Delete unneeded directory

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

diff --git a/website/archive/binaries/mac/src/disembl/biopython-1.50/Bio/FilteredReader.py b/website/archive/binaries/mac/src/disembl/biopython-1.50/Bio/FilteredReader.py
deleted file mode 100644 (file)
index ba2bb6f..0000000
--- a/website/archive/binaries/mac/src/disembl/biopython-1.50/Bio/FilteredReader.py
+++ /dev/null
@@ -1,152 +0,0 @@
-# Copyright 2001 by Katharine Lindner.  All rights reserved.\r
-# This code is part of the Biopython distribution and governed by its\r
-# license.  Please see the LICENSE file that should have been included\r
-# as part of this package.\r
-\r
-"""Code for more fancy file handles (OBSOLETE).\r
-\r
-Classes:\r
-Filtered is a decorator for File that allows the user to filter the output\r
-on a line by line basis.\r
-\r
-The FilteredReader module reads a file and applies a sequence of filters to the input\r
-The constructor sets a default filter chain, but the user can select another filter by setting\r
-Bio.FilteredReader.filter_chain.\r
-\r
-handle = open( "filename" )\r
-filtered_reader = Bio.FilteredReader( handle )\r
-filtered_reader.filter_chain = [ remove_asterisks, replace_dot_with_dash ]\r
-filtered_reasder.read()\r
-\r
-All filters in the chain must provide the same interface with a line of text as the single\r
-input parameter and altered text as the return value.\r
-\r
-This module is now considered to be obsolete, and is likely to be deprecated\r
-in a future release of Biopython, and later removed.\r
-"""\r
-\r
-\r
-def dump_saved( name, text, j ):\r
-    """Used for debugging."""\r
-    dump_file = open( name + '%d' % j, "w" )\r
-    k = 0\r
-    for i in range ( 0, len( text ), 80 ):\r
-        dump_file.write(  '%s\n' % text[ i : i + 80 ] )\r
-    dump_file.close()\r
-\r
-def remove_leading_whitespace( line ):\r
-    return line.lstrip()\r
-\r
-\r
-def remove_empty_line( line ):\r
-    stripped_line = line.strip()\r
-    if( stripped_line ):\r
-        return line[ : ]\r
-    else:\r
-        return ''\r
-\r
-def remove_useless_dot( line ):\r
-    before = line\r
-    while( 1 ):\r
-        after = before.replace( "\t.\t", "\t\t" )\r
-        if( len( before ) == len( after ) ):\r
-            break\r
-        before = after\r
-    if( after.endswith( '.' ) ):\r
-        after = after[ :-1 ]\r
-    return after\r
-\r
-def fix_punctuation( line ):\r
-    line = line.replace( "'", '' )\r
-    line = line.replace( '"', '' )\r
-    line = line.replace( ';', '\t' )\r
-    line = line.replace( 'entryname', 'id' )\r
-#    line = line.lower( )\r
-    if( line ):\r
-        return line[ : ]\r
-    else:\r
-        return ''\r
-\r
-\r
-\r
-class FilteredReader:\r
-    def __init__(self, handle ):\r
-        self._handle = handle\r
-        self._start_line = ''\r
-        self._debug_count = 0\r
-        self.filter_chain = [ remove_empty_line, remove_useless_dot, fix_punctuation ]\r
-\r
-    def __getattr__(self, attr):\r
-        return getattr(self._handle, attr)\r
-\r
-\r
-\r
-    def close(self, *args, **keywds ):\r
-        return self._handle.close( *args, **keywds)\r
-\r
-    def read( self, *args, **keywds ):\r
-        line = ''\r
-        len_expected = self._get_len_expected( args, keywds )\r
-        if( len_expected ):\r
-            filtered_text = self.read_block( len_expected )\r
-        else:\r
-            filtered_text = self.read_to_end()\r
-        return filtered_text\r
-\r
-    def read_block( self, len_expected ):\r
-\r
-        len_filtered = 0\r
-        len_adjusted -= len( self._start_line )\r
-        filtered_text = ''\r
-        while( len_filtered < len_expected ):\r
-\r
-            text_read = self._handle.read( len_adjusted )\r
-            full_text = self._start_line + text_read\r
-            lines = full_text.splitlines( 1 )\r
-            if( text_read == '' ):\r
-                filtered_text = filtered_text + self.filter( lines )\r
-                break\r
-            else:\r
-                all_but_last_line = lines[ :-1 ]\r
-                self._start_line = lines[ -1 ]\r
-                filtered_text = filtered_text + self.filter( all_but_last_line )\r
-            len_filtered_text = len( filtered_text )\r
-            len_adjusted = len_adjusted - len_filtered_text\r
-        return filtered_text[ : ]\r
-\r
-    def read_to_end( self ):\r
-        filtered_text = ''\r
-        text_read = self._handle.read()\r
-        full_text = self._start_line + text_read\r
-        lines = full_text.splitlines( 1 )\r
-        filtered_text += self.filter( lines[:] )\r
-        return filtered_text[ : ]\r
-\r
-    def _get_len_expected( self, args, keywds ):\r
-\r
-        if( len( args) > 0 ):\r
-            len_expected = args[ 0 ]\r
-            if( len_expected < 0 ):\r
-                len_expected = None\r
-        elif 'size' in keywds:\r
-            len_expected = keywds['size']\r
-        else:\r
-            len_expected = None\r
-        return len_expected\r
-\r
-    def filter( self, lines  ):\r
-        filter_chain = self.filter_chain\r
-        filtered_text = ''\r
-        for line in lines:\r
-            for filter in filter_chain:\r
-                line = filter( *( line, ) )\r
-            filtered_text += line\r
-\r
-        return filtered_text\r
-\r
-def has_trailing_linefeed( line ):\r
-    if( line.endswith( chr( 13 ) ) or \\r
-        line.endswith( chr( 10 ) ) ):\r
-        return 1\r
-    else:\r
-        return 0\r