#### Shiny UI #####

dashboardPage(skin="purple",
               dashboardHeader(title = "Drug/Target Explorer"),
               
               dashboardSidebar(
                 sidebarMenu( id = "sidebar",
                              selectInput(
                                "switch_target",
                                label="Switch to New Target",
                                choices = c(
                                  "alr",
                                  "embb",
                                  "gid",
                                  "katg",
                                  "pnca",
                                  "rpob"
                                ),
                                selected="embb"),
                              menuItem("LogoP SNP", tabName="LogoP SNP"),
                              #menuItem("Lineage Sample Count", tabName="Lineage Sample Count"),
                              menuItem("Site SNP count", tabName="Site SNP count"),
                              menuItem("Stability SNP by site", tabName="Stability SNP by site"),
                              menuItem("DM OM Plots", tabName="DM OM Plots"),
                              menuItem("Correlation", tabName="Correlation"),
                              #menuItem("Lineage Distribution", tabName="Lineage Distribution"),
                              menuItem("Consurf", tabName="Consurf"),
                              menuItem("LogoP OR", tabName="LogoP OR"),
                              menuItem("Lineage", tabName="Lineage"),
                              actionButton("force", "Refresh Plot"),
                              actionButton("force_ui", "Reset UI controls"),
                              
                              #menuItem('Stability count', tabName='Stability count'),
                              
                              # These conditionalPanel()s make extra settings appear in the sidebar when needed 
                              conditionalPanel(
                                condition="input.sidebar == 'LogoP SNP'", 
                                textInput(
                                  "omit_snp_count",
                                  "Omit SNPs",
                                  value = c(0),
                                  placeholder = "1,3,6" 
                                )
                              ),
                              # NOTE: 
                              # I *think* we can cheat here slightly and use the min/max from
                              # merged_df3[['position']] for everything because the various
                              # dataframes for a given gene/drug combination have the 
                              # same range of positions. May need fixing, especially 
                              # if we get/shrink the imported data files to something 
                              # more reasonable.
                              conditionalPanel(
                                condition="
                                  input.sidebar == 'LogoP SNP'||
                                  input.sidebar == 'Stability SNP by site' ||
                                  input.sidebar == 'Consurf' ||
                                  input.sidebar == 'LogoP OR'", 
                                sliderInput(
                                  "display_position_range"
                                  , "Display Positions"
                                  , min=1, max=150, value=c(1,150) # 150 is just a little less than the smallest pos_count
                                )
                              ),
                              
                              conditionalPanel(
                                condition="
                                  input.sidebar == 'LogoP SNP' ||
                                  input.sidebar == 'LogoP OR' ||
                                  input.sidebar == 'LogoP ED'", 
                                selectInput(
                                  "logoplot_colour_scheme", 
                                  label="Logo Plot Colour Scheme", 
                                  choices = logoPlotSchemes, 
                                  selected="chemistry"
                                )
                              ),
                              conditionalPanel(
                                condition="input.sidebar == 'Correlation'", 
                                selectInput(
                                  "corr_method", 
                                  label="Correlation Method", 
                                  choices = list("spearman", 
                                                 "pearson", 
                                                 "kendall"),
                                  selected="spearman"
                                )
                              ),
                              conditionalPanel(
                                condition="input.sidebar == 'Correlation'", 
                                numericInput(
                                  "corr_lig_dist"
                                  , "Ligand Distance Cutoff (Å)", value=1
                                )
                              ),
                              conditionalPanel(
                                condition="input.sidebar == 'Site SNP count'", 
                                numericInput(
                                  "snp_ligand_dist"
                                  , "Ligand Distance Cutoff (Å)", value=10
                                )
                              ),
                              conditionalPanel(
                                condition="input.sidebar == 'Site SNP count'", 
                                numericInput(
                                  "snp_interface_dist"
                                  , "Interface Distance Cutoff (Å)", value=10
                                )
                              ),
                              conditionalPanel(
                                condition="input.sidebar == 'Site SNP count'", 
                                numericInput(
                                  "snp_nca_dist"
                                  , "NCA Distance Cutoff (Å)", value=10
                                )
                              ),
                              
                              conditionalPanel(
                                condition="input.sidebar == 'Correlation'", 
                                checkboxGroupInput(
                                  "corr_selected",
                                  "Parameters",
                                  choiceNames = c(
                                    "DeepDDG",
                                    "Dynamut2",
                                    "FoldX",
                                    "ConSurf"#,
                                  ),
                                  choiceValues = c(
                                    "DeepDDG",
                                    "Dynamut2",
                                    "FoldX",
                                    "ConSurf"#,
                                  ),
                                  selected = c(
                                    "DeepDDG",
                                    "Dynamut2",
                                    "FoldX",
                                    "ConSurf"#,
                                  )
                                )
                              ),
                              
                              # conditionalPanel(
                              #   condition="input.sidebar == 'DM OM Plots'", 
                              #   selectInput(
                              #     "dm_om_param", 
                              #     label="Stability Parameter",
                              #     choices = keys(dm_om_map),
                              #     selected="SNAP2")
                              # ),
                              # colour_categ
                              conditionalPanel(
                                condition="input.sidebar == 'Stability SNP by site'", 
                                selectInput(
                                  "stability_snp_param",
                                  label="Stability Parameter",
                                  choices = stability_boxes_df$stability_type,
                                  selected="Average")
                              ),
                              conditionalPanel(
                                condition="input.sidebar == 'Stability SNP by site'", 
                                checkboxInput("reorder_custom_h", 
                                              label="Reorder by SNP count", 
                                              FALSE)
                              ), 
                              conditionalPanel(
                                condition="input.sidebar.match(/^Lineage.*/)", 
                                checkboxInput("all_lineages", 
                                              label="All Lineages", 
                                              FALSE)
                              ),
                              # an example of how you can match multiple things in frontend JS
                              conditionalPanel(
                                condition="input.sidebar == 'LogoP SNP' ||
                                  input.sidebar =='Stability SNP by site' ||
                                  input.sidebar =='Consurf' ||
                                  input.sidebar =='LogoP OR'",
                                actionButton("clear_ngl",
                                             "Clear Structure")
                              ),
                              conditionalPanel(
                                condition="input.sidebar == 'LogoP SNP' ||
                                  input.sidebar =='Stability SNP by site' ||
                                  input.sidebar =='Consurf' ||
                                  input.sidebar =='LogoP OR'",
                                actionButton("test_ngl",
                                             "Test NGLViewR")
                              )#,
                              
                              # downloadButton("save",
                              #                "Download Plot"
                              # )
                              # actionButton(
                              #   "reload_target",
                              #   label="Reload Target\nData (slow!)"
                              # )
                              
                 )
               ),
               #### body ####
               body <- dashboardBody(
                 
                 tabItems(
                   tabItem(tabName = "dashboard",
                           h2("Dashboard tab content")
                   ),
                   
                   tabItem(tabName = "widgets",
                           h2("Widgets tab content")
                   )
                 ),
                 # creates a 'Conditional Panel' containing a plot object from each of our 
                 # ggplot plot functions (and its associated data frame)
                 fluidRow(column(width=12,
                                 lapply(plot_functions_df$tab_name, 
                                        function(x){
                                          
                                          plot_function=plot_functions_df[
                                            plot_functions_df$tab_name==x,
                                            "plot_function"]
                                          
                                          plot_df=plot_functions_df[
                                            plot_functions_df$tab_name==x,
                                            "plot_df"]
                                          cat(paste0('\nCreating output: ', x))
                                          generate_conditionalPanel(x, plot_function, plot_df)
                                          
                                        }
                                 )
                 )
                 ),
                 # Explicit fluidRow() for Lineage plots together
                 fluidRow(
                   column(conditionalPanel(
                     condition="input.sidebar.match(/^Lineage.*/)", box(
                       title="Lineage Distribution"
                       , status = "info"
                       , width=NULL
                       , plotOutput("lineage_distP", height="700px") %>% withSpinner(color="#0dc5c1"),
                       height=800
                     )
                   ), width=6
                   ),
                   column(conditionalPanel(
                     condition="input.sidebar.match(/^Lineage.*/)", box(
                       title="Lineage SNP Diversity"
                       , status = "info"
                       , width=NULL
                       , plotOutput("lin_sc", height="700px") %>% withSpinner(color="#0dc5c1"),
                       height=800
                     )
                   ), width=6
                   )
                   
                 ),
                 # Explicit fluidRow() for Site SNP Count
                 fluidRow(
                   column(conditionalPanel(
                     condition="input.sidebar == 'Site SNP count'", 
                     box(
                       title="Site SNP count"
                       , status = "info"
                       , width=NULL
                       , plotOutput("site_snp_count_bp") %>% withSpinner(color="#0dc5c1")
                     )
                   ), width=6
                   ),
                   column(conditionalPanel(
                     condition="input.sidebar == 'Site SNP count'", 
                     box(
                       title="Ligand Distance"
                       , status = "info"
                       , width=NULL
                       , plotOutput("site_snp_count_bp_ligand") %>% withSpinner(color="#0dc5c1")
                     )
                   ), width=6
                   ),
                   column(conditionalPanel(
                     condition="input.sidebar == 'Site SNP count'", 
                     box(
                       title="Interface Distance"
                       , status = "info"
                       , width=NULL
                       , plotOutput("site_snp_count_interface") %>% withSpinner(color="#0dc5c1")
                     )
                   ), width=6
                   ),
                   column(conditionalPanel(
                     condition="input.sidebar == 'Site SNP count'", 
                     box(
                       title="RNA Distance"
                       , status = "info"
                       , width=NULL
                       , plotOutput("site_snp_count_nca") %>% withSpinner(color="#0dc5c1")
                     )
                   ), width=6
                   )
                 ),
                 
                 #   # Explicit fluidRow() for Stability Count
                 #   fluidRow(
                 #     column(
                 #       conditionalPanel(
                 #         condition="input.sidebar.match(/^Lineage.*/)",
                 #         lapply(
                 #           # FIXME: using a hardcoded target DF for this IS WRONG AND WILL BREAK
                 #           stability_boxes_df[stability_boxes_df$outcome_colname  %in% colnames(embb_merged_df3),"outcome_colname"],
                 #           function(x){
                 #             print(paste0("outcome_colname: ",x))
                 #             box(plotOutput(x), width=4)
                 #           }
                 #       ),
                 #       width=12
                 #     )
                 #   )
                 # ),
                 
                 #### fluidRow()s for "Stability Count" in the sidebar ####
                 fluidRow(
                   conditionalPanel(
                     condition="
            input.sidebar == 'LogoP SNP' || 
            input.sidebar =='Stability SNP by site' || 
            input.sidebar =='Consurf' || 
            input.sidebar =='LogoP OR'",
                     column(NGLVieweROutput("structure"),
                            width=3
                     )
                   ),
                   conditionalPanel(
                     condition="
            input.sidebar == 'LogoP SNP' || 
            input.sidebar == 'Stability SNP by site' || 
            input.sidebar == 'Site SNP count' || 
            input.sidebar == 'Consurf' || 
            input.sidebar == 'LogoP OR'",
                     column(
                       DT::dataTableOutput('table'),
                       width=9
                     )
                   )
                 ),
               )
)