created mothurOut class to handle logfiles

[mothur.git] / readcluster.cpp

diff --git a/readcluster.cpp b/readcluster.cpp
index 11b8d012a22e592d99bb71e3063c0c89a710252a..1cf9fc325b0ecdc5d222ded20346f79134f3b6b7 100644 (file)
--- a/readcluster.cpp
+++ b/readcluster.cpp
@@ -13,6 +13,7 @@
 
 ReadCluster::ReadCluster(string distfile, float c){
                globaldata = GlobalData::getInstance();
+               m = MothurOut::getInstance();
         distFile = distfile;
                cutoff = c;
 }
@@ -29,7 +30,7 @@ void ReadCluster::read(NameAssignment* nameMap){
                        
        }
        catch(exception& e) {
-               errorOut(e, "ReadCluster", "read");
+               m->errorOut(e, "ReadCluster", "read");
                exit(1);
        }
 }
@@ -63,7 +64,7 @@ void ReadCluster::convertPhylip2Column(NameAssignment* nameMap){
                }
                else{
                        list = new ListVector(nameMap->getListVector());
-                       if(nameMap->count(name)==0){        mothurOut("Error: Sequence '" + name + "' was not found in the names file, please correct"); mothurOutEndLine(); }
+                       if(nameMap->count(name)==0){        m->mothurOut("Error: Sequence '" + name + "' was not found in the names file, please correct"); m->mothurOutEndLine(); }
                }
         
                char d;
@@ -106,7 +107,7 @@ void ReadCluster::convertPhylip2Column(NameAssignment* nameMap){
                                        
                                }
                                else{
-                                       if(nameMap->count(name)==0){        mothurOut("Error: Sequence '" + name + "' was not found in the names file, please correct"); mothurOutEndLine(); }
+                                       if(nameMap->count(name)==0){        m->mothurOut("Error: Sequence '" + name + "' was not found in the names file, please correct"); m->mothurOutEndLine(); }
                                        
                                        for(int j=0;j<i;j++){
                                                in >> distance;
@@ -139,7 +140,7 @@ void ReadCluster::convertPhylip2Column(NameAssignment* nameMap){
                                        }
                                }
                                else{
-                                       if(nameMap->count(name)==0){        mothurOut("Error: Sequence '" + name + "' was not found in the names file, please correct"); mothurOutEndLine(); }
+                                       if(nameMap->count(name)==0){        m->mothurOut("Error: Sequence '" + name + "' was not found in the names file, please correct"); m->mothurOutEndLine(); }
                                        
                                        for(int j=0;j<nseqs;j++){
                                                in >> distance;
@@ -190,7 +191,7 @@ void ReadCluster::convertPhylip2Column(NameAssignment* nameMap){
                distFile = outputFile;
        }
        catch(exception& e) {
-               errorOut(e, "ReadCluster", "convertPhylip2Column");
+               m->errorOut(e, "ReadCluster", "convertPhylip2Column");
                exit(1);
        }
 }