added logfile feature

[mothur.git] / concensuscommand.cpp

diff --git a/concensuscommand.cpp b/concensuscommand.cpp
index 09e0f324268332e0f691d42b00f003aab9f9c9c9..30da32cfe05db5de942cebd213cf9cc9631cb717 100644 (file)
--- a/concensuscommand.cpp
+++ b/concensuscommand.cpp
@@ -20,44 +20,36 @@ ConcensusCommand::ConcensusCommand(string option){
                if(option == "help") { help(); abort = true; }
                
                else {
-                       if (option != "") { cout << "There are no valid parameters for the concensus command." << endl; abort = true; }
+                       if (option != "") { mothurOut("There are no valid parameters for the concensus command."); mothurOutEndLine(); abort = true; }
                        
                        //no trees were read
-                       if (globaldata->gTree.size() == 0) {    cout << "You must execute the read.tree command, before you may use the concensus command." << endl; abort = true;  }
+                       if (globaldata->gTree.size() == 0) {  mothurOut("You must execute the read.tree command, before you may use the concensus command."); mothurOutEndLine(); abort = true;  }
                        else {  t = globaldata->gTree;  }
                }
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the ConcensusCommand class Function ConcensusCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "ConcensusCommand", "ConcensusCommand");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the ConcensusCommand class function ConcensusCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }       
 }
 
 //**********************************************************************************************************************
 
 void ConcensusCommand::help(){
        try {
-               cout << "The concensus command can only be executed after a successful read.tree command." << "\n";
-               cout << "The concensus command has no parameters." << "\n";
-               cout << "The concensus command should be in the following format: concensus()." << "\n";
-               cout << "The concensus command output two files: .concensus.tre and .concensuspairs." << "\n";
-               cout << "The .concensus.tre file contains the concensus tree of the trees in your input file." << "\n";
-               cout << "The branch lengths are the percentage of trees in your input file that had the given pair." << "\n";
-               cout << "The .concensuspairs file contains a list of the internal nodes in your tree.  For each node, the pair that was used in the concensus tree " << "\n";
-               cout << "is reported with its percentage, as well as the other pairs that were seen for that node but not used and their percentages." << "\n" << "\n";         
+               mothurOut("The concensus command can only be executed after a successful read.tree command.\n");
+               mothurOut("The concensus command has no parameters.\n");
+               mothurOut("The concensus command should be in the following format: concensus().\n");
+               mothurOut("The concensus command output two files: .concensus.tre and .concensuspairs.\n");
+               mothurOut("The .concensus.tre file contains the concensus tree of the trees in your input file.\n");
+               mothurOut("The branch lengths are the percentage of trees in your input file that had the given pair.\n");
+               mothurOut("The .concensuspairs file contains a list of the internal nodes in your tree.  For each node, the pair that was used in the concensus tree \n");
+               mothurOut("is reported with its percentage, as well as the other pairs that were seen for that node but not used and their percentages.\n\n");          
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the ConcensusCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "ConcensusCommand", "help");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the ConcensusCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }       
 }
 
 //**********************************************************************************************************************
@@ -78,16 +70,6 @@ int ConcensusCommand::execute(){
                //get the possible pairings
                getSets();              
                
-               //print out pairings for testing
-               /*cout << "possible pairing " <<  endl;
-               for (it2 = nodePairs.begin(); it2 != nodePairs.end(); it2++) {
-                       for (int i = 0; i < it2->first.size(); i++) {
-                               cout << it2->first[i] << " ";
-                       }
-                       cout << '\t' << it2->second << endl;
-               }*/
-               
-               
                //open file for pairing not included in the tree
                notIncluded = getRootName(globaldata->inputFileName) + "concensuspairs";
                openOutputFile(notIncluded, out2);
@@ -170,13 +152,9 @@ int ConcensusCommand::execute(){
                return 0;
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the ConcensusCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "ConcensusCommand", "execute");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the ConcensusCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }               
 }
 
 //**********************************************************************************************************************
@@ -206,13 +184,9 @@ int ConcensusCommand::buildConcensusTree(vector<string> nodeSet) {
        
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the ConcensusCommand class Function buildConcensusTree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "ConcensusCommand", "buildConcensusTree");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the ConcensusCommand class function buildConcensusTree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }               
 }
 
 //**********************************************************************************************************************
@@ -263,13 +237,9 @@ void ConcensusCommand::getSets() {
                sort(treeSet.begin(), treeSet.end());
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the ConcensusCommand class Function getSets. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "ConcensusCommand", "getSets");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the ConcensusCommand class function getSets. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }               
 }
 
 //**********************************************************************************************************************
@@ -302,14 +272,9 @@ vector<string> ConcensusCommand::getNextAvailableSet(vector<string> bigset) {
        
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the ConcensusCommand class Function getNextAvailableSet. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "ConcensusCommand", "getNextAvailableSet");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the ConcensusCommand class function getNextAvailableSet. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }               
-
 }
 
 //**********************************************************************************************************************
@@ -337,14 +302,9 @@ vector<string> ConcensusCommand::getRestSet(vector<string> bigset, vector<string
        
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the ConcensusCommand class Function getRestSet. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "ConcensusCommand", "getRestSet");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the ConcensusCommand class function getRestSet. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }               
-
 }
 
 //**********************************************************************************************************************
@@ -366,13 +326,9 @@ bool ConcensusCommand::isSubset(vector<string> bigset, vector<string> subset) {
        
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the ConcensusCommand class Function isSubset. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "ConcensusCommand", "isSubset");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the ConcensusCommand class function isSubset. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }               
 }
 //**********************************************************************************************************************
 int ConcensusCommand::findSpot(string node) {
@@ -388,13 +344,9 @@ int ConcensusCommand::findSpot(string node) {
        
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the ConcensusCommand class Function findSpot. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "ConcensusCommand", "findSpot");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the ConcensusCommand class function findSpot. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }               
 }
 //**********************************************************************************************************************