Delete unneeded directory

[jabaws.git] / website / archive / binaries / mac / src / disembl / biopython-1.50 / Bio / File.py

diff --git a/website/archive/binaries/mac/src/disembl/biopython-1.50/Bio/File.py b/website/archive/binaries/mac/src/disembl/biopython-1.50/Bio/File.py
deleted file mode 100644 (file)
index d616f42..0000000
--- a/website/archive/binaries/mac/src/disembl/biopython-1.50/Bio/File.py
+++ /dev/null
@@ -1,180 +0,0 @@
-# Copyright 1999 by Jeffrey Chang.  All rights reserved.
-# This code is part of the Biopython distribution and governed by its
-# license.  Please see the LICENSE file that should have been included
-# as part of this package.
-
-"""Code for more fancy file handles.
-
-
-Classes:
-UndoHandle     File object decorator with support for undo-like operations.
-StringHandle   Wraps a file object around a string.
-SGMLHandle     File object that automatically strips SGML tags from data.
-
-SGMLStripper   Object that strips SGML.  This is now considered OBSOLETE, and
-               is likely to be deprecated in a future release of Biopython,
-               and later removed.
-
-"""
-import os
-import StringIO
-import sgmllib
-
-class UndoHandle:
-    """A Python handle that adds functionality for saving lines.
-
-    Saves lines in a LIFO fashion.
-
-    Added methods:
-    saveline    Save a line to be returned next time.
-    peekline    Peek at the next line without consuming it.
-
-    """
-    def __init__(self, handle):
-        self._handle = handle
-        self._saved = []
-
-    def __iter__(self):
-        return self
-
-    def next(self):
-        next = self.readline()
-        if not next:
-            raise StopIteration
-        return next
-
-    def readlines(self, *args, **keywds):
-        lines = self._saved + self._handle.readlines(*args,**keywds)
-        self._saved = []
-        return lines
-
-    def readline(self, *args, **keywds):
-        if self._saved:
-            line = self._saved.pop(0)
-        else:
-            line = self._handle.readline(*args,**keywds)
-        return line
-
-    def read(self, size=-1):
-        if size == -1:
-            saved = "".join(self._saved)
-            self._saved[:] = []
-        else:
-            saved = ''
-            while size > 0 and self._saved:
-                if len(self._saved[0]) <= size:
-                    size = size - len(self._saved[0])
-                    saved = saved + self._saved.pop(0)
-                else:
-                    saved = saved + self._saved[0][:size]
-                    self._saved[0] = self._saved[0][size:]
-                    size = 0
-        return saved + self._handle.read(size)
-
-    def saveline(self, line):
-        if line:
-            self._saved = [line] + self._saved
-
-    def peekline(self):
-        if self._saved:
-            line = self._saved[0]
-        else:
-            line = self._handle.readline()
-            self.saveline(line)
-        return line
-
-    def tell(self):
-        lengths = map(len, self._saved)
-        sum = reduce(lambda x, y: x+y, lengths, 0)
-        return self._handle.tell() - sum
-
-    def seek(self, *args):
-        self._saved = []
-        self._handle.seek(*args)
-
-    def __getattr__(self, attr):
-        return getattr(self._handle, attr)
-
-    def __enter__(self):
-        return self
-
-    def __exit__(self, type, value, traceback):
-        self._handle.close()
-
-
-# I could make this faster by using cStringIO.
-# However, cStringIO (in v1.52) does not implement the
-# readlines method.
-StringHandle = StringIO.StringIO
-
-
-
-class SGMLHandle:
-    """A Python handle that automatically strips SGML tags from data (OBSOLETE).
-
-    This module is now considered to be obsolete, and is likely to be
-    deprecated in a future release of Biopython, and later removed.
-    """
-    def __init__(self, handle):
-        """SGMLStripper(handle)
-
-        handle is a file handle to SGML-formatted data.
-        
-        """
-        self._handle = handle
-        self._stripper = SGMLStripper()
-
-    def read(self, *args, **keywds):
-        data = self._handle.read(*args, **keywds)
-        return self._stripper.strip(data)
-
-    def readline(self, *args, **keywds):
-        line = self._handle.readline(*args, **keywds)
-        return self._stripper.strip(line)
-
-    def readlines(self, *args, **keywds):
-        lines = self._handle.readlines(*args, **keywds)
-        for i in range(len(lines)):
-            lines[i] = self._stripper.strip(str)
-        return lines
-
-    def __getattr__(self, attr):
-        return getattr(self._handle, attr)
-
-
-class SGMLStripper:
-    class MyParser(sgmllib.SGMLParser):
-        def __init__(self):
-            sgmllib.SGMLParser.__init__(self)
-            self.data = ''
-        def handle_data(self, data):
-            self.data = self.data + data
-
-    def __init__(self):
-        self._parser = SGMLStripper.MyParser()
-
-    def strip(self, str):
-        """S.strip(str) -> string
-
-        Strip the SGML tags from str.
-
-        """
-        if not str:  # empty string, don't do anything.
-            return ''
-        # I need to make sure that I don't return an empty string if
-        # the buffer is not empty.  This can happen if there's a newline
-        # character embedded within a tag.  Thus, I'll first check to
-        # see if the last character is a newline.  If it is, and it's stripped
-        # away, I'll add it back.
-        is_newline = str[-1] in ['\n', '\r']
-        
-        self._parser.data = ''    # clear the parser's data (don't reset)
-        self._parser.feed(str)
-        if self._parser.data:
-            str = self._parser.data
-        elif is_newline:
-            str = '\n'
-        else:
-            str = ''
-        return str
-