<commit_before>{
    "label": "gi|117928536|ref|YP_873087.1| Holliday junction resolvase YqgF [Acidothermus cellulolyticus 11B]",
    "sequence": "MGDTAVRPGVRIGVDVGTVRIGVAVSDPDGRLAVPAETLPRDASGAGELRRLAQLVEERGAVEVVVGLPV",
    "seqcolors": {
        "data": "CCCCCCCCCCEEEEECCCCEEEEEEECCCCCEECCEEEEEECCCCCHHHHHHHHHHHHHCCCEEEECCCCCCCCCCCCCCEEEEECCCCEEEEEEECCCCCEECCEEEEEECCCCCHHHHHHHHHHHHHCCCEEEECCCC",
        "colors": {
            "C": "#DDD",
            "B": "blue",
            "X": "orange",
            "T": "#DDD",
            "S": "#DDD",
            " ": "#DDD",
            "I": "red",
            "H": "red",
            "G": "red",
            "E": "blue"
        }
    },
    "alidisplay": true,
    "alignments": [
        {
            "CS": "ALI",
            "label": "1vhx_A",
            "sequence": "RILGLDLGTKTLGVALSDEMGWTAQGIETIKNEAEGDYGLSRLSELIKDYTIDKIVLGFP",
            "description": "7.000e-14 \u003e1vhx_A 150aa 12/01/03 (X-RAY) Putative Holliday junction resolvase [BACILLUS SUBTILIS] :_: Frame:0 Round:0 Length:150",
            "start": 10,
            "seqcolors": {
                "data": "EEEEEEE SSEEEEEEE TTSSSEEEEEEEEBGGGTB  HHHHHHHHTTSEEEEEEEE    BTTB  HHHHHHHHHHHHHHHHH S EEEE  SS HHHHHHHHHHTT  HHHHHHHHHHHHHHHHHHHHHHHHT XXXXXXXXX",
                "colors": {}
            },
            "data": {},
            "dbxrefs": {
                "Test": "http://google.com"
            }
        },
        {
            "CS": "ALI",
            "label": "Hypothetical protein yqgF ",
            "sequence": "MSGTLLAFDFGTKSIGVAVGQRITGTARPLPAIKAQ-DGTPDWNIIERLLKEWQPDEIIVGLPL",
            "description": "3.000e-13 \u003e1ovq_A 138aa 03/27/03 (NMR) Hypothetical protein yqgF [ESCHERICHIA COLI] :_: Frame:0 Round:0 Length:138",
            "start": 7,
            "seqcolors": {
                "data": "   EEEEEEEETTEEEEEEEETTTTEEEEE  S  B-TTB  HHHHHHHHHHT EEEEEE     SSSS  TTHHHHHHHHHHHHHHHT  EEE    SS  SS SS   SS S    S   SSHHHHHHHHHHHHHT ",
                "colors": {}
            },
            "data": {}
        },
        {
            "CS": "ALI",
            "label": "",
            "sequence": "MSGTLLAFDFGTKSIGVAVGQRITGTARPLPAIKAQ-DGTPDWNIIERLLKEWQPDEIIVGLPL",
            "description": "1nmn_A ",
            "start": 7,
            "seqcolors": {
                "data": "X  EEEEEE  SSEEEEEEEETTTTEEEEEEEEE B-TTB  HHHHHHHHHHH  SEEEEEEEB TTS B TTHHHHHHHHHHHHHHH   EEEEEE     XXXXXXXXXXXXXXXXX  GGGHHHHHHHHHHHHTT ",
                "colors": {}
            },
            "data": {}
        },
        {
            "CS": "ALI",
            "label": "",
            "sequence": "MSGTLMAFDFGTKSIGVAVGQRITGTARPLPAIKAQ-DGTPDWNIIERLLKEWQPDEIIVGLPL",
            "description": "4.000e-13 \u003e1nu0_A 138aa 01/30/03 (X-RAY) Hypothetical protein yqgF [ESCHERICHIA COLI] :_: Frame:0 Round:0 Length:138",
            "start": 7,
            "seqcolors": {
                "data": "   EEEEEE  SSEEEEEEEETTTTEEEEEEEEEEE-TTEE HHHHHHHHHHH  SEEEEEEEE TTS B HHHHHHHHHHHHHHHHH   EEEEEEE      XXXXXXX       HHHHTTHHHHHHHHHHHHTT ",
                "colors": {}
            },
            "data": {}
        },
        {
            "CS": "ALI",
            "label": "",
            "sequence": "RVGALDVGEARIGLAVGEEGVPLASGRGYLVRKTLEE-DVEALLDFVRREGLGKLVVGLPL",
            "description": "2.000e-07 \u003e1iv0_A 98aa 03/08/02 (NMR) hypothetical protein [THERMUS THERMOPHILUS] :_: Frame:0 Round:0 Length:98",
            "start": 10,
            "seqcolors": {
                "data": " EEEEEESSSEEEEEEE S  SS   EEEEE   HHH-HHHHHHHHHHHHT  EEEEE      SSS   SSTTHHHHHHHHHTT EEEEE  S    ",
                "colors": {}
            },
            "data": {}
        }
    ],
    "qtracks": [
        {
            "label": "Disorder - original values",
            "color": "orange",
            "displayScale": true,
            "values": [
                0.803, 0.425, 0.514, 0.52, 0.249, 0.202, 0.046, 0.082, 0.059, 0.054, 0.039, 0.022, 0.013, 0.005, 0.003, 0.002, 0.002, 0.002, 0.001, 0.001, 0.001, 0.002, 0.002, 0.002, 0.002, 0.002, 0.002, 0.002, 0.003, 0.003, 0.003, 0.004, 0.004, 0.004, 0.004, 0.005, 0.005, 0.006, 0.007, 0.008, 0.008, 0.008, 0.007, 0.007, 0.008, 0.009, 0.007, 0.007, 0.006, 0.005, 0.004, 0.004, 0.004, 0.004, 0.003, 0.002, 0.002, 0.002, 0.002, 0.002, 0.001, 0.002, 0.002, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.001
            ]
        }, {
            "label": "Disorder - force non-zero",
            "color": "orange",
            "displayScale": true,
            "transform": "log",
            "forceNonZero" :true,
            "values": [
                0.803, 0.425, 0.514, 0.52, 0.249, 0.202, 0.046, 1, 0.059, 1, 0.039, 0.022, 0.013, 0.005, 0.003, 0.002, 0.002, 0.002, 0.001, 0.001, 0.001, 0.002, 0.002, 0.002, 0.002, 0.002, 0.002, 0.002, 0.003, 0.003, 0.003, 0.004, 0.004, 0.004, 0.004, 0.005, 0.005, 0.006, 0.007, 0.008, 0.008, 0.008, 0.007, 0.007, 0.008, 0.009, 0.007, 0.007, 0.006, 0.005, 0.004, 0.004, 0.004, 0.004, 0.003, 0.002, 0.002, 0.002, 0.002, 0.002, 0.001, 0.002, 0.002, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.001<commit_msg>Added sample highlight objects to test JSON.<commit_after>{
    "label": "gi|117928536|ref|YP_873087.1| Holliday junction resolvase YqgF [Acidothermus cellulolyticus 11B]",
    "sequence": "MGDTAVRPGVRIGVDVGTVRIGVAVSDPDGRLAVPAETLPRDASGAGELRRLAQLVEERGAVEVVVGLPV",
    "seqcolors": {
        "data": "CCCCCCCCCCEEEEECCCCEEEEEEECCCCCEECCEEEEEECCCCCHHHHHHHHHHHHHCCCEEEECCCCCCCCCCCCCCEEEEECCCCEEEEEEECCCCCEECCEEEEEECCCCCHHHHHHHHHHHHHCCCEEEECCCC",
        "colors": {
            "C": "#DDD",
            "B": "blue",
            "X": "orange",
            "T": "#DDD",
            "S": "#DDD",
            " ": "#DDD",
            "I": "red",
            "H": "red",
            "G": "red",
            "E": "blue"
        }
    },
    "highlights": [
        {
            "id": "PF14259",
            "start": 15,
            "end": 42,
            "color": "#bbdefb",
            "opacity": 0.9,
            "description": "15-42"
        },
        {   
            "start": 1,
            "end": 4,
            "description": "Something interesting in this region!"
        }
    ],
    "alidisplay": true,
    "alignments": [
        {
            "CS": "ALI",
            "label": "1vhx_A",
            "sequence": "RILGLDLGTKTLGVALSDEMGWTAQGIETIKNEAEGDYGLSRLSELIKDYTIDKIVLGFP",
            "description": "7.000e-14 \u003e1vhx_A 150aa 12/01/03 (X-RAY) Putative Holliday junction resolvase [BACILLUS SUBTILIS] :_: Frame:0 Round:0 Length:150",
            "start": 10,
            "seqcolors": {
                "data": "EEEEEEE SSEEEEEEE TTSSSEEEEEEEEBGGGTB  HHHHHHHHTTSEEEEEEEE    BTTB  HHHHHHHHHHHHHHHHH S EEEE  SS HHHHHHHHHHTT  HHHHHHHHHHHHHHHHHHHHHHHHT XXXXXXXXX",
                "colors": {}
            },
            "data": {},
            "dbxrefs": {
                "Test": "http://google.com"
            }
        },
        {
            "CS": "ALI",
            "label": "Hypothetical protein yqgF ",
            "sequence": "MSGTLLAFDFGTKSIGVAVGQRITGTARPLPAIKAQ-DGTPDWNIIERLLKEWQPDEIIVGLPL",
            "description": "3.000e-13 \u003e1ovq_A 138aa 03/27/03 (NMR) Hypothetical protein yqgF [ESCHERICHIA COLI] :_: Frame:0 Round:0 Length:138",
            "start": 7,
            "seqcolors": {
                "data": "   EEEEEEEETTEEEEEEEETTTTEEEEE  S  B-TTB  HHHHHHHHHHT EEEEEE     SSSS  TTHHHHHHHHHHHHHHHT  EEE    SS  SS SS   SS S    S   SSHHHHHHHHHHHHHT ",
                "colors": {}
            },
            "data": {}
        },
        {
            "CS": "ALI",
            "label": "",
            "sequence": "MSGTLLAFDFGTKSIGVAVGQRITGTARPLPAIKAQ-DGTPDWNIIERLLKEWQPDEIIVGLPL",
            "description": "1nmn_A ",
            "start": 7,
            "seqcolors": {
                "data": "X  EEEEEE  SSEEEEEEEETTTTEEEEEEEEE B-TTB  HHHHHHHHHHH  SEEEEEEEB TTS B TTHHHHHHHHHHHHHHH   EEEEEE     XXXXXXXXXXXXXXXXX  GGGHHHHHHHHHHHHTT ",
                "colors": {}
            },
            "data": {}
        },
        {
            "CS": "ALI",
            "label": "",
            "sequence": "MSGTLMAFDFGTKSIGVAVGQRITGTARPLPAIKAQ-DGTPDWNIIERLLKEWQPDEIIVGLPL",
            "description": "4.000e-13 \u003e1nu0_A 138aa 01/30/03 (X-RAY) Hypothetical protein yqgF [ESCHERICHIA COLI] :_: Frame:0 Round:0 Length:138",
            "start": 7,
            "seqcolors": {
                "data": "   EEEEEE  SSEEEEEEEETTTTEEEEEEEEEEE-TTEE HHHHHHHHHHH  SEEEEEEEE TTS B HHHHHHHHHHHHHHHHH   EEEEEEE      XXXXXXX       HHHHTTHHHHHHHHHHHHTT ",
                "colors": {}
            },
            "data": {}
        },
        {
            "CS": "ALI",
            "label": "",
            "sequence": "RVGALDVGEARIGLAVGEEGVPLASGRGYLVRKTLEE-DVEALLDFVRREGLGKLVVGLPL",
            "description": "2.000e-07 \u003e1iv0_A 98aa 03/08/02 (NMR) hypothetical protein [THERMUS THERMOPHILUS] :_: Frame:0 Round:0 Length:98",
            "start": 10,
            "seqcolors": {
                "data": " EEEEEESSSEEEEEEE S  SS   EEEEE   HHH-HHHHHHHHHHHHT  EEEEE      SSS   SSTTHHHHHHHHHTT EEEEE  S    ",
                "colors": {}
            },
            "data": {}
        }
    ],
    "qtracks": [
        {
            "label": "Disorder - original values",
            "color": "orange",
            "displayScale": true,
            "values": [
                0.803, 0.425, 0.514, 0.52, 0.249, 0.202, 0.046, 0.082, 0.059, 0.054, 0.039, 0.022, 0.013, 0.005, 0.003, 0.002, 0.002, 0.002, 0.001, 0.001, 0.001, 0.002, 0.002, 0.002, 0.002, 0.002, 0.002, 0.002, 0.003, 0.003, 0.003, 0.004, 0.004, 0.004, 0.004, 0.005, 0.005, 0.006, 0.007, 0.008, 0.008, 0.008, 0.007, 0.007, 0.008, 0.009, 0.007, 0.007, 0.006, 0.005, 0.004, 0.004, 0.004, 0.004, 0.003, 0.002, 0.002, 0.002, 0.002, 0.002, 0.001, 0.002, 0.002, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.001
            ]
        }, {
            "label": "Disorder - force non-zero",
            "color": "orange",
            "displayScale": true,
            "transform": "log",
            "forceNonZero": true,
            "values": [
                0.803, 0.425, 0.514, 0.52, 0.249, 0.202, 0.046, 1, 0.059, 1, 0.039, 0.022, 0.013, 0.005, 0.003, 0.002, 0.002, 0.002, 0.001, 0.001, 0.001, 0.002, 0.002, 0.002, 0.002, 0.002, 0.002, 0.002, 0.003, 0.003, 0.003, 0.004, 0.004, 0.004, 0.004, 0.005, 0.005, 0.006, 0.007, 0.008, 0.008, 0.008, 0.007, 0.007, 0.008, 0.009, 0.007, 0.007, 0.006, 0.005, 0.004, 0.004, 0.004, 0.004, 0.003, 0.002, 0.002, 0.002, 0.002, 0.002, 0.001, 0.002, 0.002, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.001
{'fraction_non_alphanumeric': 0.15620562340244248, 'fraction_numerical': 0.12486982864716463, 'mean_word_length': 1.7741596638655461, 'pattern_counts': {'":': 159, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 76, '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': '2333914', 'n_tokens_mistral': 5314, 'n_tokens_neox': 4139, 'n_words': 788}