worked on hcluster. made .single command run using a sharedfile. and various other...

[mothur.git] / mergefilecommand.cpp

diff --git a/mergefilecommand.cpp b/mergefilecommand.cpp
index 3342c489d9f54a55abda3bac79b60511402eaf4c..fcf63895b960fa8293df03dcff7c1e5bce28c914 100644 (file)
--- a/mergefilecommand.cpp
+++ b/mergefilecommand.cpp
@@ -35,13 +35,13 @@ MergeFileCommand::MergeFileCommand(string option){
                        }
                        
                        string fileList = validParameter.validFile(parameters, "input", false);                 
-                       if(fileList == "not found") { cout << "you must enter two or more file names" << endl;  abort=true;  }
+                       if(fileList == "not found") { mothurOut("you must enter two or more file names"); mothurOutEndLine();  abort=true;  }
                        else{   splitAtDash(fileList, fileNames);       }
                        
                        numInputFiles = fileNames.size();
                        ifstream testFile;
                        if(numInputFiles == 0){
-                               cout << "you must enter two or more file names and you entered " << fileNames.size() <<  " file names" << endl;
+                               mothurOut("you must enter two or more file names and you entered " + toString(fileNames.size()) +  " file names"); mothurOutEndLine();
                                abort=true;  
                        }
                        else{
@@ -52,18 +52,14 @@ MergeFileCommand::MergeFileCommand(string option){
                        }   
                        
                        outputFileName = validParameter.validFile(parameters, "output", false);                 
-                       if (outputFileName == "not found") { cout << "you must enter an output file name" << endl;  abort=true;  }
+                       if (outputFileName == "not found") { mothurOut("you must enter an output file name"); mothurOutEndLine();  abort=true;  }
                }
                        
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the MergeFileCommand class Function MergeFileCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "MergeFileCommand", "MergeFileCommand");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the MergeFileCommand class function MergeFileCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }       
 }
 
 //**********************************************************************************************************************
@@ -79,43 +75,36 @@ int MergeFileCommand::execute(){
                ofstream outputFile;
                openOutputFile(outputFileName, outputFile);
                
-               ifstream inputFile;
                char c;
                for(int i=0;i<numInputFiles;i++){
+                       ifstream inputFile; //declaration must be inside for loop of windows throws an error
+                       
                        openInputFile(fileNames[i], inputFile);
                        
                        while(!inputFile.eof()){        c = inputFile.get(); outputFile << c;   }
                        
                        inputFile.close();
                }
+               
+               outputFile.close();
                return 0;
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the BinSeqCommand class Function BinSeqCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "MergeFileCommand", "execute");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the BinSeqCommand class function BinSeqCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }       
-       
 }
 
 //**********************************************************************************************************************
 
 void MergeFileCommand::help(){
        try {
-               cout << "The merge.file command..." << endl;
+               mothurOut("The merge.file command..."); mothurOutEndLine();
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the MergeFileCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "MergeFileCommand", "help");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the MergeFileCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }       
-       
 }
 
 //**********************************************************************************************************************