def phog_tree(request, phog_accession, leftid1=None, leftid2=None):
tree_id = int(phog_accession[4:11])
phog_left_id = int(phog_accession[12:])
phog = TreeNode.objects.get(tree__id = tree_id, left_id = phog_left_id)
if phog == None:
return render_to_response('404.html')
else:
t = loader.get_template('phyloscope/phyloscope.html')
highlightLeftIds = ""
if leftid1 or leftid2:
if not leftid2:
highlightLeftIds = leftid1
elif not leftid1:
highlightLeftIds = leftid2
else:
highlightLeftIds = "%s %s" % (leftid1, leftid2)
colorLeftIds = ''
c = RequestContext(request, {
'json_tree': annotatedTree(phog.tree.family.__unicode__(),
tree_method=phog.tree.method),
'superorthologous_nodes': "",
'family_accession': phog.tree.family.__unicode__(),
'phog_accession': phog_accession,
'subtree_left_id': phog.left_id,
'highlight_left_ids': highlightLeftIds,
'color_left_ids': colorLeftIds,
'hide_subfam_controls': True,
'hide_ortho_controls': True,
'show_full_tree_download': False})
# add_download_form_to_context(c)
return HttpResponse(t.render(c))
def orthoscope_get(request):
t = loader.get_template('phyloscope/phyloscope.html')
subtreeLeftId = get_parameter_from_GET('subtreeLeftId', request)
highlightLeftIds = get_parameter_from_GET('highlightLeftIds', request)
colorLeftIds = get_parameter_from_GET('colorLeftIds', request)
phog_accession = get_parameter_from_GET('phog', request)
family_accession = get_parameter_from_GET('family', request)
url_tree_method = get_parameter_from_GET('treeMethod', request)
if url_tree_method == '':
url_tree_method = 'ml'
if phog_accession != "":
phog_id = int(phog_accession[4:])
phog = TreeNode.objects.get(id = phog_id)
if phog == None:
return render_to_response('404.html')
else:
c = RequestContext(request, {
'json_tree': annotatedTree(phog.tree.family.__unicode__(),
tree_method = url_tree_method),
'superorthologous_nodes': "",
'family_accession': phog.tree.alignment.family.__unicode__(),
'subtree_left_id': phog.left_id,
'highlight_left_ids': highlightLeftIds,
'color_left_ids': colorLeftIds,
'hide_subfam_controls': True,
'tree_method': url_tree_method,
'do_color_ortho': True})
return HttpResponse(t.render(c))
elif family_accession != "":
c = RequestContext(request, {
'json_tree': annotatedTree(request.GET['family'],
tree_method = url_tree_method),
'superorthologous_nodes': superorthologousNodes(
request.GET['family'], tree_method = url_tree_method),
'family_accession': request.GET['family'],
'subtree_left_id': subtreeLeftId,
'highlight_left_ids': highlightLeftIds,
'color_left_ids': colorLeftIds,
'hide_subfam_controls': True,
'do_color_ortho': True,
'tree_method': url_tree_method,
'show_family_download': False,
'show_tree_download': False})
# add_download_form_to_context(c)
return HttpResponse(t.render(c))
else:
return render_to_response('404.html')
def orthoscope(request, family_accession):
t = loader.get_template('phyloscope/phyloscope.html')
c = RequestContext(request, {'json_tree': annotatedTree(family_accession),
'family_accession': family_accession,
'superorthologous_nodes': superorthologousNodes(family_accession),
'hide_subfam_controls': True,
'do_color_ortho': True})
return HttpResponse(t.render(c))
def phyloscope(request, family_accession):
t = loader.get_template('phyloscope/phyloscope.html')
c = RequestContext(
request, {
'json_tree': annotatedTree(family_accession),
'family_accession': family_accession,
'hide_ortho_controls': True
})
return HttpResponse(t.render(c))
def phog_tree_json(request, phog_accession):
tree_id = int(phog_accession[4:11])
phog_left_id = int(phog_accession[12:])
phog = TreeNode.objects.get(tree__id = tree_id, left_id = phog_left_id)
if phog == None:
return render_to_response('404.html')
response = HttpResponse(mimetype='application/json')
response['Content-Disposition'] = 'inline; filename=%s.json' % phog_accession
response.write(annotatedTree(phog.tree.family.__unicode__(),
tree_method=phog.tree.method))
return response
def phyloscope_get(request):
t = loader.get_template('phyloscope/phyloscope.html')
mode = get_parameter_from_GET('mode', request)
subtreeLeftId = get_parameter_from_GET('subtreeLeftId', request)
highlightLeftIds = get_parameter_from_GET('highlightLeftIds', request)
colorLeftIds = get_parameter_from_GET('colorLeftIds', request)
phog_accession = get_parameter_from_GET('phog', request)
family_accession = get_parameter_from_GET('family', request)
preferred_name = get_parameter_from_GET('preferredName', request)
url_tree_method = get_parameter_from_GET('treeMethod', request)
c = RequestContext(
request, {
'json_tree': annotatedTree(family_accession, url_tree_method),
'family_accession': family_accession,
'preferred_name': preferred_name,
'url_tree_method': url_tree_method,
'hide_ortho_controls': True
})
return HttpResponse(t.render(c))