created mothurOut class to handle logfiles

[mothur.git] / tree.cpp

diff --git a/tree.cpp b/tree.cpp
index 731eb64d93f95b485f8607308e3e88345138813c..eca53d5527bbdda6dbc97ddc0c9f4e7766e15d25 100644 (file)
--- a/tree.cpp
+++ b/tree.cpp
@@ -14,6 +14,7 @@
 Tree::Tree() {
        try {
                globaldata = GlobalData::getInstance();
+               m = MothurOut::getInstance();
                
                if (globaldata->runParse == true) {  parseTreeFile();  globaldata->runParse = false;  }
 //for(int i = 0; i <   globaldata->Treenames.size(); i++) { cout << i << '\t' << globaldata->Treenames[i] << endl;  }  
@@ -44,7 +45,7 @@ Tree::Tree() {
                }
        }
        catch(exception& e) {
-               errorOut(e, "Tree", "Tree");
+               m->errorOut(e, "Tree", "Tree");
                exit(1);
        }
 }
@@ -73,7 +74,7 @@ void Tree::addNamesToCounts() {
                        
                        map<string, string>::iterator itNames = globaldata->names.find(name);
                        
-                       if (itNames == globaldata->names.end()) { mothurOut(name + " is not in your name file, please correct."); mothurOutEndLine(); exit(1);  }
+                       if (itNames == globaldata->names.end()) { m->mothurOut(name + " is not in your name file, please correct."); m->mothurOutEndLine(); exit(1);  }
                        else {
                                vector<string> dupNames;
                                splitAtComma(globaldata->names[name], dupNames);
@@ -134,7 +135,7 @@ void Tree::addNamesToCounts() {
                                
        }
        catch(exception& e) {
-               errorOut(e, "Tree", "addNamesToCounts");
+               m->errorOut(e, "Tree", "addNamesToCounts");
                exit(1);
        }
 }
@@ -148,7 +149,7 @@ int Tree::getIndex(string searchName) {
                
        }
        catch(exception& e) {
-               errorOut(e, "Tree", "getIndex");
+               m->errorOut(e, "Tree", "getIndex");
                exit(1);
        }
 }
@@ -160,7 +161,7 @@ void Tree::setIndex(string searchName, int index) {
                globaldata->gTreemap->setIndex(searchName, index);
        }
        catch(exception& e) {
-               errorOut(e, "Tree", "setIndex");
+               m->errorOut(e, "Tree", "setIndex");
                exit(1);
        }
 }
@@ -178,7 +179,7 @@ void Tree::assembleTree() {
                }
        }
        catch(exception& e) {
-               errorOut(e, "Tree", "assembleTree");
+               m->errorOut(e, "Tree", "assembleTree");
                exit(1);
        }
 }
@@ -216,7 +217,7 @@ void Tree::getCopy(Tree* copy) {
                
        }
        catch(exception& e) {
-               errorOut(e, "Tree", "getCopy");
+               m->errorOut(e, "Tree", "getCopy");
                exit(1);
        }
 }
@@ -269,7 +270,7 @@ map<string, int> Tree::mergeGroups(int i) {
                return parsimony;
        }
        catch(exception& e) {
-               errorOut(e, "Tree", "mergeGroups");
+               m->errorOut(e, "Tree", "mergeGroups");
                exit(1);
        }
 }
@@ -335,7 +336,7 @@ map<string, int> Tree::mergeUserGroups(int i, vector<string> g) {
                return parsimony;
        }
        catch(exception& e) {
-               errorOut(e, "Tree", "mergeUserGroups");
+               m->errorOut(e, "Tree", "mergeUserGroups");
                exit(1);
        }
 }
@@ -358,7 +359,7 @@ map<string,int> Tree::mergeGcounts(int position) {
                return sum;
        }
        catch(exception& e) {
-               errorOut(e, "Tree", "mergeGcounts");
+               m->errorOut(e, "Tree", "mergeGcounts");
                exit(1);
        }
 }
@@ -400,7 +401,7 @@ void Tree::randomLabels(vector<string> g) {
                }
        }
        catch(exception& e) {
-               errorOut(e, "Tree", "randomLabels");
+               m->errorOut(e, "Tree", "randomLabels");
                exit(1);
        }
 }
@@ -430,7 +431,7 @@ void Tree::randomLabels(string groupA, string groupB) {
                }
        }               
        catch(exception& e) {
-               errorOut(e, "Tree", "randomLabels");
+               m->errorOut(e, "Tree", "randomLabels");
                exit(1);
        }
 }
@@ -446,7 +447,7 @@ void Tree::randomBlengths()  {
                }
        }
        catch(exception& e) {
-               errorOut(e, "Tree", "randomBlengths");
+               m->errorOut(e, "Tree", "randomBlengths");
                exit(1);
        }
 }
@@ -503,7 +504,7 @@ void Tree::randomTopology() {
                }
        }
        catch(exception& e) {
-               errorOut(e, "Tree", "randomTopology");
+               m->errorOut(e, "Tree", "randomTopology");
                exit(1);
        }
 }
@@ -515,7 +516,7 @@ void Tree::print(ostream& out) {
                out << ";" << endl;
        }
        catch(exception& e) {
-               errorOut(e, "Tree", "print");
+               m->errorOut(e, "Tree", "print");
                exit(1);
        }
 }
@@ -527,7 +528,7 @@ void Tree::printForBoot(ostream& out) {
                out << ";" << endl;
        }
        catch(exception& e) {
-               errorOut(e, "Tree", "printForBoot");
+               m->errorOut(e, "Tree", "printForBoot");
                exit(1);
        }
 }
@@ -549,7 +550,7 @@ void Tree::createNewickFile(string f) {
                out.close();
        }
        catch(exception& e) {
-               errorOut(e, "Tree", "createNewickFile");
+               m->errorOut(e, "Tree", "createNewickFile");
                exit(1);
        }
 }
@@ -568,7 +569,7 @@ int Tree::findRoot() {
                return -1;
        }
        catch(exception& e) {
-               errorOut(e, "Tree", "findRoot");
+               m->errorOut(e, "Tree", "findRoot");
                exit(1);
        }
 }
@@ -614,7 +615,7 @@ void Tree::printBranch(int node, ostream& out, string mode) {
                
        }
        catch(exception& e) {
-               errorOut(e, "Tree", "printBranch");
+               m->errorOut(e, "Tree", "printBranch");
                exit(1);
        }
 }
@@ -710,7 +711,7 @@ void Tree::parseTreeFile() {
                filehandle.close();
        }
        catch(exception& e) {
-               errorOut(e, "Tree", "parseTreeFile");
+               m->errorOut(e, "Tree", "parseTreeFile");
                exit(1);
        }
 }
@@ -774,7 +775,7 @@ int Tree::readTreeString(ifstream& filehandle)      {
                return 0;
        }
        catch(exception& e) {
-               errorOut(e, "Tree", "readTreeString");
+               m->errorOut(e, "Tree", "readTreeString");
                exit(1);
        }
 }