Delete unneeded directory

[jabaws.git] / website / archive / binaries / mac / src / clustalw / src / fileInput / InFileStream.cpp

diff --git a/website/archive/binaries/mac/src/clustalw/src/fileInput/InFileStream.cpp b/website/archive/binaries/mac/src/clustalw/src/fileInput/InFileStream.cpp
deleted file mode 100644 (file)
index 743d024..0000000
--- a/website/archive/binaries/mac/src/clustalw/src/fileInput/InFileStream.cpp
+++ /dev/null
@@ -1,143 +0,0 @@
-/**
- * Author: Nigel Brown
- * 
- * Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.  
- */
-/**
- * InFileStream subclasses std::ifstream, adding a check for the end-of-line
- * character convention in the input file. This is then used by the getline()
- * member as the line delimiter, unless the caller supplies an explicit
- * delimiter.
- *
- * Note: This is an ugly workaround; at present various operations repeatedly
- * construct/destruct an instance and open/close a sequence file up to 12
- * times! A cleaner class will probably derive this class from something like
- * 'istream' aggregating a 'filebuf' under control of istream::seekg().
- *
- * Created: 09-02-07,Nigel Brown(EMBL)
- * 
- * Changes:
- * Mark Larkin 13-2-07: I removed the dynamic cast from the getline functions. 
- ***************************************************************************/
-#ifdef HAVE_CONFIG_H
-    #include "config.h"
-#endif
-#include <string>
-#include <fstream>
-#include <iostream>
-#include "InFileStream.h"
-using namespace std;
-
-const char LF = 0x0a;  //linefeed
-const char CR = 0x0d;  //carriage return
-
-InFileStream::InFileStream() :
-    ifstream()
-{
-    delim = '\n'; // default
-    //cout << "InFileStream() constructor 1" << endl;
-}
-
-InFileStream::InFileStream(const char *filename) :
-    ifstream(filename, ios::in), filename(filename)
-{
-    //cout << "InFileStream(f) constructor 2" << endl;
-    delim = findDelimiter();
-}
-
-//- copy-constructor: can't copy superclass private members
-//- InFileStream::InFileStream(const InFileStream &copy) :
-//-     ifstream(static_cast<const ifstream&>(copy))
-//- {
-//-     cout << "InFileStream() constructor 3" << endl;
-//-     delim = copy.delim;
-//- }
-
-void InFileStream::open(const char *filename) 
-{
-
-    this->filename = filename;
-    ifstream::open(filename, ios::in);
-    if  (ifstream::fail())
-        return;
-    delim = findDelimiter();
-}
-
-//not necessary, but for symmetry to open()
-void InFileStream::close() 
-{
-    ifstream::close();   
-}
-
-
-//getline with stored delimiter
-std::istream& InFileStream::getline(char *s, streamsize n) 
-{
-    return ifstream::getline(s, n, delim);
-}
-
-//getline with caller supplied delimiter
-std::istream& InFileStream::getline(char *s, streamsize n, char delim) 
-{
-    return ifstream::getline(s, n, delim);
-}
-
-
-/**
- * Mark 24-1-2007. I added the function findDelimiter to determine if '\r' or
- * '\n' will be used as the line delimiter when parsing the file.
- *
- * 25-01-07,Nigel Brown(EMBL): changed body of loop to check successive chars
- * in case of DOS/Windows
- *
- * 09-02-07,Nigel Brown(EMBL): moved member into new InFileStream subclassed
- * from std::ifstream, so this is called automatically for any file reader
- * that uses InFileStream in place of std::ifstream. Replaced if/then/else
- * with switch.
- */
-char InFileStream::findDelimiter()
-{
-    ifstream in;
-    int type = 0;
-    
-    in.open(filename.c_str(), ios::in);
-    if (in.fail())
-        return delim;
-    
-    in.seekg(0, ios::beg);
-
-    //look for CR or LF or CRLF (or LFCR)
-    if (in.is_open()) {
-        char c;
-        while (in.get(c)) {
-            if (c == CR)
-                type |= 1;
-            else if (c == LF)
-                type |= 2;
-            else if (type)
-                break;
-        }
-    }
-    in.close();
-
-    switch (type) {
-       case 1:
-           //cout << "file is Mac System 9" << endl;
-           delim = '\r';
-           break;
-       case 2:
-           //cout << "file is UNIX" << endl;
-           delim = '\n';
-           break;
-       case 3:
-           //cout << "file is DOS" << endl;
-           delim = '\n';
-           break;
-       default: //short or empty file
-           //cout << "file is UNIX (default)" << endl;
-           delim = '\n';
-    }
-    return delim;
-}
-
-