added logfile feature

[mothur.git] / clustercommand.cpp

diff --git a/clustercommand.cpp b/clustercommand.cpp
index eeba407eefc7bfb39a6bc60428a796f7bfb47068..593f2629ff9f1107ddaf6bd10c568047118c1070 100644 (file)
--- a/clustercommand.cpp
+++ b/clustercommand.cpp
@@ -36,7 +36,7 @@ ClusterCommand::ClusterCommand(string option){
                        
                        //error checking to make sure they read a distance file
                        if ((globaldata->gSparseMatrix == NULL) || (globaldata->gListVector == NULL)) {
-                               cout << "Before you use the cluster command, you first need to read in a distance matrix." << endl;  abort = true;
+                               mothurOut("Before you use the cluster command, you first need to read in a distance matrix."); mothurOutEndLine(); abort = true;
                        } 
                
                        //check for optional parameter and set defaults
@@ -56,7 +56,7 @@ ClusterCommand::ClusterCommand(string option){
 
                        
                        if ((method == "furthest") || (method == "nearest") || (method == "average")) { }
-                       else {cout << "Not a valid clustering method.  Valid clustering algorithms are furthest, nearest or average." << endl; abort = true; }
+                       else { mothurOut("Not a valid clustering method.  Valid clustering algorithms are furthest, nearest or average."); mothurOutEndLine(); abort = true; }
 
                        
                        if (abort == false) {
@@ -73,7 +73,7 @@ ClusterCommand::ClusterCommand(string option){
                                if(method == "furthest")        {       cluster = new CompleteLinkage(rabund, list, matrix);    tag = "fn";     }
                                else if(method == "nearest"){   cluster = new SingleLinkage(rabund, list, matrix);              tag = "nn";     }
                                else if(method == "average"){   cluster = new AverageLinkage(rabund, list, matrix);             tag = "an";     }
-                               else                                            {       cout << "error - not recognized method" << endl;        abort = true;   }       
+                               else                                            {       mothurOut("error - not recognized method"); mothurOutEndLine(); abort = true;   }       
                                
                                fileroot = getRootName(globaldata->inputFileName);
                        
@@ -88,11 +88,7 @@ ClusterCommand::ClusterCommand(string option){
                
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the ClusterCommand class Function ClusterCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the ClusterCommand class function ClusterCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "ClusterCommand", "ClusterCommand");                
                exit(1);
        }
 }
@@ -101,20 +97,16 @@ ClusterCommand::ClusterCommand(string option){
 
 void ClusterCommand::help(){
        try {
-               cout << "The cluster command can only be executed after a successful read.dist command." << "\n";
-               cout << "The cluster command parameter options are method, cuttoff and precision. No parameters are required." << "\n";
-               cout << "The cluster command should be in the following format: " << "\n";
-               cout << "cluster(method=yourMethod, cutoff=yourCutoff, precision=yourPrecision) " << "\n";
-               cout << "The acceptable cluster methods are furthest, nearest and average.  If no method is provided then furthest is assumed." << "\n" << "\n";        
+                mothurOut("The cluster command can only be executed after a successful read.dist command.\n");
+                mothurOut("The cluster command parameter options are method, cuttoff and precision. No parameters are required.\n");
+                mothurOut("The cluster command should be in the following format: \n");
+                mothurOut("cluster(method=yourMethod, cutoff=yourCutoff, precision=yourPrecision) \n");
+                mothurOut("The acceptable cluster methods are furthest, nearest and average.  If no method is provided then furthest is assumed.\n\n");
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the ClusterCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "ClusterCommand", "help");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the ClusterCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }       
 }
 
 //**********************************************************************************************************************
@@ -186,14 +178,9 @@ int ClusterCommand::execute(){
                return 0;
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the ClusterCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the ClusterCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "ClusterCommand", "execute");
                exit(1);
        }
-
 }
 
 //**********************************************************************************************************************
@@ -209,13 +196,8 @@ void ClusterCommand::printData(string label){
                oldList.print(listFile);
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the ClusterCommand class Function printData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the ClusterCommand class function printData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "ClusterCommand", "printData");
                exit(1);
        }
-
 }
 //**********************************************************************************************************************