<commit_before>package EnsEMBL::Web::ViewConfig::Gene::Compara_Tree;

use strict;
use warnings;
no warnings 'uninitialized';

use EnsEMBL::Web::Constants;

sub init {
  my ($view_config) = @_;
  $view_config->_set_defaults(qw(
    image_width          800
    width                800
    collapsability       gene
    colouring            background
    text_format          msf
    tree_format          newick_mode
    newick_mode          full_web
    nhx_mode             full
    scale                150

    group_fish            default
    group_fish_taxa       7955_8090_31033_69293_99883
    group_fish_fgcolour   royalblue4
    group_fish_bgcolour   lightblue1

    group_saurias           default
    group_saurias_taxa      28377_9031_59729
    group_saurias_fgcolour  yellow4
    group_saurias_bgcolour  lemonchiffon

    group_vertebrates           default
    group_vertebrates_taxa      7719_51511_7955_8090_31033_69293_99883_28377_9031_59729_9258_9315_9358_9361_9365_9371_9478_9544_9593_9598_9600_9606_9615_9685_9739_9785_9796_9813_9913_9978_9986_10020_10090_10116_10141_13616_30538_30608_30611_37347_42254_43179_59463_132908_8364_9483_9823
    group_vertebrates_fgcolour  tomato3
    group_vertebrates_bgcolour  ffe0f0

    group_cionas           default
    group_cionas_taxa      7719_51511

    group_low-coverage      default
    group_low-coverage_taxa 9315_9358_9361_9365_9371_9478_9593_9685_9739_9785_9813_9978_9986_10020_30538_30608_30611_37347_42254_43179_59463_132908

    group_diptera          default
    group_diptera_taxa     7159_7227_7165
    group_diptera_fgcolour 604000
    group_diptera_bgcolour ffd5d5

    group_mammals          default
    group_mammals_taxa      9258_9315_9358_9361_9365_9371_9478_9544_9593_9598_9600_9606_9615_9685_9739_9785_9796_9813_9913_9978_9986_10020_10090_10116_10141_13616_30538_30608_30611_37347_42254_43179_59463_132908_9483_9823
    group_mammals_fgcolour 005000
    group_mammals_bgcolour d0fad0

    group_primates          default
    group_primates_taxa     9478_9544_9593_9598_9600_9606_30608_30611_9483
    group_primates_fgcolour 000050
    group_primates_bgcolour f0f0ff

    group_glires           default
    group_glires_taxa      9978_9986_10020_10090_10116_10141_43179
    group_glires_fgcolour  403000
    group_glires_bgcolour  fff0e0

    group_laurasiatheria           default
    group_laurasiatheria_taxa      9615_9365_59463_42254_9796_9913_9685_9739_30538_132908_9823
    group_laurasiatheria_fgcolour  005050
    group_laurasiatheria_bgcolour  d0fafa

  ));
  
  $view_config->storable = 1;
}
<commit_msg>add nav_tree parameter<commit_after>package EnsEMBL::Web::ViewConfig::Gene::Compara_Tree;

use strict;
use warnings;
no warnings 'uninitialized';

use EnsEMBL::Web::Constants;

sub init {
  my ($view_config) = @_;
  $view_config->_set_defaults(qw(
    image_width          800
    width                800
    collapsability       gene
    colouring            background
    text_format          msf
    tree_format          newick_mode
    newick_mode          full_web
    nhx_mode             full
    scale                150

    group_fish            default
    group_fish_taxa       7955_8090_31033_69293_99883
    group_fish_fgcolour   royalblue4
    group_fish_bgcolour   lightblue1

    group_saurias           default
    group_saurias_taxa      28377_9031_59729
    group_saurias_fgcolour  yellow4
    group_saurias_bgcolour  lemonchiffon

    group_vertebrates           default
    group_vertebrates_taxa      7719_51511_7955_8090_31033_69293_99883_28377_9031_59729_9258_9315_9358_9361_9365_9371_9478_9544_9593_9598_9600_9606_9615_9685_9739_9785_9796_9813_9913_9978_9986_10020_10090_10116_10141_13616_30538_30608_30611_37347_42254_43179_59463_132908_8364_9483_9823
    group_vertebrates_fgcolour  tomato3
    group_vertebrates_bgcolour  ffe0f0

    group_cionas           default
    group_cionas_taxa      7719_51511

    group_low-coverage      default
    group_low-coverage_taxa 9315_9358_9361_9365_9371_9478_9593_9685_9739_9785_9813_9978_9986_10020_30538_30608_30611_37347_42254_43179_59463_132908

    group_diptera          default
    group_diptera_taxa     7159_7227_7165
    group_diptera_fgcolour 604000
    group_diptera_bgcolour ffd5d5

    group_mammals          default
    group_mammals_taxa      9258_9315_9358_9361_9365_9371_9478_9544_9593_9598_9600_9606_9615_9685_9739_9785_9796_9813_9913_9978_9986_10020_10090_10116_10141_13616_30538_30608_30611_37347_42254_43179_59463_132908_9483_9823
    group_mammals_fgcolour 005000
    group_mammals_bgcolour d0fad0

    group_primates          default
    group_primates_taxa     9478_9544_9593_9598_9600_9606_30608_30611_9483
    group_primates_fgcolour 000050
    group_primates_bgcolour f0f0ff

    group_glires           default
    group_glires_taxa      9978_9986_10020_10090_10116_10141_43179
    group_glires_fgcolour  403000
    group_glires_bgcolour  fff0e0

    group_laurasiatheria           default
    group_laurasiatheria_taxa      9615_9365_59463_42254_9796_9913_9685_9739_30538_132908_9823
    group_laurasiatheria_fgcolour  005050
    group_laurasiatheria_bgcolour  d0fafa

  ));
  
  $view_config->storable = 1;
  $view_config->nav_tree = 1;
}

{'fraction_non_alphanumeric': 0.018133231532735255, 'fraction_numerical': 0.26627218934911245, 'mean_word_length': 3.584426946631671, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 8, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '3953722', 'n_tokens_mistral': 2889, 'n_tokens_neox': 2037, 'n_words': 220}