TmMolStar/src/examples/alignment-provider/providers/ExternalAlignmentProvider.ts

import {
    AlignmentResponse, GroupReference,
    SequenceReference,
} from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
import {
    AlignmentCollectConfig,
    AlignmentCollectorInterface
} from "@rcsb/rcsb-saguaro-app/build/dist/RcsbCollectTools/AlignmentCollector/AlignmentCollectorInterface";
import {RcsbRequestContextManager} from "@rcsb/rcsb-saguaro-app";

import {
    RcsbModuleDataProviderInterface
} from "@rcsb/rcsb-saguaro-app/build/dist/RcsbFvWeb/RcsbFvModule/RcsbFvModuleInterface";
import {AlignmentReference} from "./AlignmentReference";
import {
    LocationProviderInterface,
    RigidTransformType, TransformMatrixType,
    TransformProviderInterface
} from "../../../RcsbFvStructure/StructureUtils/StructureLoaderInterface";
import {
    InstanceSequenceInterface
} from "@rcsb/rcsb-saguaro-app/build/dist/RcsbCollectTools/DataCollectors/MultipleInstanceSequencesCollector";
import {Alignment, AlignmentRegion, StructureAlignmentResponse} from "./alignment-response";

const alignment = {
    "info": {
        "uuid": "e6e216de-c650-4ad5-bd81-45e75dfbe180",
        "status": "COMPLETE"
    },
    "meta": {
        "alignment_mode": "pairwise",
        "alignment_method": "fatcat-rigid"
    },
    "results": [
        {
            "structures": [
                {
                    "entry_id": "101M",
                    "selection": {
                        "asym_id": "A"
                    }
                },
                {
                    "entry_id": "1ASH",
                    "selection": {
                        "asym_id": "A"
                    }
                }
            ],
            "structure_alignment": [
                {
                    "regions": [
                        [
                            {
                                "asym_id": "A",
                                "beg_seq_id": 4,
                                "beg_index": 0,
                                "length": 47
                            },
                            {
                                "asym_id": "A",
                                "beg_seq_id": 52,
                                "beg_index": 52,
                                "length": 70
                            },
                            {
                                "asym_id": "A",
                                "beg_seq_id": 124,
                                "beg_index": 128,
                                "length": 22
                            }
                        ],
                        [
                            {
                                "asym_id": "A",
                                "beg_seq_id": 1,
                                "beg_index": 0,
                                "length": 17
                            },
                            {
                                "asym_id": "A",
                                "beg_seq_id": 22,
                                "beg_index": 21,
                                "length": 61
                            },
                            {
                                "asym_id": "A",
                                "beg_seq_id": 86,
                                "beg_index": 86,
                                "length": 14
                            },
                            {
                                "asym_id": "A",
                                "beg_seq_id": 101,
                                "beg_index": 101,
                                "length": 47
                            }
                        ]
                    ],
                    "transformations": [
                        [
                            1,
                            0,
                            0,
                            0,
                            0,
                            1,
                            0,
                            0,
                            0,
                            0,
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                        ],
                        [
                            -0.7671995717115603,
                            -0.5623954843039239,
                            0.30840904072376607,
                            0,
                            -0.6011420900233072,
                            0.4627787494512096,
                            -0.6515090303739346,
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                            0.2236805864799372,
                            -0.6852351043918645,
                            -0.6931232552303105,
                            0,
                            37.48154540719762,
                            28.2044983569036,
                            -7.345065372687518,
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                        ]
                    ],
                    "summary": {
                        "scores": [
                            {
                                "value": 1.95,
                                "type": "RMSD"
                            },
                            {
                                "value": 330.13,
                                "type": "similarity-score"
                            }
                        ],
                        "n_aln_residue_pairs": 139
                    }
                }
            ],
            "sequence_alignment": [
                {
                    "regions": [
                        {
                            "asym_id": "A",
                            "beg_seq_id": 4,
                            "beg_index": 0,
                            "length": 17
                        },
                        {
                            "asym_id": "A",
                            "beg_seq_id": 21,
                            "beg_index": 21,
                            "length": 62
                        },
                        {
                            "asym_id": "A",
                            "beg_seq_id": 83,
                            "beg_index": 86,
                            "length": 14
                        },
                        {
                            "asym_id": "A",
                            "beg_seq_id": 97,
                            "beg_index": 101,
                            "length": 49
                        }
                    ],
                    "gaps": [
                        {
                            "beg_index": 17,
                            "length": 4
                        },
                        {
                            "beg_index": 83,
                            "length": 3
                        },
                        {
                            "beg_index": 100,
                            "length": 1
                        }
                    ]
                },
                {
                    "regions": [
                        {
                            "asym_id": "A",
                            "beg_seq_id": 1,
                            "beg_index": 0,
                            "length": 51
                        },
                        {
                            "asym_id": "A",
                            "beg_seq_id": 52,
                            "beg_index": 52,
                            "length": 74
                        },
                        {
                            "asym_id": "A",
                            "beg_seq_id": 126,
                            "beg_index": 128,
                            "length": 22
                        }
                    ],
                    "gaps": [
                        {
                            "beg_index": 51,
                            "length": 1
                        },
                        {
                            "beg_index": 126,
                            "length": 2
                        }
                    ]
                }
            ],
            "summary": {
                "scores": [
                    {
                        "value": 0.15,
                        "type": "sequence-identity"
                    },
                    {
                        "value": 1.94,
                        "type": "RMSD"
                    },
                    {
                        "value": 0.79,
                        "type": "TM-score"
                    },
                    {
                        "value": 330.13,
                        "type": "similarity-score"
                    },
                    {
                        "value": 0.34,
                        "type": "sequence-similarity"
                    }
                ],
                "n_aln_residue_pairs": 139,
                "n_modeled_residues": [
                    154,
                    147
                ],
                "seq_aln_len": 150,
                "aln_coverage": [
                    90,
                    95
                ]
            }
        },
        {
            "structures": [
                {
                    "entry_id": "101M",
                    "selection": {
                        "asym_id": "A"
                    }
                },
                {
                    "entry_id": "4HHB",
                    "selection": {
                        "asym_id": "A"
                    }
                }
            ],
            "structure_alignment": [
                {
                    "regions": [
                        [
                            {
                                "asym_id": "A",
                                "beg_seq_id": 2,
                                "beg_index": 0,
                                "length": 48
                            },
                            {
                                "asym_id": "A",
                                "beg_seq_id": 56,
                                "beg_index": 54,
                                "length": 93
                            }
                        ],
                        [
                            {
                                "asym_id": "A",
                                "beg_seq_id": 1,
                                "beg_index": 0,
                                "length": 141
                            }
                        ]
                    ],
                    "transformations": [
                        [
                            1,
                            0,
                            0,
                            0,
                            0,
                            1,
                            0,
                            0,
                            0,
                            0,
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                        ],
                        [
                            0.5659010881349978,
                            0.8158255303919226,
                            0.11909938038614465,
                            0,
                            0.49060456462775587,
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                            -0.8439013766543271,
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                            0.5359954069890864,
                            -0.5231116554547112,
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                    ],
                    "summary": {
                        "scores": [
                            {
                                "value": 1.41,
                                "type": "RMSD"
                            },
                            {
                                "value": 360.42,
                                "type": "similarity-score"
                            }
                        ],
                        "n_aln_residue_pairs": 141
                    }
                }
            ],
            "sequence_alignment": [
                {
                    "regions": [
                        {
                            "asym_id": "A",
                            "beg_seq_id": 2,
                            "beg_index": 0,
                            "length": 147
                        }
                    ]
                },
                {
                    "regions": [
                        {
                            "asym_id": "A",
                            "beg_seq_id": 1,
                            "beg_index": 0,
                            "length": 48
                        },
                        {
                            "asym_id": "A",
                            "beg_seq_id": 49,
                            "beg_index": 54,
                            "length": 93
                        }
                    ],
                    "gaps": [
                        {
                            "beg_index": 48,
                            "length": 6
                        }
                    ]
                }
            ],
            "summary": {
                "scores": [
                    {
                        "value": 1.63,
                        "type": "RMSD"
                    },
                    {
                        "value": 360.42,
                        "type": "similarity-score"
                    },
                    {
                        "value": 0.26,
                        "type": "sequence-identity"
                    },
                    {
                        "value": 0.83,
                        "type": "TM-score"
                    },
                    {
                        "value": 0.4,
                        "type": "sequence-similarity"
                    }
                ],
                "n_aln_residue_pairs": 141,
                "n_modeled_residues": [
                    154,
                    141
                ],
                "seq_aln_len": 147,
                "aln_coverage": [
                    92,
                    100
                ]
            }
        },
        {
            "structures": [
                {
                    "entry_id": "101M",
                    "selection": {
                        "asym_id": "A"
                    }
                },
                {
                    "entry_id": "3IA3",
                    "selection": {
                        "asym_id": "A"
                    }
                }
            ],
            "structure_alignment": [
                {
                    "regions": [
                        [
                            {
                                "asym_id": "A",
                                "beg_seq_id": 6,
                                "beg_index": 0,
                                "length": 2
                            },
                            {
                                "asym_id": "A",
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                                "length": 10
                            },
                            {
                                "asym_id": "A",
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                                "length": 7
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                            {
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                            {
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                                "length": 23
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                            {
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                                "length": 30
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                    ],
                    "transformations": [
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                    ],
                    "summary": {
                        "scores": [
                            {
                                "value": 10.35,
                                "type": "RMSD"
                            },
                            {
                                "value": 163.43,
                                "type": "similarity-score"
                            }
                        ],
                        "n_aln_residue_pairs": 83
                    }
                }
            ],
            "sequence_alignment": [
                {
                    "regions": [
                        {
                            "asym_id": "A",
                            "beg_seq_id": 6,
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                            "length": 95
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                        {
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                    "gaps": [
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                },
                {
                    "regions": [
                        {
                            "asym_id": "A",
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                        {
                            "asym_id": "A",
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                            "beg_index": 64,
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                        {
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                    "gaps": [
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            "summary": {
                "scores": [
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                        "value": 0.38,
                        "type": "TM-score"
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                        "type": "RMSD"
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                    {
                        "value": 163.43,
                        "type": "similarity-score"
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                    {
                        "value": 0.13,
                        "type": "sequence-identity"
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                    {
                        "value": 0.29,
                        "type": "sequence-similarity"
                    }
                ],
                "n_aln_residue_pairs": 83,
                "n_modeled_residues": [
                    154,
                    90
                ],
                "seq_aln_len": 154,
                "aln_coverage": [
                    54,
                    92
                ]
            }
        },
        {
            "structures": [
                {
                    "entry_id": "101M",
                    "selection": {
                        "asym_id": "A"
                    }
                },
                {
                    "entry_id": "3IA3",
                    "selection": {
                        "asym_id": "B"
                    }
                }
            ],
            "structure_alignment": [
                {
                    "regions": [
                        [
                            {
                                "asym_id": "A",
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                            {
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                            {
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                        [
                            {
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                            {
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                    ],
                    "transformations": [
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                    "summary": {
                        "scores": [
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                                "value": 278.41,
                                "type": "similarity-score"
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                            {
                                "value": 2.79,
                                "type": "RMSD"
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                        ],
                        "n_aln_residue_pairs": 133
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                }
            ],
            "sequence_alignment": [
                {
                    "regions": [
                        {
                            "asym_id": "A",
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                            "beg_index": 0,
                            "length": 4
                        },
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                            "length": 138
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                {
                    "regions": [
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                        {
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            ],
            "summary": {
                "scores": [
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                        "value": 0.66,
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                    {
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                ],
                "n_aln_residue_pairs": 133,
                "n_modeled_residues": [
                    154,
                    135
                ],
                "seq_aln_len": 143,
                "aln_coverage": [
                    86,
                    99
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            }
        }
    ]
};
const flexAlignment = {
    "info": {
        "uuid": "c74f1b38-ad36-4c24-88ea-c947eba2b965",
        "status": "COMPLETE"
    },
    "meta": {
        "alignment_mode": "pairwise",
        "alignment_method": "fatcat-flexible"
    },
    "results": [
        {
            "structures": [
                {
                    "entry_id": "1SR6",
                    "selection": {
                        "asym_id": "A"
                    }
                },
                {
                    "entry_id": "1KWO",
                    "selection": {
                        "asym_id": "A"
                    }
                }
            ],
            "structure_alignment": [
                {
                    "regions": [
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                            },
                            {
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                                "length": 163
                            },
                            {
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                            },
                            {
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                                "length": 153
                            },
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                            },
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                                "length": 54
                            },
                            {
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                                "length": 51
                            }
                        ],
                        [
                            {
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                                "length": 18
                            },
                            {
                                "asym_id": "A",
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                                "beg_index": 20,
                                "length": 174
                            },
                            {
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                                "beg_index": 198,
                                "length": 194
                            },
                            {
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                                "beg_seq_id": 410,
                                "beg_index": 395,
                                "length": 153
                            },
                            {
                                "asym_id": "A",
                                "beg_seq_id": 569,
                                "beg_index": 551,
                                "length": 56
                            },
                            {
                                "asym_id": "A",
                                "beg_seq_id": 642,
                                "beg_index": 610,
                                "length": 52
                            }
                        ]
                    ],
                    "transformations": [
                        [
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                        [
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                    "summary": {
                        "scores": [
                            {
                                "value": 1772.68,
                                "type": "similarity-score"
                            },
                            {
                                "value": 2.63,
                                "type": "RMSD"
                            }
                        ],
                        "n_aln_residue_pairs": 647
                    }
                },
                {
                    "regions": [
                        [
                            {
                                "asym_id": "A",
                                "beg_seq_id": 699,
                                "beg_index": 668,
                                "length": 3
                            },
                            {
                                "asym_id": "A",
                                "beg_seq_id": 707,
                                "beg_index": 676,
                                "length": 20
                            },
                            {
                                "asym_id": "A",
                                "beg_seq_id": 734,
                                "beg_index": 700,
                                "length": 102
                            }
                        ],
                        [
                            {
                                "asym_id": "A",
                                "beg_seq_id": 704,
                                "beg_index": 668,
                                "length": 23
                            },
                            {
                                "asym_id": "A",
                                "beg_seq_id": 734,
                                "beg_index": 700,
                                "length": 102
                            }
                        ]
                    ],
                    "transformations": [
                        [
                            1,
                            0,
                            0,
                            0,
                            0,
                            1,
                            0,
                            0,
                            0,
                            0,
                            1,
                            0,
                            0,
                            0,
                            0,
                            1
                        ],
                        [
                            0.03983531379027039,
                            -0.9969211935123139,
                            -0.06753726157621881,
                            0,
                            0.5428660722665761,
                            0.07833822385293923,
                            -0.8361576108996602,
                            0,
                            0.8388739925382667,
                            -0.0033550871152113193,
                            0.5443153204102911,
                            0,
                            10.707819252191578,
                            1.4313621373339025,
                            38.51048821786332,
                            1
                        ]
                    ],
                    "summary": {
                        "scores": [
                            {
                                "value": 2.01,
                                "type": "RMSD"
                            },
                            {
                                "value": 328.8,
                                "type": "similarity-score"
                            }
                        ],
                        "n_aln_residue_pairs": 125
                    }
                }
            ],
            "sequence_alignment": [
                {
                    "regions": [
                        {
                            "asym_id": "A",
                            "beg_seq_id": 6,
                            "beg_index": 0,
                            "length": 195
                        },
                        {
                            "asym_id": "A",
                            "beg_seq_id": 213,
                            "beg_index": 198,
                            "length": 414
                        },
                        {
                            "asym_id": "A",
                            "beg_seq_id": 643,
                            "beg_index": 612,
                            "length": 88
                        },
                        {
                            "asym_id": "A",
                            "beg_seq_id": 734,
                            "beg_index": 700,
                            "length": 102
                        }
                    ],
                    "gaps": [
                        {
                            "beg_index": 195,
                            "length": 3
                        }
                    ]
                },
                {
                    "regions": [
                        {
                            "asym_id": "A",
                            "beg_seq_id": 6,
                            "beg_index": 0,
                            "length": 18
                        },
                        {
                            "asym_id": "A",
                            "beg_seq_id": 27,
                            "beg_index": 20,
                            "length": 11
                        },
                        {
                            "asym_id": "A",
                            "beg_seq_id": 38,
                            "beg_index": 32,
                            "length": 163
                        },
                        {
                            "asym_id": "A",
                            "beg_seq_id": 210,
                            "beg_index": 195,
                            "length": 197
                        },
                        {
                            "asym_id": "A",
                            "beg_seq_id": 410,
                            "beg_index": 395,
                            "length": 153
                        },
                        {
                            "asym_id": "A",
                            "beg_seq_id": 569,
                            "beg_index": 551,
                            "length": 3
                        },
                        {
                            "asym_id": "A",
                            "beg_seq_id": 572,
                            "beg_index": 557,
                            "length": 53
                        },
                        {
                            "asym_id": "A",
                            "beg_seq_id": 642,
                            "beg_index": 610,
                            "length": 1
                        },
                        {
                            "asym_id": "A",
                            "beg_seq_id": 643,
                            "beg_index": 612,
                            "length": 55
                        },
                        {
                            "asym_id": "A",
                            "beg_seq_id": 704,
                            "beg_index": 668,
                            "length": 3
                        },
                        {
                            "asym_id": "A",
                            "beg_seq_id": 707,
                            "beg_index": 676,
                            "length": 20
                        },
                        {
                            "asym_id": "A",
                            "beg_seq_id": 734,
                            "beg_index": 700,
                            "length": 102
                        }
                    ],
                    "gaps": [
                        {
                            "beg_index": 18,
                            "length": 2
                        },
                        {
                            "beg_index": 31,
                            "length": 1
                        },
                        {
                            "beg_index": 392,
                            "length": 3
                        },
                        {
                            "beg_index": 548,
                            "length": 3
                        },
                        {
                            "beg_index": 554,
                            "length": 3
                        },
                        {
                            "beg_index": 611,
                            "length": 1
                        },
                        {
                            "beg_index": 667,
                            "length": 1
                        },
                        {
                            "beg_index": 671,
                            "length": 5
                        },
                        {
                            "beg_index": 696,
                            "length": 4
                        }
                    ]
                }
            ],
            "summary": {
                "scores": [
                    {
                        "value": 2.48,
                        "type": "RMSD"
                    },
                    {
                        "value": 0.6,
                        "type": "TM-score"
                    },
                    {
                        "value": 2076.04,
                        "type": "similarity-score"
                    },
                    {
                        "value": 0.98,
                        "type": "sequence-identity"
                    },
                    {
                        "value": 0.98,
                        "type": "sequence-similarity"
                    }
                ],
                "n_aln_residue_pairs": 772,
                "n_modeled_residues": [
                    801,
                    780
                ],
                "seq_aln_len": 802,
                "aln_coverage": [
                    96,
                    99
                ]
            }
        }
    ]
};
const alignmentExample = {
    "info": {
        "uuid": "538d54e2-039c-44c8-bd5f-bb26af9c45bb",
        "status": "COMPLETE"
    },
    "meta": {
        "alignment_mode": "pairwise",
        "alignment_method": "fatcat-rigid"
    },
    "results": [
        {
            "structures": [
                {
                    "url": "https://alphafold.ebi.ac.uk/files/AF-P41235-F1-model_v2.cif",
                    "format": "mmcif",
                    "is_binary": false,
                    "name": "AF-P41235-F1",
                    "selection": {
                        "asym_id": "A"
                    }
                },
                {
                    "entry_id": "3CBB",
                    "selection": {
                        "asym_id": "C"
                    }
                }
            ],
            "structure_alignment": [
                {
                    "regions": [
                        [
                            {
                                "asym_id": "A",
                                "beg_seq_id": 58,
                                "beg_index": 0,
                                "length": 76
                            }
                        ],
                        [
                            {
                                "asym_id": "C",
                                "beg_seq_id": 1,
                                "beg_index": 0,
                                "length": 76
                            }
                        ]
                    ],
                    "transformations": [
                        [
                            1,
                            0,
                            0,
                            0,
                            0,
                            1,
                            0,
                            0,
                            0,
                            0,
                            1,
                            0,
                            0,
                            0,
                            0,
                            1
                        ],
                        [
                            0.663932900191227,
                            -0.6410962059424273,
                            0.3849529305900804,
                            0,
                            -0.6205267418674186,
                            -0.18505769796524382,
                            0.7620368829992492,
                            0,
                            -0.4173004513190375,
                            -0.7448149455737514,
                            -0.5206832340097945,
                            0,
                            2.241812113864647,
                            17.198483576583477,
                            -52.357664887014344,
                            1
                        ]
                    ],
                    "summary": {
                        "scores": [
                            {
                                "value": 214.71,
                                "type": "similarity-score"
                            },
                            {
                                "value": 0.47,
                                "type": "RMSD"
                            }
                        ],
                        "n_aln_residue_pairs": 76
                    }
                }
            ],
            "sequence_alignment": [
                {
                    "sequence": "MRLSKTLVDMDMADYSAALDPAYTTLEFENVQVLTMGNDTSPSEGTNLNAPNSLGVSALCAICGDRATGKHYGASSCDGCKGFFRRSVRKNHMYSCRFSRQCVVDKDKRNQCRYCRLKKCFRAGMKKEAVQNERDRISTRRSSYEDSSLPSINALLQAEVLSRQITSPVSGINGDIRAKKIASIADVCESMKEQLLVLVEWAKYIPAFCELPLDDQVALLRAHAGEHLLLGATKRSMVFKDVLLLGNDYIVPRHCPELAEMSRVSIRILDELVLPFQELQIDDNEYAYLKAIIFFDPDAKGLSDPGKIKRLRSQVQVSLEDYINDRQYDSRGRFGELLLLLPTLQSITWQMIEQIQFIKLFGMAKIDNLLQEMLLGGSPSDAPHAHHPLHPHLMQEHMGTNVIVANTMPTHLSNGQMCEWPRPRGQAATPETPQPSPPGGSGSEPYKLLPGAVATIVKPLSAIPQPTITKQEVI",
                    "regions": [
                        {
                            "asym_id": "A",
                            "beg_seq_id": 58,
                            "beg_index": 0,
                            "length": 76
                        }
                    ]
                },
                {
                    "sequence": "ALCAICGDRATGKHYGASSCDGCKGFFRRSVRKNHMYSCRFSRQCVVDKDKRNQCRYCRLKKCFRAGMKKEAVQNERD",
                    "regions": [
                        {
                            "asym_id": "C",
                            "beg_seq_id": 1,
                            "beg_index": 0,
                            "length": 76
                        }
                    ]
                }
            ],
            "summary": {
                "scores": [
                    {
                        "value": 1,
                        "type": "sequence-identity"
                    },
                    {
                        "value": 214.71,
                        "type": "similarity-score"
                    },
                    {
                        "value": 1,
                        "type": "sequence-similarity"
                    },
                    {
                        "value": 0.49,
                        "type": "RMSD"
                    },
                    {
                        "value": 0.16,
                        "type": "TM-score"
                    }
                ],
                "n_aln_residue_pairs": 76,
                "n_modeled_residues": [
                    474,
                    76
                ],
                "seq_aln_len": 76,
                "aln_coverage": [
                    16,
                    100
                ]
            }
        },
        {
            "structures": [
                {
                    "url": "https://alphafold.ebi.ac.uk/files/AF-P41235-F1-model_v2.cif",
                    "format": "mmcif",
                    "is_binary": false,
                    "name": "AF-P41235-F1",
                    "selection": {
                        "asym_id": "A"
                    }
                },
                {
                    "entry_id": "1PZL",
                    "selection": {
                        "asym_id": "A"
                    }
                }
            ],
            "structure_alignment": [
                {
                    "regions": [
                        [
                            {
                                "asym_id": "A",
                                "beg_seq_id": 146,
                                "beg_index": 0,
                                "length": 21
                            },
                            {
                                "asym_id": "A",
                                "beg_seq_id": 173,
                                "beg_index": 27,
                                "length": 206
                            }
                        ],
                        [
                            {
                                "asym_id": "A",
                                "beg_seq_id": 5,
                                "beg_index": 0,
                                "length": 21
                            },
                            {
                                "asym_id": "A",
                                "beg_seq_id": 32,
                                "beg_index": 27,
                                "length": 206
                            }
                        ]
                    ],
                    "transformations": [
                        [
                            1,
                            0,
                            0,
                            0,
                            0,
                            1,
                            0,
                            0,
                            0,
                            0,
                            1,
                            0,
                            0,
                            0,
                            0,
                            1
                        ],
                        [
                            -0.010053370832324049,
                            -0.2331468555903751,
                            -0.9723895687754106,
                            0,
                            -0.5818706004499447,
                            -0.7894818469306177,
                            0.19530749524542618,
                            0,
                            -0.813219241082581,
                            0.5677684009306454,
                            -0.12772434708280683,
                            0,
                            26.741147368855113,
                            9.829205405298664,
                            85.1383381307709,
                            1
                        ]
                    ],
                    "summary": {
                        "scores": [
                            {
                                "value": 0.85,
                                "type": "RMSD"
                            },
                            {
                                "value": 638.55,
                                "type": "similarity-score"
                            }
                        ],
                        "n_aln_residue_pairs": 227
                    }
                }
            ],
            "sequence_alignment": [
                {
                    "sequence": "MRLSKTLVDMDMADYSAALDPAYTTLEFENVQVLTMGNDTSPSEGTNLNAPNSLGVSALCAICGDRATGKHYGASSCDGCKGFFRRSVRKNHMYSCRFSRQCVVDKDKRNQCRYCRLKKCFRAGMKKEAVQNERDRISTRRSSYEDSSLPSINALLQAEVLSRQITSPVSGINGDIRAKKIASIADVCESMKEQLLVLVEWAKYIPAFCELPLDDQVALLRAHAGEHLLLGATKRSMVFKDVLLLGNDYIVPRHCPELAEMSRVSIRILDELVLPFQELQIDDNEYAYLKAIIFFDPDAKGLSDPGKIKRLRSQVQVSLEDYINDRQYDSRGRFGELLLLLPTLQSITWQMIEQIQFIKLFGMAKIDNLLQEMLLGGSPSDAPHAHHPLHPHLMQEHMGTNVIVANTMPTHLSNGQMCEWPRPRGQAATPETPQPSPPGGSGSEPYKLLPGAVATIVKPLSAIPQPTITKQEVI",
                    "regions": [
                        {
                            "asym_id": "A",
                            "beg_seq_id": 146,
                            "beg_index": 0,
                            "length": 233
                        }
                    ]
                },
                {
                    "sequence": "SSYELASLPSINALLQAEVLSRQITSPVSGINGDIRAKKIASIADVCESMKEQLLVLVEWAKYIPAFCELPLDDQVALLRAHAGEHLLLGATKRSMVFKDVLLLGNDYIVPRHCPELAEMSRVSIRILDELVLPFQELQIDDNEYAYLKAIIFFDPDAKGLSDPGKIKRLRSQVQVSLEDYINDRQYDSRGRFGELLLLLPTLQSITWQMIEQIQFIKLFGMAKIDNLLQEMLLGGS",
                    "regions": [
                        {
                            "asym_id": "A",
                            "beg_seq_id": 5,
                            "beg_index": 0,
                            "length": 21
                        },
                        {
                            "asym_id": "A",
                            "beg_seq_id": 32,
                            "beg_index": 27,
                            "length": 206
                        }
                    ],
                    "gaps": [
                        {
                            "beg_index": 21,
                            "length": 6
                        }
                    ]
                }
            ],
            "summary": {
                "scores": [
                    {
                        "value": 1.1,
                        "type": "RMSD"
                    },
                    {
                        "value": 0.47,
                        "type": "TM-score"
                    },
                    {
                        "value": 638.55,
                        "type": "similarity-score"
                    },
                    {
                        "value": 1,
                        "type": "sequence-similarity"
                    },
                    {
                        "value": 0.99,
                        "type": "sequence-identity"
                    }
                ],
                "n_aln_residue_pairs": 227,
                "n_modeled_residues": [
                    474,
                    227
                ],
                "seq_aln_len": 233,
                "aln_coverage": [
                    48,
                    100
                ]
            }
        }
    ]
};

class RcsbStructuralAlignmentProvider implements AlignmentCollectorInterface {

    private alignmentResponse: AlignmentResponse | undefined = undefined;
    private readonly alignment: StructureAlignmentResponse;
    constructor(alignment: StructureAlignmentResponse) {
        this.alignment = alignment;
    }

    async collect(requestConfig: AlignmentCollectConfig, filter?: Array<string>): Promise<AlignmentResponse> {
        return new Promise(async (resolve)=>{
            resolve(await this.data());
        });
    }
    async getTargets(): Promise<string[]> {
        return new Promise(async (resolve)=>{
            resolve((await this.data()).target_alignment?.map(ta=>ta?.target_id ?? "NA") ?? [])
        })
    }
    async getAlignmentLength(): Promise<number> {
        return new Promise(async (resolve)=>{
            const ends = (await this.data() ).target_alignment?.map(ta=>ta?.aligned_regions?.[ta?.aligned_regions?.length-1]?.query_end);
            resolve(Math.max(...(ends as number[])))
        })
    }
    async getAlignment(): Promise<AlignmentResponse> {
        return new Promise(async (resolve)=>{
            resolve(this.data());
        });
    }
    private async data(): Promise<AlignmentResponse> {
        if(this.alignmentResponse)
            return this.alignmentResponse;
        return new Promise((resolve)=>{
            alignmentTransform(this.alignment).then(ar=>{
                this.alignmentResponse = ar;
                resolve(ar);
            })
        });
    }

}

class RcsbStructuralTransformProvider implements TransformProviderInterface {

    private readonly alignment: StructureAlignmentResponse;
    constructor(alignment: StructureAlignmentResponse) {
        this.alignment = alignment;
    }

    get(entryId: string, asymId?: string): RigidTransformType[] {
        const res = this.alignment.results?.find(res=>{
            const r = res.structures[1];
            return ("entry_id" in r && r.entry_id == entryId && r.selection && "asym_id" in r.selection && r.selection.asym_id == asymId)
        });
        if(res?.structure_alignment.length == 1) {
            return [{
                transform: res.structure_alignment[0].transformations[1] as TransformMatrixType
            }];
        }else if(res?.structure_alignment.length && res?.structure_alignment.length > 1){
            return res.structure_alignment.map(sa=>({
                transform: sa.transformations[1] as TransformMatrixType,
                regions: sa.regions?.[1].map(r=>[r.beg_seq_id,r.beg_seq_id+r.length-1])
            }));
        }else{
            return [{
                transform: [1,0,0,0, 0,1,0,0, 0,0,1,0, 0,0,0,1]
            }];
        }
    }

}

class RcsbStructureLocationProvider implements LocationProviderInterface {

    private readonly alignment: StructureAlignmentResponse;
    constructor(alignment: StructureAlignmentResponse) {
        this.alignment = alignment;
    }

    get(entryId:string): string|undefined {
        for(const res of this.alignment.results ?? []){
            if("url" in res.structures[0] && res.structures[0].url && res.structures[0].name == entryId ){
                return res.structures[0].url;
            }
            if("url" in res.structures[1] && res.structures[1].url && res.structures[1].name == entryId ){
                return res.structures[1].url;
            }
        }
        return undefined;
    }

}

async function alignmentTransform(alignment: StructureAlignmentResponse): Promise<AlignmentResponse> {
    if(!alignment.results)
        return {};
    const alignmentRef = await mergeAlignments(alignment.results);
    const out: AlignmentResponse = alignmentRef.buildAlignments();
    const seqs = await getSequences(alignment.results);
    out.target_alignment?.forEach(ta=>{
        const seq = seqs.find(s=>s.rcsbId===ta?.target_id)?.sequence
        if(seq && ta)
            ta.target_sequence = seq;
    });
    return out;
}

async function mergeAlignments(results: Alignment[]): Promise<AlignmentReference> {
    const result = results[0];
    if(!result)
        throw "Results not available";
    const seqs = await getSequences([result]);
    const alignmentRef = new AlignmentReference( getInstanceId(result, 0), seqs[0].sequence.length)
    results.forEach(result=>{
        if(result.sequence_alignment)
            alignmentRef.addAlignment(getInstanceId(result), transformToGapedDomain(result.sequence_alignment[0].regions), transformToGapedDomain(result.sequence_alignment[1].regions));
        else if(result.structure_alignment && result.structure_alignment[0].regions && result.structure_alignment[1].regions)
            alignmentRef.addAlignment(getInstanceId(result), transformToGapedDomain(result.structure_alignment[0].regions.flat()), transformToGapedDomain(result.structure_alignment[1].regions.flat()));
    });
    return alignmentRef;
}

function getInstanceId(result: Alignment, index: 0|1 = 1): string {
    const res = result.structures[index];
    if("entry_id" in res && res.entry_id && res.selection && "asym_id" in res.selection)
        return`${res.entry_id}.${res.selection.asym_id}`;
    else if("name" in res && res.selection &&"asym_id" in res.selection)
        return `${res.name}.${res.selection.asym_id}`;
    throw new Error("Missing entry_id and name from result");
}

function transformToGapedDomain(regions: AlignmentRegion[]): (number|undefined)[] {
    const out: (number|undefined)[]  = [];
    let prevRegionEnd = 0;
    regions.forEach(region=>{
        const beg = region.beg_index+1;
        const end = region.beg_index+region.length;
        if(beg > (prevRegionEnd+1)){
            const nGaps = beg - (prevRegionEnd+1);
            out.push(...Array(nGaps).fill(undefined));
        }
        prevRegionEnd = end;
        const seqBeg = region.beg_seq_id;
        const seqEnd = region.beg_seq_id+region.length-1;
        for(let i=seqBeg;i<=seqEnd;i++){
            out.push(i);
        }
    });
    return out;
}

async function getSequences(results: Alignment[]): Promise<InstanceSequenceInterface[]> {
    const out: InstanceSequenceInterface[] = [];
    const missingIds: string[] = [];
    const res = results[0];
    if(res.sequence_alignment?.[0].sequence) {
        out.push( {
            rcsbId: getInstanceId(res,0),
            sequence: res.sequence_alignment[0].sequence
        })
    }else{
        missingIds.push( getInstanceId(res, 0) )
    }
    results.forEach(res=>{
        if(res.sequence_alignment?.[1].sequence) {
            out.push( {
                rcsbId: getInstanceId(res,1),
                sequence: res.sequence_alignment[1].sequence
            })
        }else{
            missingIds.push( getInstanceId(res) )
        }
    });
    return  out.concat(await RcsbRequestContextManager.getInstanceSequences(missingIds));
}

const structuralAlignment: StructureAlignmentResponse = alignmentExample as StructureAlignmentResponse;

export const dataProvider: RcsbModuleDataProviderInterface = {
    alignments: {
        collector: new RcsbStructuralAlignmentProvider(structuralAlignment),
        context:{
            queryId: "structural-alignment",
            group: GroupReference.MatchingUniprotAccession,
            to: SequenceReference.PdbInstance
        }
    }
};

export const transformProvider = new RcsbStructuralTransformProvider(structuralAlignment);

export const structureLocationProvider = new RcsbStructureLocationProvider(structuralAlignment);