library(shiny)
library(shinydashboard)
library(shinyjs)

# Amino Acid Data
amino_acid_data <- data.frame(
  code = c("A", "R", "N", "D", "C", "E", "Q", "G", "H", "I", "L", "K", "M", "F", "P", "S", "T", "W", "Y", "V"),
  name = c("Alanine", "Arginine", "Asparagine", "Aspartic acid", "Cysteine", "Glutamic acid", "Glutamine", 
           "Glycine", "Histidine", "Isoleucine", "Leucine", "Lysine", "Methionine", "Phenylalanine", 
           "Proline", "Serine", "Threonine", "Tryptophan", "Tyrosine", "Valine"),
  weight = c(89.1, 174.2, 132.1, 133.1, 121.2, 147.1, 146.2, 75.1, 155.2, 131.2, 131.2, 146.2, 149.2, 
             165.2, 115.1, 105.1, 119.1, 204.2, 181.2, 117.1),
  extinction280 = c(0, 0, 0, 0, 120, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 5500, 1490, 0)
)

# UI
ui <- dashboardPage(
  dashboardHeader(title = "Protein Concentration Calculator"),
  dashboardSidebar(
    sidebarMenu(
      menuItem("Absorbance to Concentration", tabName = "absorbance"),
      menuItem("Weight to Mole", tabName = "weightToMole"),
      menuItem("Mole to Weight", tabName = "moleToWeight"),
      menuItem("Molar Concentration", tabName = "molarConcentration"),
      menuItem("Amino Acid Calculator", tabName = "aminoAcid"),
      menuItem("Extinction Calculator", tabName = "extinction")
    )
  ),
  dashboardBody(
    useShinyjs(),
    tabItems(
      # Absorbance to Concentration Tab
      tabItem(tabName = "absorbance",
              fluidRow(
                box(width = 12, title = "Absorbance to Concentration",
                    numericInput("absorbance", "Absorbance (A)", value = NULL, min = 0),
                    numericInput("extinctionCoefficient", "Extinction Coefficient (M⁻¹cm⁻¹)", value = NULL, min = 0),
                    numericInput("pathLength", "Path Length (cm)", value = 1.0, min = 0),
                    actionButton("calculateConcentration", "Calculate Concentration", class = "btn-primary"),
                    hr(),
                    conditionalPanel(
                      condition = "output.concentration !== null",
                      h4("Result:"),
                      verbatimTextOutput("concentration"),
                      h4("Step-by-Step:"),
                      verbatimTextOutput("concentrationSteps")
                    )
                )
              )
      ),
      
      # Weight to Mole Tab
      tabItem(tabName = "weightToMole",
              fluidRow(
                box(width = 12, title = "Weight to Mole",
                    numericInput("weight", "Weight (g)", value = NULL, min = 0),
                    numericInput("molarWeightWM", "Molar Weight (g/mol)", value = NULL, min = 0),
                    actionButton("calculateMole", "Calculate Mole", class = "btn-primary"),
                    hr(),
                    conditionalPanel(
                      condition = "output.weightToMoleResult !== null",
                      h4("Result:"),
                      verbatimTextOutput("weightToMoleResult"),
                      h4("Step-by-Step:"),
                      verbatimTextOutput("weightToMoleSteps")
                    )
                )
              )
      ),
      
      # Mole to Weight Tab
      tabItem(tabName = "moleToWeight",
              fluidRow(
                box(width = 12, title = "Mole to Weight",
                    numericInput("mole", "Mole", value = NULL, min = 0),
                    numericInput("molarWeightMW", "Molar Weight (g/mol)", value = NULL, min = 0),
                    actionButton("calculateWeight", "Calculate Weight", class = "btn-primary"),
                    hr(),
                    conditionalPanel(
                      condition = "output.moleToWeightResult !== null",
                      h4("Result:"),
                      verbatimTextOutput("moleToWeightResult"),
                      h4("Step-by-Step:"),
                      verbatimTextOutput("moleToWeightSteps")
                    )
                )
              )
      ),
      
      # Molar Concentration Tab
      tabItem(tabName = "molarConcentration",
              fluidRow(
                box(width = 12, title = "Molar Concentration",
                    numericInput("moleMC", "Mole", value = NULL, min = 0),
                    numericInput("volume", "Volume (L)", value = NULL, min = 0),
                    actionButton("calculateMolarConcentration", "Calculate Molar Concentration", class = "btn-primary"),
                    hr(),
                    conditionalPanel(
                      condition = "output.molarConcentration !== null",
                      h4("Result:"),
                      verbatimTextOutput("molarConcentration"),
                      h4("Step-by-Step:"),
                      verbatimTextOutput("molarConcentrationSteps")
                    )
                )
              )
      ),
      
      # Amino Acid Calculator Tab
      tabItem(tabName = "aminoAcid",
              fluidRow(
                box(width = 12, title = "Amino Acid to Molecular Weight",
                    textAreaInput("aminoAcidSequence", "Protein Sequence", "", height = "150px"),
                    actionButton("calculateMolecularWeight", "Calculate Molecular Weight", class = "btn-primary"),
                    hr(),
                    conditionalPanel(
                      condition = "output.molecularWeight !== null",
                      h4("Result:"),
                      verbatimTextOutput("molecularWeight"),
                      h4("Step-by-Step:"),
                      verbatimTextOutput("molecularWeightSteps")
                    )
                )
              )
      ),
      
      # Extinction Coefficient Calculator Tab
      tabItem(tabName = "extinction",
              fluidRow(
                box(width = 12, title = "Extinction Coefficient Calculator",
                    textAreaInput("extinctionSequence", "Protein Sequence", "", height = "150px"),
                    actionButton("calculateExtinctionCoefficient", "Calculate Extinction Coefficient", class = "btn-primary"),
                    hr(),
                    conditionalPanel(
                      condition = "output.extinctionResult !== null",
                      h4("Result:"),
                      verbatimTextOutput("extinctionResult"),
                      h4("Step-by-Step:"),
                      verbatimTextOutput("extinctionSteps")
                    )
                )
              )
      )
    ),
    # Reset Button at the bottom of each page
    fluidRow(
      column(12, align = "center", 
             actionButton("resetAll", "Reset All Fields", 
                          style = "background-color: #3c8dbc; color: white; margin-top: 20px; margin-bottom: 20px;")
      )
    )
  )
)

# Server
server <- function(input, output, session) {
  
  # Reset function for all inputs
  observeEvent(input$resetAll, {
    # Reset absorbance tab
    updateNumericInput(session, "absorbance", value = NULL)
    updateNumericInput(session, "extinctionCoefficient", value = NULL)
    updateNumericInput(session, "pathLength", value = 1.0)
    
    # Reset weight to mole tab
    updateNumericInput(session, "weight", value = NULL)
    updateNumericInput(session, "molarWeightWM", value = NULL)
    
    # Reset mole to weight tab
    updateNumericInput(session, "mole", value = NULL)
    updateNumericInput(session, "molarWeightMW", value = NULL)
    
    # Reset molar concentration tab
    updateNumericInput(session, "moleMC", value = NULL)
    updateNumericInput(session, "volume", value = NULL)
    
    # Reset amino acid calculator tab
    updateTextAreaInput(session, "aminoAcidSequence", value = "")
    
    # Reset extinction coefficient calculator tab
    updateTextAreaInput(session, "extinctionSequence", value = "")
    
    # Clear all outputs
    output$concentration <- renderText("")
    output$concentrationSteps <- renderText("")
    output$weightToMoleResult <- renderText("")
    output$weightToMoleSteps <- renderText("")
    output$moleToWeightResult <- renderText("")
    output$moleToWeightSteps <- renderText("")
    output$molarConcentration <- renderText("")
    output$molarConcentrationSteps <- renderText("")
    output$molecularWeight <- renderText("")
    output$molecularWeightSteps <- renderText("")
    output$extinctionResult <- renderText("")
    output$extinctionSteps <- renderText("")
  })
  
  # Calculate Concentration
  observeEvent(input$calculateConcentration, {
    req(input$absorbance, input$extinctionCoefficient, input$pathLength)
    
    if(input$extinctionCoefficient <= 0 || input$pathLength <= 0) {
      output$concentration <- renderText("Invalid input")
      output$concentrationSteps <- renderText("Ensure extinction coefficient and path length are greater than zero.")
      return()
    }
    
    result <- input$absorbance / (input$extinctionCoefficient * input$pathLength)
    
    output$concentration <- renderText(format(result, scientific = TRUE, digits = 6))
    output$concentrationSteps <- renderText(paste(
      "Step-by-Step:",
      "1. Concentration = Absorbance ÷ (Extinction Coefficient × Path Length)",
      paste("2.", input$absorbance, "÷ (", input$extinctionCoefficient, "×", input$pathLength, ") =", result),
      sep = "\n"
    ))
  })
  
  # Calculate Weight to Mole
  observeEvent(input$calculateMole, {
    req(input$weight, input$molarWeightWM)
    
    if(input$molarWeightWM <= 0) {
      output$weightToMoleResult <- renderText("Invalid input")
      output$weightToMoleSteps <- renderText("Ensure molar weight is greater than zero.")
      return()
    }
    
    result <- input$weight / input$molarWeightWM
    
    output$weightToMoleResult <- renderText(format(result, scientific = TRUE, digits = 6))
    output$weightToMoleSteps <- renderText(paste(
      "Step-by-Step:",
      "1. Mole = Weight ÷ Molar Weight",
      paste("2.", input$weight, "÷", input$molarWeightWM, "=", result),
      sep = "\n"
    ))
  })
  
  # Calculate Mole to Weight
  observeEvent(input$calculateWeight, {
    req(input$mole, input$molarWeightMW)
    
    if(input$molarWeightMW <= 0) {
      output$moleToWeightResult <- renderText("Invalid input")
      output$moleToWeightSteps <- renderText("Ensure molar weight is greater than zero.")
      return()
    }
    
    result <- input$mole * input$molarWeightMW
    
    output$moleToWeightResult <- renderText(format(result, scientific = TRUE, digits = 6))
    output$moleToWeightSteps <- renderText(paste(
      "Step-by-Step:",
      "1. Weight = Mole × Molar Weight",
      paste("2.", input$mole, "×", input$molarWeightMW, "=", result),
      sep = "\n"
    ))
  })
  
  # Calculate Molar Concentration
  observeEvent(input$calculateMolarConcentration, {
    req(input$moleMC, input$volume)
    
    if(input$volume <= 0) {
      output$molarConcentration <- renderText("Invalid input")
      output$molarConcentrationSteps <- renderText("Ensure volume is greater than zero.")
      return()
    }
    
    result <- input$moleMC / input$volume
    
    output$molarConcentration <- renderText(format(result, scientific = TRUE, digits = 6))
    output$molarConcentrationSteps <- renderText(paste(
      "Step-by-Step:",
      "1. Molar Concentration = Mole ÷ Volume",
      paste("2.", input$moleMC, "÷", input$volume, "=", result),
      sep = "\n"
    ))
  })
  
  # Calculate Molecular Weight from Amino Acid Sequence
  observeEvent(input$calculateMolecularWeight, {
    req(input$aminoAcidSequence)
    
    # Clean sequence - keep only letters and convert to uppercase
    cleanSequence <- toupper(gsub("[^A-Za-z]", "", input$aminoAcidSequence))
    
    if(nchar(cleanSequence) == 0) {
      output$molecularWeight <- renderText("Invalid input")
      output$molecularWeightSteps <- renderText("Please enter a valid amino acid sequence.")
      return()
    }
    
    # Split sequence into individual amino acids
    aaVector <- strsplit(cleanSequence, "")[[1]]
    
    # Count amino acids
    aaCounts <- table(aaVector)
    
    # Initialize variables for calculation
    totalWeight <- 0
    stepsText <- "Step-by-Step:\nAmino acid composition:\n"
    
    # Calculate weight for each amino acid
    for(aa in names(aaCounts)) {
      aaData <- amino_acid_data[amino_acid_data$code == aa, ]
      
      # Check if amino acid code is valid
      if(nrow(aaData) == 0) {
        output$molecularWeight <- renderText(paste("Unknown amino acid code:", aa))
        output$molecularWeightSteps <- renderText("Please check your sequence for valid amino acid codes.")
        return()
      }
      
      count <- aaCounts[aa]
      weight <- aaData$weight * count
      totalWeight <- totalWeight + weight
      
      stepsText <- paste0(stepsText, aaData$name, " (", aa, "): ", count, " × ", 
                          format(aaData$weight, nsmall = 1), " = ", 
                          format(weight, nsmall = 1), " Da\n")
    }
    
    # Account for water loss in peptide bonds
    waterMass <- 18.015
    peptideBonds <- nchar(cleanSequence) - 1
    waterLoss <- waterMass * peptideBonds
    
    totalWeight <- totalWeight - waterLoss
    
    stepsText <- paste0(stepsText, 
                        "\nWater loss from peptide bonds:\n",
                        "(", peptideBonds, " bonds × ", format(waterMass, nsmall = 3), 
                        " Da) = ", format(waterLoss, nsmall = 1), " Da\n",
                        "\nFinal molecular weight: ", format(totalWeight, nsmall = 1), " Da")
    
    output$molecularWeight <- renderText(paste0(format(totalWeight, nsmall = 1), " Da"))
    output$molecularWeightSteps <- renderText(stepsText)
  })
  
  # Calculate Extinction Coefficient
  observeEvent(input$calculateExtinctionCoefficient, {
    req(input$extinctionSequence)
    
    # Clean sequence - keep only letters and convert to uppercase
    cleanSequence <- toupper(gsub("[^A-Za-z]", "", input$extinctionSequence))
    
    if(nchar(cleanSequence) == 0) {
      output$extinctionResult <- renderText("Invalid input")
      output$extinctionSteps <- renderText("Please enter a valid amino acid sequence.")
      return()
    }
    
    # Split sequence into individual amino acids
    aaVector <- strsplit(cleanSequence, "")[[1]]
    
    # Count amino acids
    aaCounts <- table(aaVector)
    
    # Initialize variables for calculation
    totalExtinction <- 0
    stepsText <- "Step-by-Step:\nContributing amino acids:\n"
    
    # Only Trp, Tyr, and Cys contribute to extinction coefficient at 280nm
    contributingAAs <- c("W", "Y", "C")
    
    # Calculate extinction for each contributing amino acid
    for(aa in contributingAAs) {
      if(aa %in% names(aaCounts)) {
        count <- aaCounts[aa]
        aaData <- amino_acid_data[amino_acid_data$code == aa, ]
        contribution <- aaData$extinction280 * count
        totalExtinction <- totalExtinction + contribution
        
        if(count > 0) {
          stepsText <- paste0(stepsText, aaData$name, " (", aa, "): ", count, " × ", 
                              format(aaData$extinction280, nsmall = 0), " = ", 
                              format(contribution, nsmall = 0), " M⁻¹cm⁻¹\n")
        }
      }
    }
    
    stepsText <- paste0(stepsText, "\nTotal extinction coefficient: ", 
                        format(totalExtinction, nsmall = 0), " M⁻¹cm⁻¹")
    
    output$extinctionResult <- renderText(paste0(format(totalExtinction, nsmall = 0), " M⁻¹cm⁻¹"))
    output$extinctionSteps <- renderText(stepsText)
  })
}

# Run the application
shinyApp(ui = ui, server = server)