Delete unneeded directory

[jabaws.git] / website / archive / binaries / mac / src / clustalw / src / general / OutputFile.cpp

diff --git a/website/archive/binaries/mac/src/clustalw/src/general/OutputFile.cpp b/website/archive/binaries/mac/src/clustalw/src/general/OutputFile.cpp
deleted file mode 100644 (file)
index 55b505b..0000000
--- a/website/archive/binaries/mac/src/clustalw/src/general/OutputFile.cpp
+++ /dev/null
@@ -1,105 +0,0 @@
-/**
- * Author: Mark Larkin
- * 
- * Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.  
- */
-#ifdef HAVE_CONFIG_H
-    #include "config.h"
-#endif
-#include "OutputFile.h"
-#include "utils.h"
-#include "userparams.h"
-
-namespace clustalw
-{
-
-OutputFile::OutputFile()
-{
-
-}
-
-OutputFile::~OutputFile()
-{
-    // If it is open, close it and say that a file has been created!!!!!
-    if(file.get())
-    {
-        file->close();
-        utilityObject->info("%s file created:   [%s]\n", typeOfFileMsg.c_str(),
-                                name.c_str());                         
-    }
-}
-
-bool OutputFile::openFile(std::string* fileName, const std::string msg, const std::string* path, 
-                      const std::string ext, const std::string fileType)
-{
-    if (fileName->empty())
-    {
-        *fileName = getOutputFileName(msg, *path, ext);
-            
-        if(fileName->empty())
-        {
-            return false;
-        }
-    }
-
-    file.reset(new std::ofstream(fileName->c_str(), std::ofstream::trunc));
-                
-    if(!file->is_open()) 
-    {
-        utilityObject->error("Cannot open output file [%s]\n", fileName->c_str()); 
-        return false;
-    }
-    name = *fileName; 
-    typeOfFileMsg = fileType;
-    
-    return true;
-}
-
-bool OutputFile::isOpen()
-{
-    return file->is_open();
-}
-
-std::ofstream* OutputFile::getPtrToFile()
-{
-    return file.get();
-}
-                      
-std::string OutputFile::getOutputFileName(const std::string prompt, std::string path, 
-                                          const std::string fileExtension)
-{
-    std::string temp;
-    std::string _fileName; // Will return this name.
-    std::string message;
-    _fileName = path + fileExtension;
-
-    if(_fileName.compare(userParameters->getSeqName()) == 0) 
-    {
-        cerr << "WARNING: Output file name is the same as input file.\n";
-        if (userParameters->getMenuFlag()) 
-        {
-            message = "\n\nEnter new name to avoid overwriting  [" + _fileName + "]: ";
-            utilityObject->getStr(message, temp);
-            if(temp != "")
-            {
-                _fileName = temp;
-            }
-        }
-    }
-    else if (userParameters->getMenuFlag()) 
-    {
-
-        message = prompt + " [" + _fileName + "]";
-        utilityObject->getStr(message, temp);
-        if(temp != "")
-        {
-            _fileName = temp;
-        }
-    }   
-    return _fileName;
-
-}
-
-}
-
-