created mothurOut class to handle logfiles

[mothur.git] / pintail.cpp

diff --git a/pintail.cpp b/pintail.cpp
index 90c97c5e77d50f478aeb1b4bb7b1fa28713ee468..a2c72702cc7f766501f705226fe4441abcf7ed24 100644 (file)
--- a/pintail.cpp
+++ b/pintail.cpp
@@ -32,7 +32,7 @@ Pintail::~Pintail() {
                delete decalc; 
        }
        catch(exception& e) {
-               errorOut(e, "Pintail", "~Pintail");
+               m->errorOut(e, "Pintail", "~Pintail");
                exit(1);
        }
 }
@@ -66,13 +66,13 @@ void Pintail::doPrep() {
                #endif
 
                
-               mothurOut("Getting conservation... "); cout.flush();
+               m->mothurOut("Getting conservation... "); cout.flush();
                if (consfile == "") { 
-                       mothurOut("Calculating probability of conservation for your template sequences.  This can take a while...  I will output the frequency of the highest base in each position to a .freq file so that you can input them using the conservation parameter next time you run this command.  Providing the .freq file will improve speed.    "); cout.flush();
+                       m->mothurOut("Calculating probability of conservation for your template sequences.  This can take a while...  I will output the frequency of the highest base in each position to a .freq file so that you can input them using the conservation parameter next time you run this command.  Providing the .freq file will improve speed.    "); cout.flush();
                        probabilityProfile = decalc->calcFreq(templateSeqs, outputDir + getSimpleName(templateFileName)); 
-                       mothurOut("Done."); mothurOutEndLine();
-               }else                           {   probabilityProfile = readFreq();    mothurOut("Done.");               }
-               mothurOutEndLine();
+                       m->mothurOut("Done."); m->mothurOutEndLine();
+               }else                           {   probabilityProfile = readFreq();    m->mothurOut("Done.");            }
+               m->mothurOutEndLine();
                
                //make P into Q
                for (int i = 0; i < probabilityProfile.size(); i++)  {  probabilityProfile[i] = 1 - probabilityProfile[i];  }  //cout << i << '\t' << probabilityProfile[i] << endl;
@@ -135,7 +135,7 @@ void Pintail::doPrep() {
                                }
                        }
                        
-                       mothurOut("Calculating quantiles for your template.  This can take a while...  I will output the quantiles to a .quan file that you can input them using the quantiles parameter next time you run this command.  Providing the .quan file will dramatically improve speed.    "); cout.flush();
+                       m->mothurOut("Calculating quantiles for your template.  This can take a while...  I will output the quantiles to a .quan file that you can input them using the quantiles parameter next time you run this command.  Providing the .quan file will dramatically improve speed.    "); cout.flush();
                        if (processors == 1) { 
                                quantilesMembers = decalc->getQuantiles(templateSeqs, windowSizesTemplate, window, probabilityProfile, increment, 0, templateSeqs.size());
                        }else {         createProcessesQuan();          }
@@ -197,7 +197,7 @@ void Pintail::doPrep() {
                                
                        }
 
-                       mothurOut("Done."); mothurOutEndLine();
+                       m->mothurOut("Done."); m->mothurOutEndLine();
                }
                
                if (reRead) {
@@ -212,7 +212,7 @@ void Pintail::doPrep() {
                
        }
        catch(exception& e) {
-               errorOut(e, "Pintail", "doPrep");
+               m->errorOut(e, "Pintail", "doPrep");
                exit(1);
        }
 }
@@ -234,7 +234,7 @@ void Pintail::print(ostream& out, ostream& outAcc) {
                
                out << querySeq->getName() << '\t' << "div: " << deviation << "\tstDev: " << DE << "\tchimera flag: " << chimera << endl;
                if (chimera == "Yes") {
-                       mothurOut(querySeq->getName() + "\tdiv: " + toString(deviation) + "\tstDev: " + toString(DE) + "\tchimera flag: " + chimera); mothurOutEndLine();
+                       m->mothurOut(querySeq->getName() + "\tdiv: " + toString(deviation) + "\tstDev: " + toString(DE) + "\tchimera flag: " + chimera); m->mothurOutEndLine();
                        outAcc << querySeq->getName() << endl;
                }
                out << "Observed\t";
@@ -250,7 +250,7 @@ void Pintail::print(ostream& out, ostream& outAcc) {
                
        }
        catch(exception& e) {
-               errorOut(e, "Pintail", "print");
+               m->errorOut(e, "Pintail", "print");
                exit(1);
        }
 }
@@ -307,7 +307,7 @@ int Pintail::getChimeras(Sequence* query) {
                return 0;
        }
        catch(exception& e) {
-               errorOut(e, "Pintail", "getChimeras");
+               m->errorOut(e, "Pintail", "getChimeras");
                exit(1);
        }
 }
@@ -349,7 +349,7 @@ vector<float> Pintail::readFreq() {
                
        }
        catch(exception& e) {
-               errorOut(e, "Pintail", "readFreq");
+               m->errorOut(e, "Pintail", "readFreq");
                exit(1);
        }
 }
@@ -366,7 +366,7 @@ Sequence* Pintail::findPairs(Sequence* q) {
        
        }
        catch(exception& e) {
-               errorOut(e, "Pintail", "findPairs");
+               m->errorOut(e, "Pintail", "findPairs");
                exit(1);
        }
 }
@@ -406,7 +406,7 @@ void Pintail::createProcessesQuan() {
                                out.close();
                                
                                exit(0);
-                       }else { mothurOut("unable to spawn the necessary processes."); mothurOutEndLine(); exit(0); }
+                       }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
                }
                
                //force parent to wait until all the processes are done
@@ -461,7 +461,7 @@ void Pintail::createProcessesQuan() {
 #endif         
        }
        catch(exception& e) {
-               errorOut(e, "Pintail", "createProcessesQuan");
+               m->errorOut(e, "Pintail", "createProcessesQuan");
                exit(1);
        }
 }