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Update DNA Segment Map for obscure legend - Feature Request 13421 (#602)
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Fix parent-child graph for parent view
Move legend in single chromosome view to right side
Fix height of drawing area to not obscure either legend or bars
Update background colors of maternal/paternal to match other gramps views
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@GaryGriffin
GaryGriffin authored Sep 8, 2024
1 parent 834352d commit 9b64d95
Showing 1 changed file with 61 additions and 48 deletions.
109 changes: 61 additions & 48 deletions DNA/dnasegmentmap.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2020 Nick Hall
# Copyright (C) 2020-2022 Gary Griffin
# Copyright (C) 2020-2024 Gary Griffin
#
# 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
Expand Down Expand Up @@ -57,13 +57,15 @@
CONFIG = config.register_manager('DNASegmentMap')
CONFIG.register('map.chromosome-build', 37)
CONFIG.register('map.legend-swatch-offset-y', 0)
CONFIG.register('map.show_associate_id',1)
CONFIG.register('map.maternal-background', (0.926, 0.825, 0.92, 1.0))
CONFIG.register('map.paternal-background', (0.833, 0.845, 0.92, 1.0))
CONFIG.register('map.legend-single-chromosome-y-offset', 25)
CONFIG.register('map.show-centromere',0)
CONFIG.register('map.show_associate_id',0)
CONFIG.register('map.maternal-background', (0.996, 0.8, 0.941, 1.0))
CONFIG.register('map.paternal-background', (0.722, 0.808, 0.902, 1.0))
CONFIG.register('map.legend-single-chromosome-y-offset', 0)
CONFIG.register('map.show-centromere',1)
CONFIG.register('map.legend-char-height',12)
CONFIG.register('map.include-citation-notes',1)
CONFIG.register('map.include-citation-notes',0)
CONFIG.register('map.chromosome-x-scale',1.4)
CONFIG.register('map.chromosome-y-scale',1)

CONFIG.init()

Expand Down Expand Up @@ -128,10 +130,13 @@ def main(self):
if data[0][0] <= 0 : # Unrelated
side = 'U'
elif data[0][0] == 1: #parent / child
if self.dbstate.db.get_person_from_handle(data[0][1]).gender == 0:
side = 'M'
if self.dbstate.db.get_person_from_handle(data[0][1]).get_gramps_id() == active.get_gramps_id():
side = 'U'
else:
side = 'P'
if self.dbstate.db.get_person_from_handle(data[0][1]).gender == 0:
side = 'M'
else:
side = 'P'
elif (len(data) > 1 and data[0][0] == data[1][0] and data[0][2][0] != data[1][2][0]): #shares both parents
side = 'U'
elif (len(data[0][2]) == 0): # association is descendant of active
Expand Down Expand Up @@ -249,6 +254,8 @@ def __init__(self):
self.legend_single_chromosome = self._config.get('map.legend-single-chromosome-y-offset')
self.show_centromere = self._config.get('map.show-centromere')
self.legend_char_height = self._config.get('map.legend-char-height')
self.x_scale = self._config.get('map.chromosome-x-scale')
self.y_scale = self._config.get('map.chromosome-y-scale')
self._config.save()
self.chromosomesThirtySeven = (
('1', 249250621),
Expand Down Expand Up @@ -473,9 +480,10 @@ def do_draw(self, cr):
chr_height = 12
spacing = 2
self.maximum = 250000000
self.maximum *= self.x_scale
if draw_single_chromosome :
for i, label in enumerate (self.chromosomes):
if label[0] == current_chromosome: self.maximum = label[1]
if label[0] == current_chromosome: self.maximum = label[1] * self.x_scale
# Chromosome labels
self.__chrrects = []
label_width = 0
Expand All @@ -502,42 +510,43 @@ def do_draw(self, cr):
chart_width = (allocation.width - label_width) * 0.95

# Border
cr.move_to(0, offset)
cr.line_to(allocation.width, offset)
cr.stroke()
# cr.move_to(0, offset)
# cr.line_to(allocation.width, offset)
# cr.stroke()

bottom = len(self.chromosomes) * 2 * (chr_height + spacing) + offset
cr.move_to(0, bottom)
cr.line_to(allocation.width, bottom)
cr.stroke()
# cr.move_to(0, bottom)
# cr.line_to(allocation.width, bottom)
# cr.stroke()

cr.move_to(label_width, 0)
cr.line_to(label_width, bottom)
cr.stroke()
# cr.move_to(label_width, 0)
# cr.line_to(label_width, bottom)
# cr.stroke()

cr.move_to(allocation.width, 0)
cr.line_to(allocation.width, bottom)
cr.stroke()
# cr.move_to(allocation.width, 0)
# cr.line_to(allocation.width, bottom)
# cr.stroke()

# Ticks and grid lines
tick_step, maximum = 50000000, 250000000
count = 0
while count <= self.maximum:
# draw tick
tick_pos = label_width + chart_width * count / self.maximum
cr.move_to(tick_pos, bottom)
cr.line_to(tick_pos, bottom + 5)
cr.stroke()
# draw grid line
if self.grid_lines:
cr.set_dash([1, 2])
if not draw_single_chromosome :
tick_step, maximum = 50000000 , 250000000 * self.x_scale
count = 0
while count <= 250000000:
# draw tick
tick_pos = label_width + chart_width * count / self.maximum
cr.move_to(tick_pos, bottom)
cr.line_to(tick_pos, (2 * spacing) + offset)
cr.line_to(tick_pos, bottom + 5)
cr.stroke()
cr.set_dash([])
count += tick_step
# draw grid line
if self.grid_lines:
cr.set_dash([1, 2])
cr.move_to(tick_pos, bottom)
cr.line_to(tick_pos, (2 * spacing) + offset)
cr.stroke()
cr.set_dash([])
count += tick_step

offset += spacing
offset += spacing

# Chromosomes background
if not draw_single_chromosome:
Expand All @@ -550,7 +559,7 @@ def do_draw(self, cr):
# draw paternal
cr.rectangle(label_width,
i * 2 * (chr_height + spacing) + offset,
chart_width * self.centromere[i][1] / self.maximum,
chart_width * self.centromere[i][1] / self.maximum ,
chr_height)
cr.rectangle(label_width+chart_width * centloc / self.maximum,
i * 2 * (chr_height + spacing) + offset,
Expand Down Expand Up @@ -624,9 +633,9 @@ def do_draw(self, cr):

if draw_single_chromosome:
legend_offset_y = self.legend_single_chromosome * (chr_height + spacing) + offset
legend_offset_x = allocation.width * 0.10
legend_offset_x = allocation.width * 0.75
else:
legend_offset_y = 10 * (chr_height + spacing) + offset
legend_offset_y = 0 * (chr_height + spacing) + offset
legend_offset_x = allocation.width * 0.75
# legend_offset_x = allocation.width * 0.75
last_name = ''
Expand All @@ -638,8 +647,9 @@ def do_draw(self, cr):
legend_chr_height = self.legend_char_height
chromo_count = -1
row_num = 0
maximum = self.maximum
legend_count = 0
if draw_single_chromosome:
maximum = self.maximum
for chromo, start, stop, side, cms, snp, assoc_name, rgb_color, associate, handle, note in self.segments:
chromo_count += 1
try:
Expand All @@ -660,9 +670,9 @@ def do_draw(self, cr):
row_num * 2 * (chr_height + spacing) + offset,
chart_width * self.centromere[this_chromo][1] / maximum,
chr_height)
cr.rectangle(label_width + chart_width * centloc / maximum,
cr.rectangle(label_width + chart_width * centloc / maximum ,
row_num * 2 * (chr_height + spacing) + offset,
chart_width * (maximum - centloc) / maximum,
chart_width * (maximum/ self.x_scale - centloc) / maximum,
chr_height)
if self.show_centromere:
cr.move_to(label_width + chart_width * self.centromere[this_chromo][1] / self.maximum,
Expand All @@ -689,7 +699,7 @@ def do_draw(self, cr):
chr_height)
cr.rectangle(label_width+ chart_width * centloc / maximum,
row_num * 2 * (chr_height + spacing) + offset + chr_height,
chart_width* (maximum - centloc) / maximum,
chart_width* (maximum/ self.x_scale - centloc) / maximum,
chr_height)
if self.show_centromere:
cr.move_to(label_width + chart_width * self.centromere[this_chromo][1] / self.maximum,
Expand Down Expand Up @@ -758,7 +768,7 @@ def do_draw(self, cr):
# Legend entry
if last_name != assoc_name:
last_name = assoc_name

print("Single ",legend_count)
cr.rectangle(legend_offset_x - legend_chr_height - 2 * spacing,
legend_offset_y,
legend_chr_height,
Expand All @@ -777,6 +787,8 @@ def do_draw(self, cr):
legend_offset_y += legend_chr_height + 2 * spacing
PangoCairo.show_layout(cr, layout)
else: # Drawing all chromosome segments
row_num = 24
maximum = self.maximum
for chromo, start, stop, side, cms, snp, assoc_name, rgb_color, associate, handle, note in self.segments:
chromo_count += 1
try:
Expand Down Expand Up @@ -806,6 +818,7 @@ def do_draw(self, cr):
self.__notes.append(note)
# Legend entry
if last_name != assoc_name:
legend_count += 1
last_name = assoc_name
cr.rectangle(legend_offset_x - legend_chr_height - 2 * spacing,
legend_offset_y + self.legend_swatch_offset_y,
Expand All @@ -824,8 +837,8 @@ def do_draw(self, cr):
cr.set_source_rgba(*fg_color)
legend_offset_y += legend_chr_height + 2 * spacing
PangoCairo.show_layout(cr, layout)

self.set_size_request(-1, bottom + height + 5)
y_scale = max(1,row_num/20, self.y_scale, legend_count / 30 ) # rescale Y to max of user-specified and number of rows
self.set_size_request(-1, y_scale * bottom + height + 5)

def on_pointer_motion(self, _dummy, event):
"""
Expand Down

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