#' Generate the main UI for the application.
#'
#' @param options Global options for the application.
#'
#' @noRd
ui <- function(options) {
    div(
        shinyjs::useShinyjs(),
        rclipboard::rclipboardSetup(),
        navbarPage(
            id = "main_page",
            theme = bslib::bs_theme(
                version = 5,
                bootswatch = "united",
                primary = "#1964bf"
            ),
            title = "TPE-OLD candidates",
            selected = "Results",
            tabPanel(
                "Input data",
                input_page_ui("input_page", options)
            ),
            tabPanel(
                "Results",
                sidebarLayout(
                    sidebarPanel(
                        width = 3,
                        methods_ui("methods"),
                        filters_ui("filters")
                    ),
                    mainPanel(
                        width = 9,
                        tabsetPanel(
                            type = "pills",
                            tabPanel(
                                title = "Overview",
                                div(
                                    style = "margin-top: 16px",
                                    plotly::plotlyOutput(
                                        "rank_plot",
                                        width = "100%",
                                        height = "600px"
                                    )
                                )
                            ),
                            tabPanel(
                                title = "Methods & Distribution",
                                div(
                                    style = "margin-top: 16px",
                                    plotly::plotlyOutput(
                                        "rankings_plot",
                                        width = "100%",
                                        height = "600px"
                                    )
                                )
                            ),
                            tabPanel(
                                title = "Comparison",
                                div(
                                    style = "margin-top: 16px",
                                    plotly::plotlyOutput(
                                        "boxplot",
                                        width = "100%",
                                        height = "600px"
                                    )
                                )
                            ),
                            tabPanel(
                                title = "Scores by position",
                                div(
                                    style = "margin-top: 16px",
                                    selectInput(
                                        "positions_plot_chromosome_name",
                                        label = NULL,
                                        choices = chromosome_choices()
                                    ),
                                    plotly::plotlyOutput(
                                        "positions_plot",
                                        width = "100%",
                                        height = "600px"
                                    )
                                )
                            ),
                            tabPanel(
                                title = "Detailed results",
                                results_ui("results")
                            ),
                            tabPanel(
                                title = "g:Profiler",
                                div(
                                    style = "margin-top: 16px",
                                    plotly::plotlyOutput("gost_plot"),
                                ),
                                div(
                                    style = "margin-top: 16px",
                                    DT::DTOutput("gost_details")
                                )
                            ),
                            tabPanel(
                                title = "DisGeNET",
                                div(
                                    style = "margin-top: 16px",
                                    DT::DTOutput("disgenet")
                                )
                            )
                        )
                    )
                )
            ),
            tabPanel(
                title = "Publication"
            )
        )
    )
}

#' Generate a named list for choosing chromosomes.
#' @noRd
chromosome_choices <- function() {
    choices <- purrr::lmap(
        unique(geposan::genes$chromosome),
        function(name) {
            choice <- list(name)

            names(choice) <- paste0(
                "Chromosome ",
                name
            )

            choice
        }
    )

    choices[order(suppressWarnings(sapply(choices, as.integer)))]
}