created mothurOut class to handle logfiles

[mothur.git] / ccode.cpp

diff --git a/ccode.cpp b/ccode.cpp
index 28e9723f6c19984b3e6cb9dbcfc869c0d75d6ffe..00a30e5b6c0db1f58cb90b3c564703b7d3d77f6d 100644 (file)
--- a/ccode.cpp
+++ b/ccode.cpp
@@ -38,8 +38,6 @@ void Ccode::printHeader(ostream& out) {
 void Ccode::print(ostream& out, ostream& outAcc) {
        try {
                
-               mothurOutEndLine();
-               
                ofstream out2;
                openOutputFileAppend(mapInfo, out2);
                
@@ -111,7 +109,7 @@ void Ccode::print(ostream& out, ostream& outAcc) {
                out << endl;    
                        
                if (results) {
-                       mothurOut(querySeq->getName() + " was found have at least one chimeric window."); mothurOutEndLine();
+                       m->mothurOut(querySeq->getName() + " was found have at least one chimeric window."); m->mothurOutEndLine();
                        outAcc << querySeq->getName() << endl;
                }
 
@@ -121,7 +119,7 @@ void Ccode::print(ostream& out, ostream& outAcc) {
                
        }
        catch(exception& e) {
-               errorOut(e, "Ccode", "print");
+               m->errorOut(e, "Ccode", "print");
                exit(1);
        }
 }
@@ -224,7 +222,7 @@ int Ccode::getChimeras(Sequence* query) {
                return 0;
        }
        catch(exception& e) {
-               errorOut(e, "Ccode", "getChimeras");
+               m->errorOut(e, "Ccode", "getChimeras");
                exit(1);
        }
 }
@@ -306,7 +304,7 @@ void Ccode::trimSequences(Sequence* query) {
 
                
                //check to make sure that is not whole seq
-               if ((rearPos - frontPos - 1) <= 0) {  mothurOut("Error, when I trim your sequences, the entire sequence is trimmed."); mothurOutEndLine(); exit(1);  }
+               if ((rearPos - frontPos - 1) <= 0) {  m->mothurOut("Error, when I trim your sequences, the entire sequence is trimmed."); m->mothurOutEndLine(); exit(1);  }
                
                map<int, int> tempTrim;
                tempTrim[frontPos] = rearPos;
@@ -326,7 +324,7 @@ void Ccode::trimSequences(Sequence* query) {
                spotMap = newMap;
        }
        catch(exception& e) {
-               errorOut(e, "Ccode", "trimSequences");
+               m->errorOut(e, "Ccode", "trimSequences");
                exit(1);
        }
 }
@@ -341,13 +339,13 @@ vector<int> Ccode::findWindows() {
        
                //default is wanted = 10% of total length
                if (windowSizes > length) { 
-                       mothurOut("You have slected a window larger than your sequence length after all filters, masks and trims have been done. I will use the default 10% of sequence length.");
+                       m->mothurOut("You have slected a window larger than your sequence length after all filters, masks and trims have been done. I will use the default 10% of sequence length.");
                        windowSizes = length / 10;
                }else if (windowSizes == 0) { windowSizes = length / 10;  }
                else if (windowSizes > (length * 0.20)) {
-                       mothurOut("You have selected a window that is larger than 20% of your sequence length.  This is not recommended, but I will continue anyway."); mothurOutEndLine();
+                       m->mothurOut("You have selected a window that is larger than 20% of your sequence length.  This is not recommended, but I will continue anyway."); m->mothurOutEndLine();
                }else if (windowSizes < (length * 0.05)) {
-                       mothurOut("You have selected a window that is smaller than 5% of your sequence length.  This is not recommended, but I will continue anyway."); mothurOutEndLine();
+                       m->mothurOut("You have selected a window that is smaller than 5% of your sequence length.  This is not recommended, but I will continue anyway."); m->mothurOutEndLine();
                }
                
                //save starting points of each window
@@ -361,7 +359,7 @@ vector<int> Ccode::findWindows() {
                return win;
        }
        catch(exception& e) {
-               errorOut(e, "Ccode", "findWindows");
+               m->errorOut(e, "Ccode", "findWindows");
                exit(1);
        }
 }
@@ -416,7 +414,7 @@ int Ccode::getDiff(string seqA, string seqB) {
        
        }
        catch(exception& e) {
-               errorOut(e, "Ccode", "getDiff");
+               m->errorOut(e, "Ccode", "getDiff");
                exit(1);
        }
 }
@@ -486,12 +484,12 @@ void Ccode::removeBadReferenceSeqs(vector<SeqDist>& seqs) {
                        seqs = goodSeqs;
                        
                }else { //warn, but dont remove any
-                       mothurOut(querySeq->getName() + " does not have an adaquate number of reference sequences that are within 20% and 0.5% similarity.  I will continue, but please check."); mothurOutEndLine();  
+                       m->mothurOut(querySeq->getName() + " does not have an adaquate number of reference sequences that are within 20% and 0.5% similarity.  I will continue, but please check."); m->mothurOutEndLine();  
                }
 
        }
        catch(exception& e) {
-               errorOut(e, "Ccode", "removeBadReferenceSeqs");
+               m->errorOut(e, "Ccode", "removeBadReferenceSeqs");
                exit(1);
        }
 }
@@ -531,7 +529,7 @@ vector<SeqDist>  Ccode::findClosest(Sequence* q, int numWanted) {
 
        }
        catch(exception& e) {
-               errorOut(e, "Ccode", "findClosestSides");
+               m->errorOut(e, "Ccode", "findClosestSides");
                exit(1);
        }
 }
@@ -618,7 +616,7 @@ void Ccode::getAverageRef(vector<SeqDist> ref) {
                
        }
        catch(exception& e) {
-               errorOut(e, "Ccode", "getAverageRef");
+               m->errorOut(e, "Ccode", "getAverageRef");
                exit(1);
        }
 }
@@ -687,7 +685,7 @@ void Ccode::getAverageQuery (vector<SeqDist> ref, Sequence* query) {
                }
        }
        catch(exception& e) {
-               errorOut(e, "Ccode", "getAverageQuery");
+               m->errorOut(e, "Ccode", "getAverageQuery");
                exit(1);
        }
 }
@@ -713,7 +711,7 @@ void Ccode::findVarianceRef() {
                }
        }
        catch(exception& e) {
-               errorOut(e, "Ccode", "findVarianceRef");
+               m->errorOut(e, "Ccode", "findVarianceRef");
                exit(1);
        }
 }
@@ -738,7 +736,7 @@ void Ccode::findVarianceQuery() {
 
        }
        catch(exception& e) {
-               errorOut(e, "Ccode", "findVarianceQuery");
+               m->errorOut(e, "Ccode", "findVarianceQuery");
                exit(1);
        }
 }
@@ -800,7 +798,7 @@ void Ccode::determineChimeras() {
                
        }
        catch(exception& e) {
-               errorOut(e, "Ccode", "determineChimeras");
+               m->errorOut(e, "Ccode", "determineChimeras");
                exit(1);
        }
 }
@@ -845,13 +843,13 @@ float Ccode::getT(int numseq) {
         else if (numseq > 2) tvalue = 2.353;
         else if (numseq > 1) tvalue = 2.920;
                else if (numseq <= 1) {
-                       mothurOut("Two or more reference sequences are required, your data will be flawed.\n"); mothurOutEndLine();
+                       m->mothurOut("Two or more reference sequences are required, your data will be flawed.\n"); m->mothurOutEndLine();
                }
                
                return tvalue;
        }
        catch(exception& e) {
-               errorOut(e, "Ccode", "getT");
+               m->errorOut(e, "Ccode", "getT");
                exit(1);
        }
 }
@@ -897,13 +895,13 @@ float Ccode::getF(int numseq) {
         else if (numseq > 1) fvalue = 18.5;
         else if (numseq > 0) fvalue = 161;
                else if (numseq <= 0) {
-                       mothurOut("Two or more reference sequences are required, your data will be flawed.\n"); mothurOutEndLine();
+                       m->mothurOut("Two or more reference sequences are required, your data will be flawed.\n"); m->mothurOutEndLine();
         }
                
                return fvalue;
        }
        catch(exception& e) {
-               errorOut(e, "Ccode", "getF");
+               m->errorOut(e, "Ccode", "getF");
                exit(1);
        }
 }