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# coding: UTF-8
# Copyright 2009, 2010 Thomas Jourdan
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
import ka_utils
"""Generate HTML describing the genome."""
import os
import sys
import traceback
import ka_debug
import exon_color
import exon_position
import exon_direction
class HtmlFormater(object):
"""Html formater
inv: self._indent >= 0
"""
generator = u'Minimal Kandid'
def __init__(self, base_name, unique_id, base_folder):
"""Constructor for HTML formater."""
self._base_name = base_name.replace(' ', '_')
self.unique_id = unique_id
self._base_folder = base_folder.replace(' ', '_')
self._indent = 0
self._page = u''
self.produced_files_list = []
self.id_count = 0
self._header_occured = False # debugging only
self._footer_occured = False # debugging only
file_path = os.path.join(base_folder, unique_id)
if not os.path.exists(file_path):
try:
os.mkdir(file_path)
except:
ka_debug.err('creating directory [%s] [%s] [%s]' % \
(file_path, sys.exc_info()[0], sys.exc_info()[1]))
traceback.print_exc(file=sys.__stderr__)
def _escape(self, text):
"""Quote special characters '<' and '&'.
This must be done to produce correct HTML.
pre: text is not None
"""
utext = unicode(text)
quoted = u''
for uchar in utext:
if uchar in [u'<']:
quoted += u'<'
elif uchar in [u'&']:
quoted += u'&'
else:
quoted += uchar
return quoted
def _append(self, lines):
"""Append lines to HTML page.
pre: lines is not None
"""
indenting = u' '*(2*self._indent)
for line in lines:
self._page += indenting + line + u'\n'
def _append_escaped(self, text):
"""Append text to HTML page.
pre: text is not None
"""
self._page += self._escape(text)
def _get_id(self):
"""Returns a unique id.
All elements generated are decorated with an id.
We need this to use the HTML page like a tree widget.
"""
self.id_count += 1
return u'id_' + unicode(self.id_count)
def get_absolutename(self, extension, postfix=None):
"""Returns absolute path appended by filename
of the generated HTML page."""
return os.path.join(self.get_pathname(),
self.get_filename(extension, postfix))
def get_pathname(self):
"""Returns absolute path."""
return os.path.join(self._base_folder,
self.unique_id)
def get_filename(self, extension, postfix=None):
"""Returns the filename only of the generated HTML page."""
postfix = '' if postfix is None else '_' + postfix
return self._base_name + postfix + '.' + extension
def header(self, title):
"""Generate starting sequence to the HTML page.
pre: not self._header_occured
pre: not self._footer_occured
"""
self._append( (
u'<?xml version="1.0" encoding="UTF-8"?>',
u'<?xml-stylesheet href="../treestyles.css" type="text/css"?>',
u'<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.1//EN"',
u' "http://www.w3.org/TR/xhtml11/DTD/xhtml11.dtd">',
u'',
u'<html xml:lang="en" xmlns="http://www.w3.org/1999/xhtml">',
u'<head>',
u' <meta name="generator" content="' + HtmlFormater.generator +'" />',
u'',
u' <title>' + title + u'</title>',
u' <link rel="stylesheet" href="../treestyles.css" type="text/css" />',
u' <script type="text/javascript" src="../marktree.js">',
u'//<![CDATA[',
u'',
u' //]]>',
u' </script>',
u'</head>',
u'',
u'<body>',
u' <div class="basetop">',
u' <a href="#" onclick="expandAll(document.getElementById(\'base\'))">Expand</a> -',
u' <a href="#" onclick="collapseAll(document.getElementById(\'base\'))">Collapse</a>',
u' </div>',
u'',
u' <div id="base" class="basetext">',
u'',
u' <ul>',
) )
self._header_occured = True
def footer(self):
"""Generate finishing sequence to the HTML page.
pre: self._indent == 0
pre: self._header_occured
pre: not self._footer_occured
"""
self._append( (
u' </ul>',
u' </div>',
u'</body>',
u'</html>',
) )
self._footer_occured = True
def _begin_list_item(self, identification):
"""Start a list item.
pre: self._header_occured
pre: not self._footer_occured
"""
self._append( (
u' <li class="basic" id="id_' + identification + u'" >',
u' <span>',
) )
def _end_list_item(self):
"""Close a list item.
pre: self._header_occured
pre: not self._footer_occured
"""
self._append( (
u' </span>',
u' </li>',
) )
def _image_item(self, filename, width, height, description, newline=True):
"""Append an image tag to the page.
pre: filename is not None
pre: width is not None
pre: height is not None
pre: description is not None
"""
if newline:
self._append( (
u' <br />',
) )
self._append( (
u' <img style="background-color:#000000" src="' + filename + u'"' \
+ u' width="' + unicode(width) + u'"' \
+ u' height="' + unicode(height) + u'"' \
+ u' alt="' + description + u'"'
+ u' title="' + description + u'" border="1" />',
) )
def begin_list(self, text):
"""Start a list.
pre: self._header_occured
pre: not self._footer_occured
pre: text is not None
"""
self._indent += 1
self._append( (
u' <li class="col" id="' + self._get_id() + u'">',
self._escape(text),
u' <ul class="subexp">',
) )
def end_list(self):
"""Close a list.
pre: self._header_occured
pre: not self._footer_occured
"""
self._append( (
u' </ul>',
u' </li>',
) )
self._indent -= 1
def text_item(self, text):
"""Generate an item for using in text lists.
pre: self._header_occured
pre: not self._footer_occured
pre: text is not None
"""
self._begin_list_item(self._get_id())
self._append_escaped(text)
self._end_list_item()
def text_list(self, title, text_list):
"""Generate a text list.
pre: self._header_occured
pre: not self._footer_occured
pre: text_list is not None
"""
self._begin_list_item(self._get_id())
self._append_escaped(title)
for text in text_list:
self._append_escaped(text + u', ')
self._end_list_item()
def color_item(self, color, text, alpha=True):
"""Generate a preview icon showing colors.
pre: self._header_occured
pre: not self._footer_occured
pre: color is not None
pre: text is not None
"""
identification = self._get_id()
pathname = self.get_absolutename('png', postfix=identification)
filename = self.get_filename('png', postfix=identification)
surface = exon_color.Color.make_icon(color.rgba, alpha,
ka_utils.ICON_WIDTH, ka_utils.ICON_HEIGHT)
surface.write_to_png(pathname)
self.produced_files_list.append(pathname)
description = color.explain(alpha)
self._begin_list_item(identification)
self._append_escaped(text)
self._image_item(filename, ka_utils.ICON_WIDTH, ka_utils.ICON_HEIGHT,
description)
self._end_list_item()
def alpha_item(self, alpha, text):
"""Generate a preview icon showing transparency.
pre: self._header_occured
pre: not self._footer_occured
pre: alpha is not None
pre: text is not None
"""
identification = self._get_id()
pathname = self.get_absolutename('png', postfix=identification)
filename = self.get_filename('png', postfix=identification)
surface = exon_color.Color.make_icon((1.0, 1.0, 1.0, alpha), True,
ka_utils.ICON_WIDTH, ka_utils.ICON_HEIGHT)
surface.write_to_png(pathname)
self.produced_files_list.append(pathname)
description = '%d%% opaque' % (100*alpha)
self._begin_list_item(self._get_id())
self._append_escaped(text)
self._image_item(filename, ka_utils.ICON_WIDTH, ka_utils.ICON_HEIGHT,
description)
self._end_list_item()
def color_array(self, color_list, text, alpha=True):
"""Generate some preview icons showing colors.
pre: self._header_occured
pre: not self._footer_occured
pre: color_list is not None
pre: text is not None
"""
self._begin_list_item(self._get_id())
self._append_escaped(text)
self._append( (u' <br />',) )
for color in color_list:
identification = self._get_id()
pathname = self.get_absolutename('png', postfix=identification)
filename = self.get_filename('png', postfix=identification)
surface = color.make_icon(color.rgba, alpha,
ka_utils.ICON_WIDTH, ka_utils.ICON_HEIGHT)
surface.write_to_png(pathname)
self.produced_files_list.append(pathname)
description = color.explain(alpha)
self._image_item(filename,
ka_utils.ICON_WIDTH, ka_utils.ICON_HEIGHT,
description, newline=False)
self._end_list_item()
def position_item(self, position, text):
"""Generate a preview icon showing a position.
pre: self._header_occured
pre: not self._footer_occured
pre: position is not None
pre: text is not None
"""
self.position_array([position], text)
def position_array(self, position_list, text):
"""Generate some preview icons showing positions.
pre: self._header_occured
pre: not self._footer_occured
pre: position_list is not None
pre: text is not None
"""
description = u'['
for position in position_list:
description += position.explain() + u'; '
description += u']'
self._begin_list_item(self._get_id())
self._append_escaped(text + u' ' + description)
identification = self._get_id()
pathname = self.get_absolutename('png', postfix=identification)
filename = self.get_filename('png', postfix=identification)
surface = exon_position.Position.make_icon(position_list,
ka_utils.ICON_WIDTH, ka_utils.ICON_HEIGHT)
surface.write_to_png(pathname)
self.produced_files_list.append(pathname)
self._image_item(filename, ka_utils.ICON_WIDTH, ka_utils.ICON_HEIGHT,
description)
self._end_list_item()
def direction_item(self, direction, text):
"""Generate a preview icon showing one direction vectors.
pre: self._header_occured
pre: not self._footer_occured
pre: direction is not None
pre: text is not None
"""
self.direction_array([direction], text)
def direction_array(self, direction_list, text):
"""Generate some preview icons showing direction vectors.
pre: self._header_occured
pre: not self._footer_occured
pre: direction_list is not None
pre: text is not None
"""
description = u'['
for direction in direction_list:
description += direction.explain() + u'; '
description += u']'
self._begin_list_item(self._get_id())
self._append_escaped(text + u' ' + description)
identification = self._get_id()
pathname = self.get_absolutename('png', postfix=identification)
filename = self.get_filename('png', postfix=identification)
surface = exon_direction.Direction.make_icon(direction_list,
ka_utils.ICON_WIDTH, ka_utils.ICON_HEIGHT)
surface.write_to_png(pathname)
self.produced_files_list.append(pathname)
self._image_item(filename, ka_utils.ICON_WIDTH, ka_utils.ICON_HEIGHT,
description)
self._end_list_item()
def surface_item(self, surface, text, description):
"""Generate a preview icon of the layers surface.
pre: self._header_occured
pre: not self._footer_occured
pre: surface is not None
pre: text is not None
pre: description is not None
"""
identification = self._get_id()
pathname = self.get_absolutename('png', postfix=identification)
filename = self.get_filename('png', postfix=identification)
surface.write_to_png(pathname)
self.produced_files_list.append(pathname)
width = surface.get_width()
height = surface.get_height()
self._begin_list_item(self._get_id())
self._append_escaped(text)
self._image_item(filename, width, height, description)
self._end_list_item()
def write_html_file(self, file_path):
"""Write HTML to the file system.
pre: self._header_occured
pre: self._footer_occured
pre: self._indent == 0
pre: file_path is not None
"""
out_file = None
try:
out_file = open(file_path, 'w')
out_file.write(self._page.encode('utf-8'))
self.produced_files_list.append(file_path)
except:
ka_debug.err('failed writing [%s] [%s] [%s]' % \
(file_path, sys.exc_info()[0], sys.exc_info()[1]))
traceback.print_exc(file=sys.__stderr__)
finally:
if out_file:
out_file.close()
|
