created mothurOut class to handle logfiles

[mothur.git] / chimera.cpp

diff --git a/chimera.cpp b/chimera.cpp
index e7253ec27d25c47157527c0f386ffb84fba4d55d..820b475ef32575a1d690d568b73ce4936a8f603b 100644 (file)
--- a/chimera.cpp
+++ b/chimera.cpp
@@ -50,11 +50,11 @@ string Chimera::createFilter(vector<Sequence*> seqs, float t) {
                        //cout << "a = " << a[i] <<  " t = " << t[i] <<  " g = " << g[i] <<  " c = " << c[i] << endl;
                }
 
-               mothurOut("Filter removed " + toString(numColRemoved) + " columns.");  mothurOutEndLine();
+               m->mothurOut("Filter removed " + toString(numColRemoved) + " columns.");  m->mothurOutEndLine();
                return filterString;
        }
        catch(exception& e) {
-               errorOut(e, "Chimera", "createFilter");
+               m->errorOut(e, "Chimera", "createFilter");
                exit(1);
        }
 }
@@ -80,7 +80,7 @@ map<int, int> Chimera::runFilter(Sequence* seq) {
                return maskMap;
        }
        catch(exception& e) {
-               errorOut(e, "Chimera", "runFilter");
+               m->errorOut(e, "Chimera", "runFilter");
                exit(1);
        }
 }
@@ -88,9 +88,10 @@ map<int, int> Chimera::runFilter(Sequence* seq) {
 vector<Sequence*> Chimera::readSeqs(string file) {
        try {
        
-               mothurOut("Reading sequences... "); cout.flush();
+               m->mothurOut("Reading sequences... "); cout.flush();
                ifstream in;
                openInputFile(file, in);
+               
                vector<Sequence*> container;
                int count = 0;
                length = 0;
@@ -110,12 +111,12 @@ vector<Sequence*> Chimera::readSeqs(string file) {
                }
                
                in.close();
-               mothurOut("Done."); mothurOutEndLine();
+               m->mothurOut("Done."); m->mothurOutEndLine();
                
                return container;
        }
        catch(exception& e) {
-               errorOut(e, "Chimera", "readSeqs");
+               m->errorOut(e, "Chimera", "readSeqs");
                exit(1);
        }
 }
@@ -143,7 +144,7 @@ void Chimera::setMask(string filename) {
                }
        }
        catch(exception& e) {
-               errorOut(e, "Chimera", "setMask");
+               m->errorOut(e, "Chimera", "setMask");
                exit(1);
        }
 }
@@ -186,7 +187,7 @@ vector< vector<float> > Chimera::readQuantiles() {
                
        }
        catch(exception& e) {
-               errorOut(e, "Chimera", "readQuantiles");
+               m->errorOut(e, "Chimera", "readQuantiles");
                exit(1);
        }
 }
@@ -204,14 +205,14 @@ Sequence* Chimera::getSequence(string name) {
                        }
                }
                
-               if(spot == -1) { mothurOut("Error: Could not find sequence."); mothurOutEndLine(); return NULL; }
+               if(spot == -1) { m->mothurOut("Error: Could not find sequence."); m->mothurOutEndLine(); return NULL; }
                
                temp = new Sequence(templateSeqs[spot]->getName(), templateSeqs[spot]->getAligned());
                
                return temp;
        }
        catch(exception& e) {
-               errorOut(e, "Chimera", "getSequence");
+               m->errorOut(e, "Chimera", "getSequence");
                exit(1);
        }
 }