added logfile feature

[mothur.git] / deconvolutecommand.cpp

diff --git a/deconvolutecommand.cpp b/deconvolutecommand.cpp
index fba2d27ebf470c968f50f64c71c54917f0e8f5df..a936c820b56f88609e621894565359892384224a 100644 (file)
--- a/deconvolutecommand.cpp
+++ b/deconvolutecommand.cpp
@@ -35,7 +35,7 @@ DeconvoluteCommand::DeconvoluteCommand(string option) {
                        //check for required parameters
                        inFastaName = validParameter.validFile(parameters, "fasta", true);
                        if (inFastaName == "not open") { abort = true; }
-                       else if (inFastaName == "not found") { inFastaName = ""; cout << "fasta is a required parameter for the unique.seqs command." << endl; abort = true;  } 
+                       else if (inFastaName == "not found") { inFastaName = ""; mothurOut("fasta is a required parameter for the unique.seqs command."); mothurOutEndLine(); abort = true;  }  
                        
                        oldNameMapFName = validParameter.validFile(parameters, "name", true);
                        if (oldNameMapFName == "not open") { abort = true; }
@@ -44,11 +44,7 @@ DeconvoluteCommand::DeconvoluteCommand(string option) {
 
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the DeconvoluteCommand class Function DeconvoluteCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the DeconvoluteCommand class function DeconvoluteCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "DeconvoluteCommand", "DeconvoluteCommand");
                exit(1);
        }
 }
@@ -56,21 +52,17 @@ DeconvoluteCommand::DeconvoluteCommand(string option) {
 
 void DeconvoluteCommand::help(){
        try {
-               cout << "The unique.seqs command reads a fastafile and creates a namesfile." << "\n";
-               cout << "It creates a file where the first column is the groupname and the second column is a list of sequence names who have the same sequence. " << "\n";
-               cout << "If the sequence is unique the second column will just contain its name. " << "\n";
-               cout << "The unique.seqs command parameter is fasta and it is required." << "\n";
-               cout << "The unique.seqs command should be in the following format: " << "\n";
-               cout << "unique.seqs(fasta=yourFastaFile) " << "\n";    
+               mothurOut("The unique.seqs command reads a fastafile and creates a namesfile.\n");
+               mothurOut("It creates a file where the first column is the groupname and the second column is a list of sequence names who have the same sequence. \n");
+               mothurOut("If the sequence is unique the second column will just contain its name. \n");
+               mothurOut("The unique.seqs command parameter is fasta and it is required.\n");
+               mothurOut("The unique.seqs command should be in the following format: \n");
+               mothurOut("unique.seqs(fasta=yourFastaFile) \n");       
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the DeconvoluteCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "DeconvoluteCommand", "help");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the DeconvoluteCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }       
 }
 
 /**************************************************************************************/
@@ -94,11 +86,7 @@ int DeconvoluteCommand::execute() {
                return 0;
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the DeconvoluteCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the DeconvoluteCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "DeconvoluteCommand", "execute");
                exit(1);
        }
 }