created mothurOut class to handle logfiles

[mothur.git] / slayer.cpp

diff --git a/slayer.cpp b/slayer.cpp
index 66db22b6a36ae9a0f7f9dd383201cd3852a120b2..2d079cd6ac10ae5ed4aeea0454ff3f0e984561e8 100644 (file)
--- a/slayer.cpp
+++ b/slayer.cpp
@@ -11,7 +11,7 @@
 
 /***********************************************************************/
 Slayer::Slayer(int win, int increment, int parentThreshold, float div, int i, int snp) :
-               windowSize(win), windowStep(increment), parentFragmentThreshold(parentThreshold), divRThreshold(div), iters(i), percentSNPSample(snp){}
+               windowSize(win), windowStep(increment), parentFragmentThreshold(parentThreshold), divRThreshold(div), iters(i), percentSNPSample(snp){ m = MothurOut::getInstance(); }
 /***********************************************************************/
 string Slayer::getResults(Sequence* query, vector<Sequence*> refSeqs) {
        try {
@@ -98,7 +98,7 @@ string Slayer::getResults(Sequence* query, vector<Sequence*> refSeqs) {
                }
        }
        catch(exception& e) {
-               errorOut(e, "Slayer", "getResults");
+               m->errorOut(e, "Slayer", "getResults");
                exit(1);
        }
 }
@@ -130,7 +130,7 @@ vector<data_struct> Slayer::runBellerophon(Sequence* q, Sequence* pA, Sequence*
        
                //check window size
                if (length < (2*windowSize+windowStep)) { 
-                       mothurOut("Your window size is too large for " + q->getName() + ". I will make the window size " + toString(length/4) + " which is 1/4 the filtered length."); mothurOutEndLine();      
+                       m->mothurOut("Your window size is too large for " + q->getName() + ". I will make the window size " + toString(length/4) + " which is 1/4 the filtered length."); m->mothurOutEndLine();        
                        windowSize = length / 4;
                }
                
@@ -208,7 +208,7 @@ vector<data_struct> Slayer::runBellerophon(Sequence* q, Sequence* pA, Sequence*
                
        }
        catch(exception& e) {
-               errorOut(e, "Slayer", "runBellerophon");
+               m->errorOut(e, "Slayer", "runBellerophon");
                exit(1);
        }
 }
@@ -257,7 +257,7 @@ vector<snps> Slayer::getSNPS(string parentA, string query, string parentB, int l
                
        }
        catch(exception& e) {
-               errorOut(e, "Slayer", "getSNPS");
+               m->errorOut(e, "Slayer", "getSNPS");
                exit(1);
        }
 }
@@ -342,7 +342,7 @@ void Slayer::bootstrapSNPS(vector<snps> left, vector<snps> right, float& BSA, fl
        
        }
        catch(exception& e) {
-               errorOut(e, "Slayer", "bootstrapSNPS");
+               m->errorOut(e, "Slayer", "bootstrapSNPS");
                exit(1);
        }
 }
@@ -363,7 +363,7 @@ float Slayer::snpQA(vector<snps> data) {
                return percentID;
        }
        catch(exception& e) {
-               errorOut(e, "Slayer", "snpQA");
+               m->errorOut(e, "Slayer", "snpQA");
                exit(1);
        }
 }
@@ -385,7 +385,7 @@ float Slayer::snpQB(vector<snps> data) {
 
        }
        catch(exception& e) {
-               errorOut(e, "Slayer", "snpQB");
+               m->errorOut(e, "Slayer", "snpQB");
                exit(1);
        }
 }
@@ -406,7 +406,7 @@ float Slayer::snpAB(vector<snps> data) {
 
        }
        catch(exception& e) {
-               errorOut(e, "Slayer", "snpAB");
+               m->errorOut(e, "Slayer", "snpAB");
                exit(1);
        }
 }
@@ -428,7 +428,7 @@ float Slayer::computePercentID(string queryFrag, string parent, int left, int ri
                return percentID;
        }
        catch(exception& e) {
-               errorOut(e, "Slayer", "computePercentID");
+               m->errorOut(e, "Slayer", "computePercentID");
                exit(1);
        }
 }
@@ -494,7 +494,7 @@ map<int, int> Slayer::verticalFilter(vector<Sequence*> seqs) {
                return maskMap;
        }
        catch(exception& e) {
-               errorOut(e, "Slayer", "verticalFilter");
+               m->errorOut(e, "Slayer", "verticalFilter");
                exit(1);
        }
 }