created mothurOut class to handle logfiles

[mothur.git] / bellerophon.cpp

diff --git a/bellerophon.cpp b/bellerophon.cpp
index 17859dc710309b7535e234aec56791bc7a8ee1b2..02b282926bbb2dbe1eae2ed61997c2cbe4bccb8b 100644 (file)
--- a/bellerophon.cpp
+++ b/bellerophon.cpp
@@ -21,7 +21,7 @@ Bellerophon::Bellerophon(string name, string o)  {
                outputDir = o;
        }
        catch(exception& e) {
-               errorOut(e, "Bellerophon", "Bellerophon");
+               m->errorOut(e, "Bellerophon", "Bellerophon");
                exit(1);
        }
 }
@@ -39,33 +39,33 @@ void Bellerophon::print(ostream& out, ostream& outAcc) {
                        if (pref[i].score[0] > 1.0) { 
                                above1++; 
                                outAcc << pref[i].name << endl;
-                               mothurOut(pref[i].name + " is a suspected chimera at breakpoint " + toString(pref[i].midpoint)); mothurOutEndLine();
-                               mothurOut("It's score is " + toString(pref[i].score[0]) + " with suspected left parent " + pref[i].leftParent[0] + " and right parent " + pref[i].rightParent[0]); mothurOutEndLine();
+                               m->mothurOut(pref[i].name + " is a suspected chimera at breakpoint " + toString(pref[i].midpoint)); m->mothurOutEndLine();
+                               m->mothurOut("It's score is " + toString(pref[i].score[0]) + " with suspected left parent " + pref[i].leftParent[0] + " and right parent " + pref[i].rightParent[0]); m->mothurOutEndLine();
                        }
                }
                
                //output results to screen
-               mothurOutEndLine();
-               mothurOut("Sequence with preference score above 1.0: " + toString(above1)); mothurOutEndLine();
+               m->mothurOutEndLine();
+               m->mothurOut("Sequence with preference score above 1.0: " + toString(above1)); m->mothurOutEndLine();
                int spot;
                spot = pref.size()-1;
-               mothurOut("Minimum:\t" + toString(pref[spot].score[0])); mothurOutEndLine();
+               m->mothurOut("Minimum:\t" + toString(pref[spot].score[0])); m->mothurOutEndLine();
                spot = pref.size() * 0.975;
-               mothurOut("2.5%-tile:\t" + toString(pref[spot].score[0])); mothurOutEndLine();
+               m->mothurOut("2.5%-tile:\t" + toString(pref[spot].score[0])); m->mothurOutEndLine();
                spot = pref.size() * 0.75;
-               mothurOut("25%-tile:\t" + toString(pref[spot].score[0])); mothurOutEndLine();
+               m->mothurOut("25%-tile:\t" + toString(pref[spot].score[0])); m->mothurOutEndLine();
                spot = pref.size() * 0.50;
-               mothurOut("Median: \t" + toString(pref[spot].score[0])); mothurOutEndLine();
+               m->mothurOut("Median: \t" + toString(pref[spot].score[0])); m->mothurOutEndLine();
                spot = pref.size() * 0.25;
-               mothurOut("75%-tile:\t" + toString(pref[spot].score[0])); mothurOutEndLine();
+               m->mothurOut("75%-tile:\t" + toString(pref[spot].score[0])); m->mothurOutEndLine();
                spot = pref.size() * 0.025;
-               mothurOut("97.5%-tile:\t" + toString(pref[spot].score[0])); mothurOutEndLine();
+               m->mothurOut("97.5%-tile:\t" + toString(pref[spot].score[0])); m->mothurOutEndLine();
                spot = 0;
-               mothurOut("Maximum:\t" + toString(pref[spot].score[0])); mothurOutEndLine();
+               m->mothurOut("Maximum:\t" + toString(pref[spot].score[0])); m->mothurOutEndLine();
 
        }
        catch(exception& e) {
-               errorOut(e, "Bellerophon", "print");
+               m->errorOut(e, "Bellerophon", "print");
                exit(1);
        }
 }
@@ -96,28 +96,28 @@ int Bellerophon::getChimeras() {
                }
                
                distCalculator = new eachGapDist();
-               
+cout << "fastafile = " << fastafile << endl;           
                //read in sequences
                seqs = readSeqs(fastafile);
-               
-               if (unaligned) { mothurOut("Your sequences need to be aligned when you use the bellerophon method."); mothurOutEndLine(); return 1;  }
+       cout << "here:"<< endl; 
+               if (unaligned) { m->mothurOut("Your sequences need to be aligned when you use the bellerophon method."); m->mothurOutEndLine(); return 1;  }
                
                int numSeqs = seqs.size();
                
-               if (numSeqs == 0) { mothurOut("Error in reading you sequences."); mothurOutEndLine(); exit(1); }
+               if (numSeqs == 0) { m->mothurOut("Error in reading you sequences."); m->mothurOutEndLine(); exit(1); }
                
                //set default window to 25% of sequence length
                string seq0 = seqs[0]->getAligned();
                if (window == 0) { window = seq0.length() / 4;  }
                else if (window > (seq0.length() / 2)) {  
-                       mothurOut("Your sequence length is = " + toString(seq0.length()) + ". You have selected a window size greater than the length of half your aligned sequence. I will run it with a window size of " + toString((seq0.length() / 2))); mothurOutEndLine();
+                       m->mothurOut("Your sequence length is = " + toString(seq0.length()) + ". You have selected a window size greater than the length of half your aligned sequence. I will run it with a window size of " + toString((seq0.length() / 2))); m->mothurOutEndLine();
                        window = (seq0.length() / 2);
                }
                
                if (increment > (seqs[0]->getAlignLength() - (2*window))) { 
                        if (increment != 10) {
                        
-                               mothurOut("You have selected a increment that is too large. I will use the default."); mothurOutEndLine();
+                               m->mothurOut("You have selected a increment that is too large. I will use the default."); m->mothurOutEndLine();
                                increment = 10;
                                if (increment > (seqs[0]->getAlignLength() - (2*window))) {  increment = 0;  }
                                
@@ -234,7 +234,7 @@ int Bellerophon::getChimeras() {
                
        }
        catch(exception& e) {
-               errorOut(e, "Bellerophon", "getChimeras");
+               m->errorOut(e, "Bellerophon", "getChimeras");
                exit(1);
        }
 }
@@ -259,7 +259,7 @@ int Bellerophon::createSparseMatrix(int startSeq, int endSeq, SparseMatrix* spar
                return 1;
        }
        catch(exception& e) {
-               errorOut(e, "Bellerophon", "createSparseMatrix");
+               m->errorOut(e, "Bellerophon", "createSparseMatrix");
                exit(1);
        }
 }
@@ -382,7 +382,7 @@ void Bellerophon::generatePreferences(vector<SeqMap> left, vector<SeqMap> right,
 
        }
        catch(exception& e) {
-               errorOut(e, "Bellerophon", "generatePreferences");
+               m->errorOut(e, "Bellerophon", "generatePreferences");
                exit(1);
        }
 }