{% comment %}

Modal to align sequence

Input:
- id: prefix of element identifiers

{% endcomment %}

<div class="modal fade"
     id="{{ id }}_alignment"
     tabindex="-1"
     data-bs-backdrop="static"
     data-bs-keyboard="false"
     aria-labelledby="{{ id }}_{{ type }}_modal_label"
     aria-hidden="true">
    <div class="modal-dialog modal-lg">
        <div class="modal-content">
            <div class="modal-header">
                <h1 class="modal-title fs-5">Sequence alignment</h1>
                <span class="ms-2 me-5 small">{{ species.get_html_link }}</span>

                <div class="ms-auto d-flex align-items-center">
                    <button type="button"
                            class="btn-close"
                            data-bs-dismiss="modal"
                            aria-label="Close"></button>
                </div>
            </div>
            <div class="modal-body">
                <div class="row mb-2 small">
                    <label class="col-lg-2 col-form-label small">Aligner</label>
                    <div class="col-lg-10">
                        <a class="form-control-plaintext"
                           target="_blank"
                           href="https://github.com/bbuchfink/diamond">
                            DIAMOND {{ DIAMOND_VERSION }}
                            <i class="fa fa-2xs fa-arrow-up-right-from-square"></i>
                        </a>
                    </div>
                </div>

                <div class="row mb-2 small">
                    <label class="col-lg-2 col-form-label small">Proteome</label>
                    <div class="col-lg-10">
                        <span class="form-control-plaintext">
                            <img class="rounded"
                                 width="20px"
                                 height="100%"
                                 src="{{ species.image_url }}"
                                 alt="Image of {{ species }}">
                            {{ species.get_html }}

                            {% if species.proteome %}
                                <a class="ps-1"
                                   href="{% url 'download_file' species.proteome.slug %}">{{ species.proteome.ext|upper }}</a>
                            {% endif %}
                        </span>
                    </div>
                </div>

                <div class="row mb-2 small">
                    <label class="col-lg-2 col-form-label small">Type</label>
                    <div class="col-lg-10">
                        <div class="btn-group btn-group-sm mb-3 w-100" role="group">
                            <input type="radio"
                                   class="btn-check"
                                   name="{{ id }}_type"
                                   id="{{ id }}_type_nucleotides"
                                   autocomplete="off"
                                   value="nucleotides">
                            <label class="btn btn-outline-primary" for="{{ id }}_type_nucleotides">Nucleotides</label>

                            <input type="radio"
                                   class="btn-check"
                                   name="{{ id }}_type"
                                   id="{{ id }}_type_aminoacids"
                                   autocomplete="off"
                                   value="aminoacids"
                                   checked>
                            <label class="btn btn-outline-primary" for="{{ id }}_type_aminoacids">Amino acids</label>
                        </div>
                    </div>
                </div>

                <div class="row mb-2 small">
                    <label for="{{ id }}_query" class="col-lg-2 col-form-label small">Sequences</label>
                    <div class="col-lg-10">
                        <div class="sequence-input border border-secondary-subtle rounded">
                            <textarea type="textarea" id="{{ id }}_query" rows="6" required class="sequence-textarea form-control font-monospace border-0 rounded-top p-2" placeholder="FASTA sequences (maximum of {{ MAX_ALIGNMENT_SEQS }})">
                            </textarea>
                            <div class="d-flex justify-content-between small py-1 px-2 border-top border-secondary-subtle bg-light rounded-bottom">
                                <button type="button"
                                        class="btn btn-link btn-sm"
                                        onclick="document.getElementById('{{ id }}_upload').click();">
                                    <span class="small">
                                        <i class="fa fa-file-lines"></i>
                                        Load from FASTA file...
                                    </span>
                                </button>
                                <span>
                                    <span id="{{ id }}_count">0</span>
                                    out of {{ MAX_ALIGNMENT_SEQS }} sequences
                                </span>
                            </div>
                        </div>

                        <input class="form-control d-none" type="file" id="{{ id }}_upload">
                    </div>
                </div>
            </div>

            <div id="{{ id }}_alertContainer"></div>
            <template id="{{ id }}_errorTemplate">
                <div role="alert"
                     class="alert alert-danger alert-dismissible fade show m-2">
                    <i class="fa fa-triangle-exclamation"></i>
                    <strong class="alert-title">Title</strong>
                    <span class="alert-description">Description</span>
                    <button type="button"
                            class="btn-close"
                            data-bs-dismiss="alert"
                            aria-label="Close"></button>
                </div>
            </template>

            <div class="modal-footer justify-content-between">
                <p class="text-muted small">
                    <i class="fa fa-info-circle"></i>
                    Alignment results are saved as gene lists.
                </p>
                <span>
                    <button id="{{ id }}_{{ type }}_editor_btn"
                            type="button"
                            class="btn btn-outline-primary"
                            href="javascript:void(0);"
                            data-bs-toggle="modal"
                            data-bs-target="#{{ id }}_{{ type }}_editor">
                        Show gene lists
                    </button>
                    <button type="submit"
                            class="btn btn-primary"
                            id="{{ id }}_align_btn"
                            disabled>
                        <span id="{{ id }}_align_spinner"
                              class="spinner-border spinner-border-sm d-none"></span>
                        Align
                    </button>
                </span>
            </div>
        </div>
    </div>
</div>

<script type="module">
    {% load static %}
    import { uploadSequenceFile, highlightSequenceText, alignSequence }
        from "{% static 'app/dist/atlas/modals/alignment.js' %}";

    const id = "{{ id }}",
          maxMB = {{ MAX_FILE_SIZE }},
          maxSeqs = {{ MAX_ALIGNMENT_SEQS }};
    uploadSequenceFile(id, maxMB, maxSeqs);
    highlightSequenceText(id, maxSeqs);
    alignSequence(id, "{{species}}", "{{type}}");
</script>