDataArray->count) % 100 != 0){     pDataArray->m->mothurOut("Processing sequence: " + toString(pDataArray->count)); pDataArray->m->mothurOutEndLine();             }
+               if((pDataArray->count) % 100 != 0){     pDataArray->m->mothurOutJustToScreen("Processing sequence: " + toString(pDataArray->count)+"\n");               }
                
                delete myclassify;
                inFASTA.close();

diff --git a/clusterfragmentscommand.cpp b/clusterfragmentscommand.cpp
index ef199ccdf0a11efba99eaf0299ff50413b70b89f..1b8cc71706710a3c80d53f6ff2fd877d07d98103 100644 (file)
--- a/clusterfragmentscommand.cpp
+++ b/clusterfragmentscommand.cpp
@@ -262,10 +262,10 @@ int ClusterFragmentsCommand::execute(){
                                alignSeqs[i].active = 0;
                                
                        }//end if active i
-                       if(i % 100 == 0)        { m->mothurOut(toString(i) + "\t" + toString(numSeqs - count) + "\t" + toString(count)); m->mothurOutEndLine(); }
+                       if(i % 100 == 0)        { m->mothurOutJustToScreen(toString(i) + "\t" + toString(numSeqs - count) + "\t" + toString(count)+"\n");       }
                }
                
-               if(numSeqs % 100 != 0)  { m->mothurOut(toString(numSeqs) + "\t" + toString(numSeqs - count) + "\t" + toString(count)); m->mothurOutEndLine();   }
+               if(numSeqs % 100 != 0)  { m->mothurOutJustToScreen(toString(numSeqs) + "\t" + toString(numSeqs - count) + "\t" + toString(count)+"\n"); }
        
                
                string fileroot = outputDir + m->getRootName(m->getSimpleName(fastafile));

diff --git a/distancecommand.cpp b/distancecommand.cpp
index 19094e9e76ee76981b9d5bd501df3876d401b387..9243df3873a9687d43da9da940b32da1ce9a5091 100644 (file)
--- a/distancecommand.cpp
+++ b/distancecommand.cpp
@@ -675,11 +675,11 @@ int DistanceCommand::driver(int startLine, int endLine, string dFileName, float
                        if (output == "lt") { outFile << endl; }
                        
                        if(i % 100 == 0){
-                               m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
+                               m->mothurOutJustToScreen(toString(i) + "\t" + toString(time(NULL) - startTime)+"\n"); 
                        }
                        
                }
-               m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
+               m->mothurOutJustToScreen(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)+"\n");
                
                outFile.close();
                delete distCalculator;
@@ -745,11 +745,11 @@ int DistanceCommand::driver(int startLine, int endLine, string dFileName, string
                        outFile << endl; 
                        
                        if(i % 100 == 0){
-                               m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
+                               m->mothurOutJustToScreen(toString(i) + "\t" + toString(time(NULL) - startTime)+"\n");
                        }
                        
                }
-               m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
+               m->mothurOutJustToScreen(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)+"\n");
                
                outFile.close();
                delete distCalculator;
@@ -812,8 +812,7 @@ int DistanceCommand::driverMPI(int startLine, int endLine, MPI_File& outMPI, flo
                        }
                        
                        if(i % 100 == 0){
-                               m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
-                               cout << i << '\t' << (time(NULL) - startTime) << endl;
+                               m->mothurOutJustToScreen(toString(i) + "\t" + toString(time(NULL) - startTime)+"\n"); 
                        }
                        
                         
@@ -829,8 +828,7 @@ int DistanceCommand::driverMPI(int startLine, int endLine, MPI_File& outMPI, flo
                        
                }
                
-               m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
-               cout << (endLine-1) << '\t' << (time(NULL) - startTime) << endl;        
+               m->mothurOutJustToScreen(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)+"\n");
                delete distCalculator;
                return 1;
        }
@@ -907,9 +905,7 @@ int DistanceCommand::driverMPI(int startLine, int endLine, string file, unsigned
 
                
                        if(i % 100 == 0){
-                               m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
-                               cout << i << '\t' << (time(NULL) - startTime) << endl;
-                       }
+                               m->mothurOutJustToScreen(toString(i) + "\t" + toString(time(NULL) - startTime)+"\n");                   }
                        
                        
                        //send results to parent
@@ -923,8 +919,8 @@ int DistanceCommand::driverMPI(int startLine, int endLine, string file, unsigned
                        delete buf;
                }
                
-               m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
-               cout << (endLine-1) << '\t' << (time(NULL) - startTime) << endl;
+               m->mothurOutJustToScreen(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)+"\n");
+               
                MPI_File_close(&outMPI);
                delete distCalculator;
                
@@ -1002,8 +998,7 @@ int DistanceCommand::driverMPI(int startLine, int endLine, string file, unsigned
 
                
                        if(i % 100 == 0){
-                               m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
-                               cout << i << '\t' << (time(NULL) - startTime) << endl;
+                               m->mothurOutJustToScreen(toString(i) + "\t" + toString(time(NULL) - startTime)+"\n"); 
                        }
                        
                        
@@ -1018,8 +1013,8 @@ int DistanceCommand::driverMPI(int startLine, int endLine, string file, unsigned
                        delete buf;
                }
                
-               m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
-               cout << (endLine-1) << '\t' << (time(NULL) - startTime) << endl;
+               m->mothurOutJustToScreen(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)+"\n");
+               
                MPI_File_close(&outMPI);
                delete distCalculator;
                return 1;

diff --git a/distancecommand.h b/distancecommand.h
index af55406b372dbf0f56a546be4de2bc87f5072614..2f53232b5943d835e8c27adf7374a5e3a8ce168f 100644 (file)
--- a/distancecommand.h
+++ b/distancecommand.h
@@ -119,11 +119,10 @@ static DWORD WINAPI MyDistThreadFunction(LPVOID lpParam){
                                if (pDataArray->output == "lt") { outFile << endl; }
                                
                                if(i % 100 == 0){
-                                       pDataArray->m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); pDataArray->m->mothurOutEndLine();
-                               }
+                                       pDataArray->m->mothurOutJustToScreen(toString(i) + "\t" + toString(time(NULL) - startTime)+"\n");                               }
                                pDataArray->count++;
                        }
-                       pDataArray->m->mothurOut(toString(pDataArray->count) + "\t" + toString(time(NULL) - startTime)); pDataArray->m->mothurOutEndLine();
+                       pDataArray->m->mothurOutJustToScreen(toString(pDataArray->count) + "\t" + toString(time(NULL) - startTime)+"\n");
                }else{
                        if(pDataArray->startLine == 0){ outFile << pDataArray->alignDB.getNumSeqs() << endl;    }
                        
@@ -148,11 +147,11 @@ static DWORD WINAPI MyDistThreadFunction(LPVOID lpParam){
                                outFile << endl; 
                                
                                if(i % 100 == 0){
-                                       pDataArray->m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); pDataArray->m->mothurOutEndLine();
+                                       pDataArray->m->mothurOutJustToScreen(toString(i) + "\t" + toString(time(NULL) - startTime)+"\n"); 
                                }
                                pDataArray->count++;
                        }
-                       pDataArray->m->mothurOut(toString(pDataArray->count) + "\t" + toString(time(NULL) - startTime)); pDataArray->m->mothurOutEndLine();
+                       pDataArray->m->mothurOutJustToScreen(toString(pDataArray->count) + "\t" + toString(time(NULL) - startTime)+"\n"); 
                }
                
                outFile.close();

diff --git a/filterseqscommand.cpp b/filterseqscommand.cpp
index b17d9ed6799d9c8287664cf63241b0fde01bf40e..8b68988884acb408d0e72c5c3fa407a7b9f241b6 100644 (file)
--- a/filterseqscommand.cpp
+++ b/filterseqscommand.cpp
@@ -558,7 +558,7 @@ int FilterSeqsCommand::driverMPIRun(int start, int num, MPI_File& inMPI, MPI_Fil
 
                        }
                        
-                       if((i+1) % 100 == 0){   cout << (i+1) << endl;   m->mothurOutJustToLog(toString(i+1) + "\n");   }
+                       if((i+1) % 100 == 0){   cout << (i+1) << endl;          }
                }
                
                if(outputString != ""){ //output to file 
@@ -572,7 +572,7 @@ int FilterSeqsCommand::driverMPIRun(int start, int num, MPI_File& inMPI, MPI_Fil
                        delete buf;
                }
                
-               if((num) % 100 != 0){   cout << (num) << endl;   m->mothurOutJustToLog(toString(num) + "\n");   }
+               if((num) % 100 != 0){   cout << (num) << endl;          }
                        
                return 0;
        }
@@ -623,10 +623,10 @@ int FilterSeqsCommand::driverRunFilter(string F, string outputFilename, string i
                        #endif
                        
                        //report progress
-                       if((count) % 100 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine();           }
+                       if((count) % 100 == 0){ m->mothurOutJustToScreen(toString(count)+"\n");         }
                }
                //report progress
-               if((count) % 100 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine();           }
+               if((count) % 100 != 0){ m->mothurOutJustToScreen(toString(count)+"\n");                 }
                
                
                out.close();
@@ -1006,10 +1006,10 @@ int FilterSeqsCommand::driverCreateFilter(Filters& F, string filename, linePair*
                        #endif
                        
                        //report progress
-                       if((count) % 100 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine();           }
+                       if((count) % 100 == 0){ m->mothurOutJustToScreen(toString(count)+"\n");                 }
                }
                //report progress
-               if((count) % 100 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine();           }
+               if((count) % 100 != 0){ m->mothurOutJustToScreen(toString(count)+"\n");         }
                in.close();
                
                return count;
@@ -1052,11 +1052,11 @@ int FilterSeqsCommand::MPICreateFilter(int start, int num, Filters& F, MPI_File&
                        cout.flush();
                                                
                        //report progress
-                       if((i+1) % 100 == 0){   cout << (i+1) << endl;   m->mothurOutJustToLog(toString(i+1) + "\n");   }
+                       if((i+1) % 100 == 0){   cout << (i+1) << endl;          }
                }
                
                //report progress
-               if((num) % 100 != 0){   cout << num << endl; m->mothurOutJustToLog(toString(num) + "\n");       }
+               if((num) % 100 != 0){   cout << num << endl;    }
                
                return 0;
        }

diff --git a/filterseqscommand.h b/filterseqscommand.h
index 90c13f8ee82722570d129d74874b519cc4ee9a60..ed7cfd1f98ddb6f44c8c7f690447d8dea1d4f6f0 100644 (file)
--- a/filterseqscommand.h
+++ b/filterseqscommand.h
@@ -168,10 +168,10 @@ static DWORD WINAPI MyCreateFilterThreadFunction(LPVOID lpParam){
                        }\r
             pDataArray->count++;\r
             //report progress\r
-                       if((i) % 100 == 0){     pDataArray->m->mothurOut(toString(i)); pDataArray->m->mothurOutEndLine();               }\r
+                       if((i) % 100 == 0){     pDataArray->m->mothurOutJustToScreen(toString(i)+"\n");                 }\r
                }\r
                \r
-        if((pDataArray->count) % 100 != 0){    pDataArray->m->mothurOut(toString(pDataArray->count)); pDataArray->m->mothurOutEndLine();               }\r
+        if((pDataArray->count) % 100 != 0){    pDataArray->m->mothurOutJustToScreen(toString(pDataArray->count)+"\n");                 }\r
         \r
                in.close();\r
                \r
@@ -223,10 +223,10 @@ static DWORD WINAPI MyRunFilterThreadFunction(LPVOID lpParam){
             }\r
             pDataArray->count++;\r
             //report progress\r
-                       if((i) % 100 == 0){     pDataArray->m->mothurOut(toString(i)); pDataArray->m->mothurOutEndLine();               }\r
+                       if((i) % 100 == 0){     pDataArray->m->mothurOutJustToScreen(toString(i)+"\n");                 }\r
                }\r
                \r
-        if((pDataArray->count) % 100 != 0){    pDataArray->m->mothurOut(toString(pDataArray->count)); pDataArray->m->mothurOutEndLine();               }\r
+        if((pDataArray->count) % 100 != 0){    pDataArray->m->mothurOutJustToScreen(toString(pDataArray->count)+"\n");                 }\r
         \r
                in.close();\r
         out.close();\r

diff --git a/matrixoutputcommand.cpp b/matrixoutputcommand.cpp
index 310e32bf23e048c73ae37579ac2e8e2d1cb8b0ff..a53a3dcb92837f112771f44ef39219d9e36a277a 100644 (file)
--- a/matrixoutputcommand.cpp
+++ b/matrixoutputcommand.cpp
@@ -652,7 +652,7 @@ int MatrixOutputCommand::process(vector<SharedRAbundVector*> thisLookup){
             }
             
             if (subsample && (thisIter != 0)) {  
-                if((thisIter) % 100 == 0){     m->mothurOut(toString(thisIter)); m->mothurOutEndLine();                }
+                if((thisIter) % 100 == 0){     m->mothurOutJustToScreen(toString(thisIter)+"\n");              }
                 calcDistsTotals.push_back(calcDists);
                 for (int i = 0; i < calcDists.size(); i++) {
                     for (int j = 0; j < calcDists[i].size(); j++) {

diff --git a/mothurout.cpp b/mothurout.cpp
index 0efa551565c6e18001cd6ed53e0643a50f525f37..fc16d204b142e5a6f55783f56bc52aafb8e6a4d1 100644 (file)
--- a/mothurout.cpp
+++ b/mothurout.cpp
@@ -348,6 +348,27 @@ void MothurOut::mothurOut(string output) {
        }
 }
 /*********************************************************************************************/
+void MothurOut::mothurOutJustToScreen(string output) {
+       try {
+               
+#ifdef USE_MPI
+        int pid;
+        MPI_Comm_rank(MPI_COMM_WORLD, &pid);
+        
+        if (pid == 0) { //only one process should output to screen
+#endif
+            logger() << output;
+            
+#ifdef USE_MPI
+        }
+#endif
+       }
+       catch(exception& e) {
+               errorOut(e, "MothurOut", "MothurOut");
+               exit(1);
+       }
+}
+/*********************************************************************************************/
 void MothurOut::mothurOutEndLine() {
        try {
                #ifdef USE_MPI

diff --git a/mothurout.h b/mothurout.h
index 4a46e051b67bb08caee8c4d97f3947c366d01926..643ecd58a149aebc1ac88f500d4658de98d5e145 100644 (file)
--- a/mothurout.h
+++ b/mothurout.h
@@ -40,6 +40,7 @@ class MothurOut {
                void mothurOutEndLine(); //writes to cout and the logfile
                void mothurOut(string, ofstream&); //writes to the ofstream, cout and the logfile
                void mothurOutEndLine(ofstream&); //writes to the ofstream, cout and the logfile
+        void mothurOutJustToScreen(string); //writes to cout
                void mothurOutJustToLog(string);
                void errorOut(exception&, string, string);
                void closeLog();

diff --git a/myseqdist.cpp b/myseqdist.cpp
index 78255d8f73d894c7cb4032d925b684843094bee7..28538959a80d8b2a600c33a4c1ff0ed0a77fb75c 100644 (file)
--- a/myseqdist.cpp
+++ b/myseqdist.cpp
@@ -219,11 +219,11 @@ int correctDist::driver(int start, int end, string distFileName){
                        }
                        distFile << endl;
                        
-                       if(i % 100 == 0){ m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine(); }
+                       if(i % 100 == 0){ m->mothurOutJustToScreen(toString(i) + "\t" + toString(time(NULL) - startTime)+"\n"); }
                }
                distFile.close();
                
-               if((end-1) % 100 != 0){ m->mothurOut(toString(end-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine(); }
+               if((end-1) % 100 != 0){ m->mothurOutJustToScreen(toString(end-1) + "\t" + toString(time(NULL) - startTime)+"\n"); }
                m->mothurOut("Done.\n");
                
                return 0;

diff --git a/pairwiseseqscommand.cpp b/pairwiseseqscommand.cpp
index c9e5ecfdfda727427793e98aaed0270cdcd6e046..7d96e31d1eefb534729e421b266092db1536aa46 100644 (file)
--- a/pairwiseseqscommand.cpp
+++ b/pairwiseseqscommand.cpp
@@ -689,11 +689,11 @@ int PairwiseSeqsCommand::driver(int startLine, int endLine, string dFileName, fl
                        if (output == "lt") { outFile << endl; }
                        
                        if(i % 100 == 0){
-                               m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
+                               m->mothurOutJustToScreen(toString(i) + "\t" + toString(time(NULL) - startTime)+"\n");
                        }
                        
                }
-               m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
+               m->mothurOutJustToScreen(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)+"\n");
                
                outFile.close();
         delete alignment;
@@ -783,11 +783,11 @@ int PairwiseSeqsCommand::driver(int startLine, int endLine, string dFileName, st
                        outFile << endl; 
                        
                        if(i % 100 == 0){
-                               m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
+                               m->mothurOutJustToScreen(toString(i) + "\t" + toString(time(NULL) - startTime)+"\n"); 
                        }
                        
                }
-               m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
+               m->mothurOutJustToScreen(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)+"\n");
                
                outFile.close();
         delete alignment;

diff --git a/pairwiseseqscommand.h b/pairwiseseqscommand.h
index defccb5227104798667b49c879617bf9d1811200..cb68e7fa8ef44ce231284e11f3f9a669396d6a44 100644 (file)
--- a/pairwiseseqscommand.h
+++ b/pairwiseseqscommand.h
@@ -199,11 +199,11 @@ static DWORD WINAPI MyPairwiseSquareThreadFunction(LPVOID lpParam){
                        outFile << endl; 
                        
                        if(i % 100 == 0){
-                               pDataArray->m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); pDataArray->m->mothurOutEndLine();
+                               pDataArray->m->mothurOutJustToScreen(toString(i) + "\t" + toString(time(NULL) - startTime)+"\n"); 
                        }
                        
                }
-               pDataArray->m->mothurOut(toString(pDataArray->count) + "\t" + toString(time(NULL) - startTime)); pDataArray->m->mothurOutEndLine();
+               pDataArray->m->mothurOutJustToScreen(toString(pDataArray->count) + "\t" + toString(time(NULL) - startTime)+"\n");
                
                outFile.close();
         delete alignment;
@@ -302,11 +302,11 @@ static DWORD WINAPI MyPairwiseThreadFunction(LPVOID lpParam){
                        if (pDataArray->output == "lt") { outFile << endl; }
                        
                        if(i % 100 == 0){
-                               pDataArray->m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); pDataArray->m->mothurOutEndLine();
+                               pDataArray->m->mothurOutJustToScreen(toString(i) + "\t" + toString(time(NULL) - startTime)+"\n"); 
                        }
                        
                }
-               pDataArray->m->mothurOut(toString(pDataArray->end-1) + "\t" + toString(time(NULL) - startTime)); pDataArray->m->mothurOutEndLine();
+               pDataArray->m->mothurOutJustToScreen(toString(pDataArray->end-1) + "\t" + toString(time(NULL) - startTime)+"\n");
                
                outFile.close();
         delete alignment;

diff --git a/pcrseqscommand.h b/pcrseqscommand.h
index 16c1e29be5f9cbba00180a55a746bbe923b3cbdb..581675efa046b400b547e46ab64988e83a199714 100644 (file)
--- a/pcrseqscommand.h
+++ b/pcrseqscommand.h
@@ -265,10 +265,10 @@ static DWORD WINAPI MyPcrThreadFunction(LPVOID lpParam){
                        }
                                                
                        //report progress
-                       if((i+1) % 100 == 0){   pDataArray->m->mothurOut("Processing sequence: " + toString(i+1)); pDataArray->m->mothurOutEndLine();           }
+                       if((i+1) % 100 == 0){   pDataArray->m->mothurOutJustToScreen("Processing sequence: " + toString(i+1)+"\n");     }
                }
                //report progress
-               if((pDataArray->count) % 100 != 0){     pDataArray->m->mothurOut("Thread Processing sequence: " + toString(pDataArray->count)); pDataArray->m->mothurOutEndLine();              }
+               if((pDataArray->count) % 100 != 0){     pDataArray->m->mothurOutJustToScreen("Thread Processing sequence: " + toString(pDataArray->count)+"\n");                }
                
                goodFile.close();
                inFASTA.close();

diff --git a/prcseqscommand.cpp b/prcseqscommand.cpp
index cf93cb796104aa90428e5466546c9839789216f7..8db6c24ff05ce4a5a23bc11a9021b208f5e65d55 100644 (file)
--- a/prcseqscommand.cpp
+++ b/prcseqscommand.cpp
@@ -696,10 +696,10 @@ int PcrSeqsCommand::driverPcr(string filename, string goodFasta, string badFasta
 #endif
                        
                        //report progress
-                       if((count) % 100 == 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
+                       if((count) % 100 == 0){ m->mothurOutJustToScreen("Processing sequence: " + toString(count)+"\n");               }
                }
                //report progress
-               if((count) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
+               if((count) % 100 != 0){ m->mothurOutJustToScreen("Processing sequence: " + toString(count)+"\n");       }
                
         badFile.close();
                goodFile.close();

diff --git a/preclustercommand.cpp b/preclustercommand.cpp
index c2564c1f769a835fd85559f10811672eb6a34e0d..bbf8df27ac5ee691f091f150638b781f85486a11 100644 (file)
--- a/preclustercommand.cpp
+++ b/preclustercommand.cpp
@@ -597,7 +597,7 @@ int PreClusterCommand::process(string newMapFile){
                     out << "ideal_seq_" << (i+1) << '\t' << alignSeqs[i].numIdentical << endl << chunk << endl;;
                     
                 }//end if active i
-                if(i % 100 == 0)       { m->mothurOut(toString(i) + "\t" + toString(numSeqs - count) + "\t" + toString(count)); m->mothurOutEndLine(); }
+                if(i % 100 == 0)       { m->mothurOutJustToScreen(toString(i) + "\t" + toString(numSeqs - count) + "\t" + toString(count)+"\n");       }
             }
         }else {
             map<int, string> mapFile;
@@ -632,7 +632,7 @@ int PreClusterCommand::process(string newMapFile){
                     }//end abundance check
                 }//end for loop j
                 
-                if(i % 100 == 0)       { m->mothurOut(toString(i) + "\t" + toString(numSeqs - count) + "\t" + toString(count)); m->mothurOutEndLine(); }
+                if(i % 100 == 0)       { m->mothurOutJustToScreen(toString(i) + "\t" + toString(numSeqs - count) + "\t" + toString(count)+"\n");       }
             }
             
             for (int i = 0; i < numSeqs; i++) {

diff --git a/preclustercommand.h b/preclustercommand.h
index 12dd2d2556fcef245794ff178171920f7f5f0b37..2b93328e64a038695a3abbd10cfe9be1165b783d 100644 (file)
--- a/preclustercommand.h
+++ b/preclustercommand.h
@@ -301,7 +301,7 @@ static DWORD WINAPI MyPreclusterThreadFunction(LPVOID lpParam){
                         out << "ideal_seq_" << (i+1) << '\t' << alignSeqs[i].numIdentical << endl << chunk << endl;
                         
                     }//end if active i
-                    if(i % 100 == 0)   { pDataArray->m->mothurOut(toString(i) + "\t" + toString(numSeqs - count) + "\t" + toString(count)); pDataArray->m->mothurOutEndLine(); }
+                    if(i % 100 == 0)   { pDataArray->m->mothurOutJustToScreen(toString(i) + "\t" + toString(numSeqs - count) + "\t" + toString(count)+"\n");   }
                 }
                 
             }else {
@@ -344,7 +344,7 @@ static DWORD WINAPI MyPreclusterThreadFunction(LPVOID lpParam){
                         }//end abundance check
                     }//end for loop j
                     
-                    if(i % 100 == 0)   { pDataArray->m->mothurOut(toString(i) + "\t" + toString(numSeqs - count) + "\t" + toString(count)); pDataArray->m->mothurOutEndLine(); }
+                    if(i % 100 == 0)   { pDataArray->m->mothurOutJustToScreen(toString(i) + "\t" + toString(numSeqs - count) + "\t" + toString(count)+"\n");   }
                 }
                 
                 for (int i = 0; i < numSeqs; i++) {

diff --git a/screenseqscommand.cpp b/screenseqscommand.cpp
index 3718c9a9c0cf843d9f91311b8b7b3cdee814f455..d2fbe935356a2f0752efa683a893a5892e1b2eb2 100644 (file)
--- a/screenseqscommand.cpp
+++ b/screenseqscommand.cpp
@@ -2409,10 +2409,10 @@ int ScreenSeqsCommand::driver(linePair filePos, string goodFName, string badAccn
                        #endif
                        
                        //report progress
-                       if((count) % 100 == 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
+                       if((count) % 100 == 0){ m->mothurOutJustToScreen("Processing sequence: " + toString(count)+"\n");               }
                }
                //report progress
-               if((count) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
+               if((count) % 100 != 0){ m->mothurOutJustToScreen("Processing sequence: " + toString(count)+"\n");       }
                
                        
                goodFile.close();
@@ -2504,7 +2504,7 @@ int ScreenSeqsCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File&
                        }
                        
                        //report progress
-                       if((i) % 100 == 0){     m->mothurOut("Processing sequence: " + toString(i)); m->mothurOutEndLine();             }
+                       if((i) % 100 == 0){     m->mothurOutJustToScreen("Processing sequence: " + toString(i)+"\n");           }
                }
                                
                return 1;

diff --git a/screenseqscommand.h b/screenseqscommand.h
index e2906900980ac7d1897b9e0976435401fb35c8be..aeaddae1300207aff7ef713858e9ee760be52e12 100644 (file)
--- a/screenseqscommand.h
+++ b/screenseqscommand.h
@@ -449,10 +449,10 @@ static DWORD WINAPI MySumScreenThreadFunction(LPVOID lpParam){
     
                        }               
             //report progress
-                       if((i+1) % 100 == 0){   pDataArray->m->mothurOut("Processing sequence: " + toString(i+1)); pDataArray->m->mothurOutEndLine();           }
+                       if((i+1) % 100 == 0){   pDataArray->m->mothurOutJustToScreen("Processing sequence: " + toString(i+1)+"\n");             }
                }
                //report progress
-               if((pDataArray->count) % 100 != 0){     pDataArray->m->mothurOut("Processing sequence: " + toString(pDataArray->count)); pDataArray->m->mothurOutEndLine();             }
+               if((pDataArray->count) % 100 != 0){     pDataArray->m->mothurOutJustToScreen("Processing sequence: " + toString(pDataArray->count)+"\n");               }
                
 
                

diff --git a/seqerrorcommand.cpp b/seqerrorcommand.cpp
index 2bd7054afc33c4f0600683a1b8ebe50a2fd338c4..203a71ede5544a3d1c5e2eba73072fa825445aac 100644 (file)
--- a/seqerrorcommand.cpp
+++ b/seqerrorcommand.cpp
@@ -881,7 +881,7 @@ int SeqErrorCommand::driver(string filename, string qFileName, string rFileName,
                                if (queryFile.eof()) { break; }
                        #endif
                        
-                       if(index % 100 == 0){   m->mothurOut(toString(index));  m->mothurOutEndLine(); }
+                       if(index % 100 == 0){   m->mothurOutJustToScreen(toString(index)+"\n");  }
                }
                queryFile.close();
                outChimeraReport.close();
@@ -892,7 +892,7 @@ int SeqErrorCommand::driver(string filename, string qFileName, string rFileName,
                else if(qFileName != "" && aligned == false){   qualFile.close();                       }
         
                //report progress
-               m->mothurOut(toString(index));  m->mothurOutEndLine();
+               m->mothurOutJustToScreen(toString(index)+"\n"); 
                
                return index;
        }

diff --git a/seqsummarycommand.cpp b/seqsummarycommand.cpp
index 90a66f8f633212cf69a2930914a1911c5bca1cb1..6d8336cb40217a9547791e69765230dff0dabe62 100644 (file)
--- a/seqsummarycommand.cpp
+++ b/seqsummarycommand.cpp
@@ -494,13 +494,8 @@ int SeqSummaryCommand::driverCreateSummary(vector<int>& startPosition, vector<in
                        #else
                                if (in.eof()) { break; }
                        #endif
-                       
-                       //report progress
-                       //if((count) % 100 == 0){       m->mothurOut(toString(count)); m->mothurOutEndLine();           }
                }
-               //report progress
-               //if((count) % 100 != 0){       m->mothurOut(toString(count)); m->mothurOutEndLine();           }
-               
+                               
                in.close();
                
                return count;

diff --git a/shhhercommand.cpp b/shhhercommand.cpp
index 63157820390d18e1ef598a8bf58932964cc6f369..e970bab34f9276a680bce6e29faa9cf829684e12 100644 (file)
--- a/shhhercommand.cpp
+++ b/shhhercommand.cpp
@@ -858,7 +858,7 @@ string ShhherCommand::flowDistMPI(int startSeq, int stopSeq){
                                }
                        }
                        if(i % 100 == 0){
-                               m->mothurOut(toString(i) + '\t' + toString(time(NULL) - begTime) + '\t' + toString((clock()-begClock)/CLOCKS_PER_SEC) + '\n');
+                               m->mothurOutJustToScreen(toString(i) + '\t' + toString(time(NULL) - begTime) + '\t' + toString((clock()-begClock)/CLOCKS_PER_SEC) + '\n');
                        }
                }
                
@@ -867,7 +867,7 @@ string ShhherCommand::flowDistMPI(int startSeq, int stopSeq){
                
                if (m->control_pressed) { return fDistFileName; }
                
-               m->mothurOut(toString(stopSeq) + '\t' + toString(time(NULL) - begTime) + '\t' + toString((clock()-begClock)/CLOCKS_PER_SEC) + '\n');
+               m->mothurOutJustToScreen(toString(stopSeq) + '\t' + toString(time(NULL) - begTime) + '\t' + toString((clock()-begClock)/CLOCKS_PER_SEC) + '\n');
 
                ofstream distFile(fDistFileName.c_str());
                distFile << outStream.str();            
@@ -2545,9 +2545,8 @@ int ShhherCommand::flowDistParentFork(int numFlowCells, string distFileName, int
                                }
                        }
                        if(i % 100 == 0){
-                               m->mothurOut(toString(i) + "\t" + toString(time(NULL) - begTime));
-                               m->mothurOut("\t" + toString((clock()-begClock)/CLOCKS_PER_SEC));
-                               m->mothurOutEndLine();
+                               m->mothurOutJustToScreen(toString(i) + "\t" + toString(time(NULL) - begTime));
+                               m->mothurOutJustToScreen("\t" + toString((clock()-begClock)/CLOCKS_PER_SEC)+"\n");
                        }
                }
                
@@ -2557,9 +2556,8 @@ int ShhherCommand::flowDistParentFork(int numFlowCells, string distFileName, int
                
                if (m->control_pressed) {}
                else {
-                       m->mothurOut(toString(stopSeq-1) + "\t" + toString(time(NULL) - begTime));
-                       m->mothurOut("\t" + toString((clock()-begClock)/CLOCKS_PER_SEC));
-                       m->mothurOutEndLine();
+                       m->mothurOutJustToScreen(toString(stopSeq-1) + "\t" + toString(time(NULL) - begTime));
+                       m->mothurOutJustToScreen("\t" + toString((clock()-begClock)/CLOCKS_PER_SEC)+"\n");
                }
         
         return 0;

diff --git a/unifracunweightedcommand.cpp b/unifracunweightedcommand.cpp
index ab8afd07ffd96728e6204d2f9b2bbd2adc719787..272ae8255b6566e0f2c0ff04489580a9a36acdfd 100644 (file)
--- a/unifracunweightedcommand.cpp
+++ b/unifracunweightedcommand.cpp
@@ -421,7 +421,7 @@ int UnifracUnweightedCommand::execute() {
                 delete newCt;
                 delete subSampleTree;
                 
-                if((thisIter+1) % 100 == 0){   m->mothurOut(toString(thisIter+1)); m->mothurOutEndLine();              }
+                if((thisIter+1) % 100 == 0){   m->mothurOutJustToScreen(toString(thisIter+1)+"\n");            }
             }
             if (subsample) { m->mothurOut("It took " + toString(time(NULL) - startSubsample) + " secs to run the subsampling."); m->mothurOutEndLine(); }
             

diff --git a/unifracweightedcommand.cpp b/unifracweightedcommand.cpp
index 81ea326e67665cb006500ed8d04f273b15fca2b4..3b0c53b7437111cfe5045663a8c78370274b939e 100644 (file)
--- a/unifracweightedcommand.cpp
+++ b/unifracweightedcommand.cpp
@@ -408,7 +408,7 @@ int UnifracWeightedCommand::execute() {
                 delete newCt;
                 delete subSampleTree;
                 
-                if((thisIter+1) % 100 == 0){   m->mothurOut(toString(thisIter+1)); m->mothurOutEndLine();              }
+                if((thisIter+1) % 100 == 0){   m->mothurOutJustToScreen(toString(thisIter+1)+"\n");    }
             }
             
             if (m->control_pressed) { delete ct; for (int i = 0; i < T.size(); i++) { delete T[i]; } if (random) { delete output; } outSum.close(); for (int i = 0; i < outputNames.size(); i++) {     m->mothurRemove(outputNames[i]);  } return 0; }