changed groupfile in classify.seqs to reflect multiple fasta files

[mothur.git] / mergefilecommand.cpp

diff --git a/mergefilecommand.cpp b/mergefilecommand.cpp
index d5973394e5a097e879bf1526689d137266a417c1..a076281035ff08fdb2ba0af591dce24f726cd636 100644 (file)
--- a/mergefilecommand.cpp
+++ b/mergefilecommand.cpp
@@ -11,7 +11,7 @@
 
 //**********************************************************************************************************************
 
-MergeFileCommand::MergeFileCommand(string option){
+MergeFileCommand::MergeFileCommand(string option)  {
        try {
                abort = false;
                
@@ -39,7 +39,7 @@ MergeFileCommand::MergeFileCommand(string option){
                        if (inputDir == "not found"){   inputDir = "";          }
                        
                        string fileList = validParameter.validFile(parameters, "input", false);                 
-                       if(fileList == "not found") { mothurOut("you must enter two or more file names"); mothurOutEndLine();  abort=true;  }
+                       if(fileList == "not found") { m->mothurOut("you must enter two or more file names"); m->mothurOutEndLine();  abort=true;  }
                        else{   splitAtDash(fileList, fileNames);       }
                        
                        //if the user changes the output directory command factory will send this info to us in the output parameter 
@@ -49,7 +49,7 @@ MergeFileCommand::MergeFileCommand(string option){
                        numInputFiles = fileNames.size();
                        ifstream testFile;
                        if(numInputFiles == 0){
-                               mothurOut("you must enter two or more file names and you entered " + toString(fileNames.size()) +  " file names"); mothurOutEndLine();
+                               m->mothurOut("you must enter two or more file names and you entered " + toString(fileNames.size()) +  " file names"); m->mothurOutEndLine();
                                abort=true;  
                        }
                        else{
@@ -66,13 +66,13 @@ MergeFileCommand::MergeFileCommand(string option){
                        }   
                        
                        outputFileName = validParameter.validFile(parameters, "output", false);                 
-                       if (outputFileName == "not found") { mothurOut("you must enter an output file name"); mothurOutEndLine();  abort=true;  }
+                       if (outputFileName == "not found") { m->mothurOut("you must enter an output file name"); m->mothurOutEndLine();  abort=true;  }
                        else if (outputDir != "") { outputFileName = outputDir + getSimpleName(outputFileName); }
                }
                        
        }
        catch(exception& e) {
-               errorOut(e, "MergeFileCommand", "MergeFileCommand");
+               m->errorOut(e, "MergeFileCommand", "MergeFileCommand");
                exit(1);
        }
 }
@@ -96,16 +96,30 @@ int MergeFileCommand::execute(){
                        
                        openInputFile(fileNames[i], inputFile);
                        
-                       while(!inputFile.eof()){        c = inputFile.get(); outputFile << c;   }
+                       while(!inputFile.eof()){        
+                               if (m->control_pressed) { inputFile.close(); outputFile.close(); remove(outputFileName.c_str()); return 0;  }
+                       
+                               c = inputFile.get(); 
+                               //-1 is eof char
+                               if (int(c) != -1) { outputFile << c; }   
+                       }
                        
                        inputFile.close();
                }
                
                outputFile.close();
+               
+               if (m->control_pressed) { remove(outputFileName.c_str()); return 0;  }
+               
+               m->mothurOutEndLine();
+               m->mothurOut("Output File Name: "); m->mothurOutEndLine();
+               m->mothurOut(outputFileName); m->mothurOutEndLine();    
+               m->mothurOutEndLine();
+
                return 0;
        }
        catch(exception& e) {
-               errorOut(e, "MergeFileCommand", "execute");
+               m->errorOut(e, "MergeFileCommand", "execute");
                exit(1);
        }
 }
@@ -114,10 +128,10 @@ int MergeFileCommand::execute(){
 
 void MergeFileCommand::help(){
        try {
-               mothurOut("The merge.file command..."); mothurOutEndLine();
+               m->mothurOut("The merge.file command..."); m->mothurOutEndLine();
        }
        catch(exception& e) {
-               errorOut(e, "MergeFileCommand", "help");
+               m->errorOut(e, "MergeFileCommand", "help");
                exit(1);
        }
 }