added logfile feature

[mothur.git] / readtreecommand.cpp

diff --git a/readtreecommand.cpp b/readtreecommand.cpp
index d301b1366d5f8965a2c84151940d5773b5d71854..2a3c5d0cdf264ce0c4ecf614b4c3fd46d0ffe51c 100644 (file)
--- a/readtreecommand.cpp
+++ b/readtreecommand.cpp
@@ -38,12 +38,12 @@ ReadTreeCommand::ReadTreeCommand(string option){
                        //check for required parameters
                        treefile = validParameter.validFile(parameters, "tree", true);
                        if (treefile == "not open") { abort = true; }
-                       else if (treefile == "not found") { treefile = ""; cout << "tree is a required parameter for the read.tree command." << endl; abort = true;  }  
+                       else if (treefile == "not found") { treefile = ""; mothurOut("tree is a required parameter for the read.tree command."); mothurOutEndLine(); abort = true;  }   
                        else {  globaldata->setTreeFile(treefile);  globaldata->setFormat("tree");      }
                        
                        groupfile = validParameter.validFile(parameters, "group", true);
                        if (groupfile == "not open") { abort = true; }  
-                       else if (groupfile == "not found") { groupfile = ""; cout << "group is a required parameter for the read.tree command." << endl; abort = true;  }
+                       else if (groupfile == "not found") { groupfile = ""; mothurOut("group is a required parameter for the read.tree command."); mothurOutEndLine(); abort = true;   }
                        else {  
                                globaldata->setGroupFile(groupfile); 
                                //read in group map info.
@@ -60,11 +60,7 @@ ReadTreeCommand::ReadTreeCommand(string option){
                }
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the ReadTreeCommand class Function ReadTreeCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the ReadTreeCommand class function ReadTreeCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "ReadTreeCommand", "ReadTreeCommand");              
                exit(1);
        }
 }
@@ -72,26 +68,22 @@ ReadTreeCommand::ReadTreeCommand(string option){
 
 void ReadTreeCommand::help(){
        try {
-               cout << "The read.tree command must be run before you execute a unifrac.weighted, unifrac.unweighted. " << "\n";
-               cout << "It also must be run before using the parsimony command, unless you are using the randomtree parameter." << "\n";
-               cout << "The read.tree command should be in the following format: read.tree(tree=yourTreeFile, group=yourGroupFile)." << "\n";
-               cout << "The tree and group parameters are both required." << "\n";
-               cout << "Note: No spaces between parameter labels (i.e. tree), '=' and parameters (i.e.yourTreefile)." << "\n" << "\n";
+               mothurOut("The read.tree command must be run before you execute a unifrac.weighted, unifrac.unweighted. \n");
+               mothurOut("It also must be run before using the parsimony command, unless you are using the randomtree parameter.\n");
+               mothurOut("The read.tree command should be in the following format: read.tree(tree=yourTreeFile, group=yourGroupFile).\n");
+               mothurOut("The tree and group parameters are both required.\n");
+               mothurOut("Note: No spaces between parameter labels (i.e. tree), '=' and parameters (i.e.yourTreefile).\n\n");
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the ReadTreeCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "ReadTreeCommand", "help"); 
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the ReadTreeCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }       
 }
 
 //**********************************************************************************************************************
 
 ReadTreeCommand::~ReadTreeCommand(){
-       delete read;
+       if (abort == false) { delete read; }
 }
 
 //**********************************************************************************************************************
@@ -105,10 +97,10 @@ int ReadTreeCommand::execute(){
                
                readOk = read->read(); 
                
-               if (readOk != 0) { cout << "Read Terminated." << endl; globaldata->gTree.clear(); delete globaldata->gTreemap; return 0; }
+               if (readOk != 0) { mothurOut("Read Terminated."); mothurOutEndLine(); globaldata->gTree.clear(); delete globaldata->gTreemap; return 0; }
                
                vector<Tree*> T = globaldata->gTree;
-               
+
                //assemble users trees
                for (int i = 0; i < T.size(); i++) {
                        T[i]->assembleTree();
@@ -126,7 +118,7 @@ int ReadTreeCommand::execute(){
                                
                                //then you did not find it so report it 
                                if (count == globaldata->Treenames.size()) { 
-                                       cout << treeMap->namesOfSeqs[i] << " is in your namefile and not in your tree. It will be disregarded." << endl;
+                                       mothurOut(treeMap->namesOfSeqs[i] + " is in your namefile and not in your tree. It will be disregarded."); mothurOutEndLine();
                                }
                        }
                }
@@ -134,11 +126,7 @@ int ReadTreeCommand::execute(){
                return 0;
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the ReadTreeCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the ReadTreeCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "ReadTreeCommand", "execute");      
                exit(1);
        }
 }