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Add newick example files

pull/492/head
Franklin Delehelle 2023-02-19 08:39:50 +07:00 committed by Wilfred Hughes
parent a0b9df0e29
commit 21ded51e90
4 changed files with 1368 additions and 0 deletions
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1
manual/src/languages_supported.md
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@ -33,6 +33,7 @@ with `difft --list-languages`.
| Kotlin | [fwcd/tree-sitter-kotlin](https://github.com/fwcd/tree-sitter-kotlin) |
| Lua | [nvim-treesitter/tree-sitter-lua](https://github.com/nvim-treesitter/tree-sitter-lua) |
| Make | [alemuller/tree-sitter-make](https://github.com/alemuller/tree-sitter-make) |
| Newick | [delehef/tree-sitter-newick](https://github.com/delehef/tree-sitter-newick) |
| Nix | [cstrahan/tree-sitter-nix](https://github.com/cstrahan/tree-sitter-nix) |
| OCaml | [tree-sitter/tree-sitter-ocaml](https://github.com/tree-sitter/tree-sitter-ocaml) |
| Perl | [ganezdragon/tree-sitter-perl](https://github.com/ganezdragon/tree-sitter-perl) |

3
sample_files/compare.expected vendored
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@ -130,6 +130,9 @@ sample_files/nested_slider_before.rs sample_files/nested_slider_after.rs
sample_files/nesting_before.el sample_files/nesting_after.el
9fcf6b8adf148cdae47bc3a5f8068e41 -
sample_files/newick_before.nwk sample_files/newick_after.nwk
4778aef7b901b2cc7f9ad3601f87864d -
sample_files/nix_before.nix sample_files/nix_after.nix
09a56752c1eb7f3f5c10d631a01973fc -

903
sample_files/newick_after.nwk vendored
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@ -0,0 +1,903 @@
(
(
(
Drosophila_melanogaster,
Caenorhabditis_elegans
)
,
(
(
Ciona_intestinalis,
Ciona_savignyi
)
,
(
(
Eptatretus_burgeri,
Petromyzon_marinus
)
,
(
(
(
(
(
(
(
(
(
(
(
Astyanax_mexicanus,
Pygocentrus_nattereri
)
,
Electrophorus_electricus
)
,
Ictalurus_punctatus
)
,
(
(
(
Cyprinus_carpio_carpio,
Sinocyclocheilus_grahami
)
,
Carassius_auratus
)
,
Danio_rerio
)
)
,
(
Clupea_harengus,
Denticeps_clupeoides
)
)
,
(
(
(
(
(
(
(
(
(
(
Kryptolebias_marmoratus,
Nothobranchius_furzeri
)
,
(
(
Fundulus_heteroclitus,
Cyprinodon_variegatus
)
,
(
(
(
Poecilia_latipinna,
Poecilia_formosa
)
,
Poecilia_reticulata
)
,
Xiphophorus_maculatus
)
)
)
,
(
(
Oryzias_javanicus,
Oryzias_melastigma
)
,
(
Oryzias_latipes,
Oryzias_sinensis
)
)
)
,
(
(
(
(
(
(
(
Maylandia_zebra,
Astatotilapia_calliptera
)
,
Pundamilia_nyererei
)
,
Haplochromis_burtoni
)
,
Neolamprologus_brichardi
)
,
Oreochromis_niloticus
)
,
Amphilophus_citrinellus
)
,
(
(
(
Amphiprion_percula,
Amphiprion_ocellaris
)
,
Acanthochromis_polyacanthus
)
,
Stegastes_partitus
)
)
)
,
(
(
(
Cynoglossus_semilaevis,
Scophthalmus_maximus
)
,
(
(
Seriola_dumerili,
Seriola_lalandi_dorsalis
)
,
Lates_calcarifer
)
)
,
(
(
Anabas_testudineus,
Betta_splendens
)
,
Mastacembelus_armatus
)
)
)
,
(
(
(
(
(
Cyclopterus_lumpus,
Gasterosteus_aculeatus
)
,
(
Cottoperca_gobio,
Sander_lucioperca
)
)
,
(
(
Larimichthys_crocea,
Dicentrarchus_labrax
)
,
Sparus_aurata
)
)
,
Labrus_bergylta
)
,
(
Tetraodon_nigroviridis,
Takifugu_rubripes
)
)
)
,
Hippocampus_comes
)
,
Myripristis_murdjan
)
,
Gadus_morhua
)
,
(
(
(
(
(
Oncorhynchus_kisutch,
Oncorhynchus_tshawytscha
)
,
Oncorhynchus_mykiss
)
,
(
Salmo_salar,
Salmo_trutta
)
)
,
Hucho_hucho
)
,
Esox_lucius
)
)
)
,
(
Scleropages_formosus,
Paramormyrops_kingsleyae
)
)
,
Lepisosteus_oculatus
)
,
Erpetoichthys_calabaricus
)
,
(
(
(
Leptobrachium_leishanense,
Xenopus_tropicalis
)
,
(
(
(
(
(
(
(
(
Erinaceus_europaeus,
Sorex_araneus
)
,
(
(
(
(
(
Rhinolophus_ferrumequinum,
Myotis_lucifugus
)
,
Pteropus_vampyrus
)
,
(
Equus_caballus,
Equus_asinus_asinus
)
)
,
(
(
(
(
(
(
(
Ovis_aries_reference_breed,
Capra_hircus_reference_breed
)
,
(
(
(
Bos_indicus_x_Bos_taurus,
Bos_taurus
)
,
(
Bos_mutus,
Bos_grunniens
)
)
,
Bison_bison_bison
)
)
,
Moschus_moschiferus
)
,
Cervus_hanglu_yarkandensis
)
,
(
(
(
(
(
Monodon_monoceros,
Delphinapterus_leucas
)
,
Phocoena_sinus
)
,
Tursiops_truncatus
)
,
Physeter_catodon
)
,
Balaenoptera_musculus
)
)
,
(
(
(
(
(
(
(
Sus_scrofa_breed_jinhua,
Sus_scrofa_breed_meishan
)
,
Sus_scrofa_breed_rongchang
)
,
Sus_scrofa_breed_tibetan
)
,
Sus_scrofa_breed_bamei
)
,
Sus_scrofa_breed_wuzhishan
)
,
(
(
Sus_scrofa_reference_breed,
Sus_scrofa_breed_usmarc
)
,
(
(
(
Sus_scrofa_breed_hampshire,
Sus_scrofa_breed_berkshire
)
,
Sus_scrofa_breed_landrace
)
,
(
Sus_scrofa_breed_largewhite,
Sus_scrofa_breed_pietrain
)
)
)
)
,
Catagonus_wagneri
)
)
,
(
Camelus_dromedarius,
Vicugna_pacos
)
)
)
,
(
(
(
(
(
Ursus_maritimus,
Ursus_americanus
)
,
Ailuropoda_melanoleuca_reference_isolate
)
,
(
Neogale_vison,
Mustela_putorius_furo
)
)
,
(
(
Canis_lupus_familiaris_breed_Labrador_retriever,
Canis_lupus_dingo
)
,
Vulpes_vulpes
)
)
,
(
(
(
Panthera_leo,
Panthera_pardus
)
,
Panthera_tigris_altaica
)
,
Felis_catus
)
)
)
)
,
(
(
(
(
(
(
(
(
(
(
(
Cricetulus_griseus,
Mesocricetus_auratus
)
,
Peromyscus_maniculatus_bairdii
)
,
Microtus_ochrogaster
)
,
(
(
(
(
(
Mus_spicilegus,
Mus_spretus_strain_SPRET/EiJ
)
,
(
(
(
(
(
(
(
Mus_musculus_reference_CL57BL6_strain,
Mus_musculus_strain_C57BL/6NJ
)
,
Mus_musculus_strain_NZO/HlLtJ
)
,
(
(
(
(
Mus_musculus_strain_A/J,
Mus_musculus_strain_BALB/cJ
)
,
(
(
Mus_musculus_strain_C3H/HeJ,
Mus_musculus_strain_CBA/J
)
,
Mus_musculus_strain_DBA/2J
)
)
,
Mus_musculus_strain_AKR/J
)
,
(
Mus_musculus_strain_FVB/NJ,
Mus_musculus_strain_NOD/ShiLtJ
)
)
)
,
(
Mus_musculus_strain_129S1/SvImJ,
Mus_musculus_strain_LP/J
)
)
,
Mus_musculus_domesticus_strain_WSB/EiJ
)
,
Mus_musculus_musculus_strain_PWK/PhJ
)
,
Mus_musculus_castaneus_strain_CAST/EiJ
)
)
,
Mus_caroli_strain_CAROLI_EIJ
)
,
Mus_pahari_strain_PAHARI_EIJ
)
,
Rattus_norvegicus_strain_BN/NHsdMcwi
)
)
,
Nannospalax_galili
)
,
Jaculus_jaculus
)
,
Dipodomys_ordii
)
,
(
(
(
(
Chinchilla_lanigera,
Cavia_porcellus
)
,
Heterocephalus_glaber
)
,
Octodon_degus
)
,
(
(
(
Urocitellus_parryii,
Ictidomys_tridecemlineatus
)
,
Marmota_marmota_marmota
)
,
Sciurus_vulgaris
)
)
)
,
(
Oryctolagus_cuniculus,
Ochotona_princeps
)
)
,
Tupaia_belangeri
)
,
(
(
(
(
(
(
(
(
(
Pan_troglodytes,
Pan_paniscus
)
,
Homo_sapiens
)
,
Gorilla_gorilla_gorilla
)
,
Pongo_abelii
)
,
Nomascus_leucogenys
)
,
(
(
(
(
(
Cercocebus_atys,
Mandrillus_leucophaeus
)
,
Papio_anubis
)
,
(
(
Macaca_mulatta,
Macaca_fascicularis
)
,
Macaca_nemestrina
)
)
,
Chlorocebus_sabaeus
)
,
(
Rhinopithecus_roxellana,
Rhinopithecus_bieti
)
)
)
,
(
(
(
Cebus_imitator,
Saimiri_boliviensis_boliviensis
)
,
Callithrix_jacchus
)
,
Aotus_nancymaae
)
)
,
Carlito_syrichta
)
,
(
(
(
Prolemur_simus,
Propithecus_coquereli
)
,
Microcebus_murinus
)
,
Otolemur_garnettii
)
)
)
)
,
(
Dasypus_novemcinctus,
Choloepus_hoffmanni
)
)
,
(
(
Loxodonta_africana,
Procavia_capensis
)
,
Echinops_telfairi
)
)
,
(
(
(
(
Vombatus_ursinus,
Phascolarctos_cinereus
)
,
Notamacropus_eugenii
)
,
Sarcophilus_harrisii
)
,
Monodelphis_domestica
)
)
,
Ornithorhynchus_anatinus
)
,
(
(
(
(
(
(
(
Notechis_scutatus,
Pseudonaja_textilis
)
,
Laticauda_laticaudata
)
,
Naja_naja
)
,
Anolis_carolinensis_reference_strain
)
,
(
Salvator_merianae,
Podarcis_muralis
)
)
,
Sphenodon_punctatus
)
,
(
(
(
(
(
(
(
Gallus_gallus_reference_breed,
Meleagris_gallopavo_reference_strain
)
,
Coturnix_japonica
)
,
(
Anas_platyrhynchos_platyrhynchos,
Anser_brachyrhynchus
)
)
,
(
(
Aquila_chrysaetos_chrysaetos,
Strigops_habroptila
)
,
(
(
(
(
Serinus_canaria,
Taeniopygia_guttata
)
,
Geospiza_fortis
)
,
Parus_major
)
,
Ficedula_albicollis
)
)
)
,
Struthio_camelus_australis
)
,
Crocodylus_porosus
)
,
(
(
(
Gopherus_evgoodei,
Chelonoidis_abingdonii
)
,
(
Terrapene_carolina_triunguis,
Chrysemys_picta_bellii
)
)
,
Pelodiscus_sinensis
)
)
)
)
)
,
Latimeria_chalumnae
)
)
,
Callorhinchus_milii
)
)
)
)
,
Saccharomyces_cerevisiae;

461
sample_files/newick_before.nwk vendored
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@ -0,0 +1,461 @@
(
(
(
Drosophila_melanogaster,
Caenorhabditis_elegans
)
,
(
(
Ciona_intestinalis,
Ciona_savignyi
)
,
(
(
Eptatretus_burgeri,
Petromyzon_marinus
)
,
(
(
(
(
Danio_rerio,
Astyanax_mexicanus
)
,
(
(
(
(
(
Poecilia_formosa,
Xiphophorus_maculatus
)
,
Oryzias_latipes
)
,
Oreochromis_niloticus
)
,
(
(
Tetraodon_nigroviridis,
Takifugu_rubripes
)
,
Gasterosteus_aculeatus
)
)
,
Gadus_morhua
)
)
,
Lepisosteus_oculatus
)
,
(
(
(
(
(
(
(
(
(
(
(
(
(
(
(
(
(
(
(
(
Cricetulus_griseus_chok1gshd,
Cricetulus_griseus_crigri
)
,
Mesocricetus_auratus
)
,
Peromyscus_maniculatus_bairdii
)
,
Microtus_ochrogaster
)
,
(
(
(
(
(
(
(
(
(
(
(
(
(
Mus_musculus,
Mus_musculus_BALB/cJ
)
,
(
(
Mus_musculus_C3H/HeJ,
Mus_musculus_CBA/J
)
,
Mus_musculus_DBA/2J
)
)
,
Mus_musculus_AKR/J
)
,
(
(
Mus_musculus_FVB/NJ,
Mus_musculus_NOD/ShiLtJ
)
,
Mus_musculus_domesticus_WSB/EiJ
)
)
,
(
Mus_musculus_129S1/SvImJ,
Mus_musculus_LP/J
)
)
,
(
Mus_musculus_reference_CL57BL6,
Mus_musculus_C57BL/6NJ
)
)
,
Mus_musculus_NZO/HlLtJ
)
,
Mus_musculus_musculus_PWK/PhJ
)
,
Mus_musculus_castaneus_CAST/EiJ
)
,
Mus_spretus
)
,
Mus_caroli
)
,
Mus_pahari
)
,
Rattus_norvegicus
)
)
,
Nannospalax_galili
)
,
Jaculus_jaculus
)
,
Dipodomys_ordii
)
,
(
(
(
(
(
Cavia_porcellus,
Cavia_aperea
)
,
Chinchilla_lanigera
)
,
Octodon_degus
)
,
(
(
Heterocephalus_glaber_female,
Heterocephalus_glaber_male
)
,
Fukomys_damarensis
)
)
,
Ictidomys_tridecemlineatus
)
)
,
(
Oryctolagus_cuniculus,
Ochotona_princeps
)
)
,
Tupaia_belangeri
)
,
(
(
(
(
(
(
(
(
(
Pan_troglodytes,
Pan_paniscus
)
,
Homo_sapiens
)
,
Gorilla_gorilla
)
,
Pongo_abelii
)
,
Nomascus_leucogenys
)
,
(
(
(
(
(
Cercocebus_atys,
Mandrillus_leucophaeus
)
,
Papio_anubis
)
,
(
(
Macaca_fascicularis,
Macaca_mulatta
)
,
Macaca_nemestrina
)
)
,
Chlorocebus_sabaeus
)
,
(
(
Rhinopithecus_roxellana,
Rhinopithecus_bieti
)
,
Colobus_angolensis_palliatus
)
)
)
,
(
(
(
Cebus_capucinus,
Saimiri_boliviensis_boliviensis
)
,
Callithrix_jacchus
)
,
Aotus_nancymaae
)
)
,
Carlito_syrichta
)
,
(
(
Microcebus_murinus,
Propithecus_coquereli
)
,
Otolemur_garnettii
)
)
)
,
(
(
Erinaceus_europaeus,
Sorex_araneus
)
,
(
(
(
(
(
(
Sus_scrofa,
Vicugna_pacos
)
,
(
(
Ovis_aries,
Capra_hircus
)
,
Bos_taurus
)
)
,
Tursiops_truncatus
)
,
Equus_caballus
)
,
(
(
(
Ailuropoda_melanoleuca,
Mustela_putorius_furo
)
,
Canis_familiaris
)
,
(
(
Panthera_pardus,
Panthera_tigris_altaica
)
,
Felis_catus
)
)
)
,
(
Pteropus_vampyrus,
Myotis_lucifugus
)
)
)
)
,
(
Dasypus_novemcinctus,
Choloepus_hoffmanni
)
)
,
(
(
Loxodonta_africana,
Procavia_capensis
)
,
Echinops_telfairi
)
)
,
(
(
Sarcophilus_harrisii,
Notamacropus_eugenii
)
,
Monodelphis_domestica
)
)
,
Ornithorhynchus_anatinus
)
,
(
(
(
(
(
Gallus_gallus,
Meleagris_gallopavo
)
,
Anas_platyrhynchos
)
,
(
Ficedula_albicollis,
Taeniopygia_guttata
)
)
,
Pelodiscus_sinensis
)
,
Anolis_carolinensis
)
)
,
Xenopus_tropicalis
)
,
Latimeria_chalumnae
)
)
)
)
)
,
Saccharomyces_cerevisiae
)
;