def write_svg(self, fh):
"""
Write this termimus to the SVG file.
Parameters:
fh - open filehandle to write SVG XML text to
Return value:
None
"""
if self.domain_id:
domainid = self.domain_id
else:
domainid = ''
#shape='flowEndOfProc'
shape = 'rect' # FIXME errors with flowEndOfProc, even without ports
clr = rgb_tuple_to_hex_str(self.get_color(), SHAPE_ALPHA)
style = 'fill:#' + rgb_tuple_to_hex_str(self.get_color()) + ';'
fh.write(' <dunnart:node id="' + str(self.xmlid) + '" ' +
'dunnart:label="' + self.label + '" ' + 'dunnart:width="' +
str(self.width) + '" ' + 'dunnart:height="' +
str(self.height) + '" ' + 'dunnart:xPos="' + str(self.xpos) +
'" ' + 'dunnart:yPos="' + str(self.ypos) + '" ' +
'dunnart:fillColour="' + clr + '" ' + # color
'style="' + style + '" ' + # color
'dunnart:type="' + shape + '" ' + PTGRAPH_NS + ':' +
'chainId="' + self.get_chainid() + '" ' + PTGRAPH_NS + ':' +
'domainId="' + domainid + '" ' + PTGRAPH_NS + ':' +
'hovertext="chain ' + self.chainid + '" ' +
'onclick="handleClickEvent(evt)"' + '/>\n')
def write_svg(self, fh):
"""
Write this termimus to the SVG file.
Parameters:
fh - open filehandle to write SVG XML text to
Return value:
None
"""
if self.domain_id:
domainid = self.domain_id
else:
domainid = ''
#shape='flowEndOfProc'
shape='rect' # FIXME errors with flowEndOfProc, even without ports
clr = rgb_tuple_to_hex_str(self.get_color(), SHAPE_ALPHA)
style = 'fill:#' + rgb_tuple_to_hex_str(self.get_color()) + ';'
fh.write(' <dunnart:node id="'+str(self.xmlid)+'" ' +
'dunnart:label="' + self.label + '" ' +
'dunnart:width="' + str(self.width) + '" ' +
'dunnart:height="' + str(self.height) +'" ' +
'dunnart:xPos="' + str(self.xpos) + '" ' +
'dunnart:yPos="' + str(self.ypos) + '" ' +
'dunnart:fillColour="' + clr + '" ' + # color
'style="' + style + '" ' + # color
'dunnart:type="' + shape + '" ' +
PTGRAPH_NS + ':' + 'chainId="' +
self.get_chainid() + '" ' +
PTGRAPH_NS + ':' + 'domainId="' +
domainid + '" ' +
PTGRAPH_NS + ':' + 'hovertext="chain ' + self.chainid + '" ' +
'onclick="handleClickEvent(evt)"' +
'/>\n')
def write_svg(self, fh):
"""
Write this strand to the SVG file.
Mostly there are Dunnart namespace attributes for Dunnart to use
in layout out diagram, but also some proorigami namespace attributes
that are ignored by Dunnart but retained in its finished diagram
SVG output to be used by interactive SVG for hover text showing
residues and so on.
Parameters:
fh - open filehandle to write SVG XML text to
Return value:
None
"""
shape = 'bioStrand'
if self.get_reversed():
reversed_str = "1"
else:
reversed_str = "0"
clr = rgb_tuple_to_hex_str(self.get_color(), SHAPE_ALPHA)
style = 'fill:#' + rgb_tuple_to_hex_str(self.get_color()) + ';'
(residue_names,
residue_ids) = get_residue_strings(self.resname_list, self.resid_list)
if self.get_sheet_id():
sheetid = self.get_sheet_id()
else:
sheetid = ''
if self.domain_id:
domainid = self.domain_id
else:
domainid = ''
fh.write(' <dunnart:node id="' + str(self.xmlid) + '" ' +
'dunnart:label="' + self.label + '" ' + 'dunnart:width="' +
str(self.width) + '" ' + 'dunnart:height="' +
str(self.height) + '" ' + 'dunnart:xPos="' + str(self.xpos) +
'" ' + 'dunnart:yPos="' + str(self.ypos) + '" ' +
'dunnart:reversed="' + reversed_str + '" ' +
'dunnart:fillColour="' + clr + '" ' + # color
'style="' + style + '" ' + # color
'dunnart:type="' + shape + '" ' + PTGRAPH_NS + ':' +
'residueNames="' + residue_names + '" ' + PTGRAPH_NS + ':' +
'residueSeqNums="' + residue_ids + '" ' + PTGRAPH_NS + ':' +
'sseseqnum="' + self.sseseqnum + '" ' + PTGRAPH_NS + ':' +
'chainId="' + self.get_chainid() + '" ' + PTGRAPH_NS + ':' +
'sheetId="' + sheetid + '" ' + PTGRAPH_NS + ':' +
'domainId="' + domainid + '" ' +
# hovertext is updated by Javascript in interactive SVG
PTGRAPH_NS + ':' + 'hovertext="' + self.nodeid + '" ' +
PTGRAPH_NS + ':' + 'selected="0" ' + 'dunnart:headLabel="' +
self.headLabel + '" ' + 'dunnart:tailLabel="' +
self.tailLabel + '" '
'onmousemove="updateHoverText(evt)" ' +
'onclick="handleClickEvent(evt)"' + ' />\n')
def set_color(self, color):
"""
Label this node with color (r,g,b) tuple. See comments in __init__
Parameters: color - (r,g,b) color tuple
Return value: None
Uses data members (write): color, color_hex
"""
self.color = color
self.color_hex = rgb_tuple_to_hex_str(color)
def set_color(self, color):
"""
Label this node with color (r,g,b) tuple. See comments in __init__
Parameters: color - (r,g,b) color tuple
Return value: None
Uses data members (write): color, color_hex
"""
self.color = color
self.color_hex = rgb_tuple_to_hex_str(color)
def write_svg(self, fh):
"""
Write this strand to the SVG file.
Mostly there are Dunnart namespace attributes for Dunnart to use
in layout out diagram, but also some proorigami namespace attributes
that are ignored by Dunnart but retained in its finished diagram
SVG output to be used by interactive SVG for hover text showing
residues and so on.
Parameters:
fh - open filehandle to write SVG XML text to
Return value:
None
"""
shape = 'bioStrand'
if self.get_reversed():
reversed_str = "1"
else:
reversed_str = "0"
clr = rgb_tuple_to_hex_str(self.get_color(), SHAPE_ALPHA)
style = 'fill:#' + rgb_tuple_to_hex_str(self.get_color()) + ';'
(residue_names, residue_ids) = get_residue_strings(self.resname_list,
self.resid_list)
if self.get_sheet_id():
sheetid = self.get_sheet_id()
else:
sheetid = ''
if self.domain_id:
domainid = self.domain_id
else:
domainid = ''
fh.write(' <dunnart:node id="'+str(self.xmlid)+'" ' +
'dunnart:label="' + self.label + '" ' +
'dunnart:width="' + str(self.width) + '" ' +
'dunnart:height="' + str(self.height) +'" ' +
'dunnart:xPos="' + str(self.xpos) + '" ' +
'dunnart:yPos="' + str(self.ypos) + '" ' +
'dunnart:reversed="' + reversed_str + '" ' +
'dunnart:fillColour="' + clr + '" ' + # color
'style="' + style + '" ' + # color
'dunnart:type="' + shape + '" ' +
PTGRAPH_NS + ':' + 'residueNames="' +
residue_names + '" ' +
PTGRAPH_NS + ':' + 'residueSeqNums="' +
residue_ids +
'" ' +
PTGRAPH_NS + ':' + 'sseseqnum="' +
self.sseseqnum + '" ' +
PTGRAPH_NS + ':' + 'chainId="' +
self.get_chainid() + '" ' +
PTGRAPH_NS + ':' + 'sheetId="' +
sheetid + '" ' +
PTGRAPH_NS + ':' + 'domainId="' +
domainid + '" ' +
# hovertext is updated by Javascript in interactive SVG
PTGRAPH_NS + ':' + 'hovertext="' + self.nodeid + '" ' +
PTGRAPH_NS + ':' + 'selected="0" ' +
'dunnart:headLabel="' + self.headLabel + '" ' +
'dunnart:tailLabel="' + self.tailLabel + '" '
'onmousemove="updateHoverText(evt)" ' +
'onclick="handleClickEvent(evt)"' +
' />\n')
