/* Standardize all button styling */
button {
  background-color: #2e2e2e;
  color: #e0e0e0;
  border: 1px solid #555;
  border-radius: 4px;
  padding: 10px 15px;
  font-size: 16px;
  cursor: pointer;
  transition: background 0.3s ease, border-color 0.3s ease;
  outline: none;
}

button:hover {
  background-color: #222;
  border-color: #777;
}

button:active {
  background-color: #1e1e1e;
  border-color: #666;
}

/* Standardize form elements: dropdowns, search bars, file inputs */
select,
input[type="text"],
input[type="file"] {
  background-color: #1e1e1e;
  color: #e0e0e0;
  border: 1px solid #555;
  border-radius: 4px;
  padding: 8px 12px;
  font-size: 16px;
  transition: background 0.3s ease, border-color 0.3s ease;
}

select:focus,
input[type="text"]:focus {
  border-color: #0072B2;
  outline: none;
}

.apexcharts-menu,
.apexcharts-menu * {
  color: #000 !important;
  text-align: center;
}

/* Base styling */
body {
  font-family: 'Helvetica Neue', Arial, sans-serif;
  background: #121212;
  margin: 20px;
  color: #e0e0e0;
  text-align: center;
}

h1 {
  text-align: center;
  color: #f0f0f0;
}

.container {
  width: 90%;
  max-width: 1240px;
  margin: auto;
  padding: 2%;
  background: #1e1e1e;
  border-radius: 10px;
  box-shadow: 0 4px 12px rgba(0, 0, 0, 0.5);
}

.text-center {
  text-align: center;
}

/* Tab styling */
.tab-bar {
  display: flex;
  flex-wrap: wrap;
  gap: 10px;
  margin-bottom: 20px;
}

@media (max-width: 768px) {
  .tab-bar {
    flex-direction: column;
  }

  .container {
    padding: 10px;
  }

  #igvContainer {
    height: calc(100vh - 200px);
  }

  #chartCanvas,
  #pairsChartCanvas {
    min-height: 200px;
  }
}

.tab-bar button {
  flex: 1;
}

.tab-bar button.active {
  background-color: #0072B2;
}

.tab-content {
  display: none;
}

.tab-content.active {
  display: block;
}

/* Viewer Tab styling */
#chartCanvas {
  margin-top: 20px;
  background: transparent;
  min-height: 300px;
}

.chart-heading {
  margin-top: 24px;
  margin-bottom: 12px;
  font-size: 24px;
  font-weight: 600;
  color: #e0e0e0;
}

.chart-title-link {
  color: inherit;
  text-decoration: underline;
}

.chart-title-link:hover,
.chart-title-link:focus {
  color: #4fc3f7;
}

#legend {
  margin-top: 20px;
  display: flex;
  justify-content: center;
  gap: 20px;
  font-size: 16px;
}

#legend div {
  display: flex;
  align-items: center;
}

#legend div span {
  margin-left: 5px;
}

.legend-box {
  width: 20px;
  height: 20px;
  border: 1px solid #fff;
}

.legend-box--significant {
  background-color: #4fc3f7;
}

.legend-box--nonsignificant {
  background-color: #ffb74d;
}

.legend-box--pairs-primary {
  background-color: #4fc3f7;
}

.legend-box--pairs-primary-light {
  background-color: #a9e3f7;
}

.legend-box--pairs-secondary {
  background-color: #ffb74d;
}

.legend-box--pairs-secondary-light {
  background-color: #ffd8a5;
}

.chart-info-row {
  display: flex;
  justify-content: flex-end;
  margin: 10px 0;
  gap: 10px;
}

.chart-action-button {
  padding: 8px 14px;
  font-size: 14px;
  text-transform: uppercase;
  letter-spacing: 0.5px;
}

.chart-action-button:disabled {
  opacity: 0.5;
  cursor: not-allowed;
}

.pairs-legend {
  margin-top: 10px;
  display: flex;
  gap: 15px;
  justify-content: center;
}

.legend-entry {
  display: flex;
  align-items: center;
  gap: 5px;
}

.info-button {
  width: 32px;
  height: 32px;
  border-radius: 50%;
  font-weight: bold;
  font-size: 18px;
  padding: 0;
  line-height: 1;
}

.info-button:focus {
  outline: 2px solid #80bfff;
  outline-offset: 2px;
}

/* Data Tables styling */
#tableList {
  margin-bottom: 20px;
}

#tableList table {
  width: 100%;
  border-collapse: collapse;
  margin-bottom: 10px;
}

#tableList th,
#tableList td {
  border: 1px solid #555;
  padding: 8px;
  text-align: left;
}

#tableList th {
  background-color: #2e2e2e;
}

#tableDisplay {
  max-height: 400px;
  overflow-x: auto;
  overflow-y: auto;
  border: 1px solid #555;
}

#tableDisplay table {
  width: 100%;
  border-collapse: collapse;
}

#tableDisplay th,
#tableDisplay td {
  border: 1px solid #555;
  padding: 5px;
}

#tableDisplay th {
  background-color: #2e2e2e;
}

/* asRNA/mRNA pairs styling */
.upload-group {
  margin-bottom: 15px;
}

.upload-group label {
  display: block;
  margin-bottom: 5px;
  font-weight: bold;
}

.upload-group input {
  width: auto;
}

.status-message {
  color: #D55E00;
  margin-top: 5px;
}

.pairs-section {
  margin-top: 20px;
}

.pairs-section h2 {
  margin-bottom: 15px;
}

.pairs-table {
  width: 100%;
  border-collapse: collapse;
  margin-top: 10px;
}

.pairs-table th,
.pairs-table td {
  padding: 8px 12px;
  border: 1px solid #555;
  text-align: left;
}

.pairs-table th {
  background-color: #2e2e2e;
}

.significant {
  font-weight: bold;
}

/* Genome Viewer Tab styling */
#igvContainer {
  width: 100%;
  height: calc(100vh - 150px);
  margin: auto;
  background: #ffffff;
  border-radius: 10px;
  box-shadow: 0 4px 12px rgba(0, 0, 0, 0.5);
  padding: 10px;
}

#igvContainer svg text,
#igvContainer svg tspan {
  fill: #000 !important;
  color: #000 !important;
}

#igvContainer .igv-container {
  background-color: #000000 !important;
}

#igvContainer .igv-track-label {
  color: #000 !important;
}

#igvContainer .igv-track {
  border: 1px solid #000 !important;
}

#igvContainer .igv-axis,
#igvContainer .igv-popover-label,
#igvContainer .igv-popover-content {
  color: #000 !important;
}

#igvContainer .igv-control-pane,
#igvContainer .igv-menu-bar-container {
  background-color: #ffffff !important;
}

#igvContainer .igv-locus-bar {
  background-color: #000 !important;
}

#igvContainer .igv-locus-label,
#igvContainer .igv-locus-input {
  background-color: #000000 !important;
  color: #000 !important;
}

#igvContainer .igv-icon,
#igvContainer .igv-glyph-count,
#igvContainer .igv-zoom-handles path {
  fill: #000 !important;
  stroke: #000 !important;
}

#igvContainer .igv-popover {
  background-color: #000 !important;
  border: 1px solid #000 !important;
  border-radius: 6px !important;
  color: #000 !important;
}

#igvContainer .igv-track-label,
#igvContainer .igv-track-label * {
  color: #000 !important;
  fill: #000 !important;
}

#igvContainer .igv-popover,
#igvContainer .igv-popover * {
  color: #000 !important;
}

/* Processing Site Motifs Tab Styles */
#motifsTab .motifs-container {
  display: grid;
  grid-template-columns: repeat(auto-fit, minmax(600px, 1fr));
  gap: 20px;
  margin-top: 20px;
}

#motifsTab .section {
  background: #1e1e1e;
  border: 1px solid #333;
  border-radius: 8px;
  display: flex;
  flex-direction: column;
  overflow: hidden;
}

#motifsTab .section-top,
#motifsTab .section-bottom {
  flex: 1;
  padding: 15px;
}

#motifsTab .section-top {
  display: flex;
  justify-content: center;
  align-items: center;
  background: #2e2e2e;
}

#motifsTab .svg-wrapper {
  background: #ffffff;
  max-width: 100%;
  height: auto;
  border: 4px solid #ccc;
  border-radius: 4px;
  padding: 5px;
  display: inline-block;
}

#motifsTab .svg-wrapper img {
  width: 100%;
  height: auto;
  display: block;
}

#motifsTab .section-bottom {
  background: #2e2e2e;
  display: flex;
  flex-direction: column;
  border-top: 1px solid #333;
}

#motifsTab .section-bottom select {
  margin-bottom: 10px;
  padding: 10px;
  font-size: 16px;
  border: 1px solid #555;
  border-radius: 4px;
  background: #1e1e1e;
  color: #e0e0e0;
  transition: background 0.3s ease, border-color 0.3s ease;
}

#motifsTab .section-bottom select:hover {
  background: #222;
  border-color: #777;
}

#motifsTab .btn-container {
  margin-bottom: 10px;
  display: flex;
  gap: 10px;
}

#motifsTab .btn-container button {
  flex: 1;
  padding: 10px;
  font-size: 14px;
  border: 1px solid #555;
  border-radius: 4px;
  background: #1e1e1e;
  color: #e0e0e0;
  cursor: pointer;
  transition: background 0.3s ease, border-color 0.3s ease;
}

#motifsTab .btn-container button:hover {
  background: #222;
  border-color: #777;
}

#motifsTab .section-bottom pre {
  flex: 1;
  padding: 15px;
  background: #1e1e1e;
  border: 1px solid #555;
  border-radius: 4px;
  overflow: auto;
  white-space: pre-wrap;
  color: #e0e0e0;
  font-size: 14px;
}

/* Save Chart Button Styles */
.save-chart-btn {
  margin-top: 10px;
}

/* Additional styles for arCOG analysis */
.arCOG-container {
  max-width: 1200px;
  margin: auto;
  background-color: #1e1e1e;
  padding: 10px 20px 20px 20px;
  border-radius: 8px;
  box-shadow: 0 4px 12px rgba(0, 0, 0, 0.5);
}

.arCOG-header-controls {
  display: flex;
  flex-wrap: wrap;
  justify-content: space-between;
  align-items: flex-start;
  gap: 10px;
  padding: 10px 0;
}

.arCOG-left {
  display: flex;
  flex-direction: column;
}

.arcog-input-header {
  display: flex;
  align-items: center;
  gap: 8px;
}

.arcog-input-header label {
  margin-bottom: 0;
}

.arCOG-left label {
  font-size: 14px;
  font-weight: bold;
  margin-bottom: 2px;
}

.arCOG-middle {
  display: flex;
  flex-direction: column;
  align-items: flex-start;
}

.arCOG-middle label {
  font-size: 14px;
  font-weight: bold;
  margin-bottom: 2px;
}

.arCOG-middle select {
  padding: 6px;
  font-size: 14px;
  border: 1px solid #555;
  border-radius: 4px;
  background-color: #222;
  color: #e0e0e0;
  outline: none;
  width: 350px;
  height: 200px;
}

.arCOG-right {
  display: flex;
  flex-direction: column;
  gap: 5px;
}

.arCOG-right button {
  width: 200px;
}

.arCOG-header-controls input[type="file"],
.arCOG-header-controls select {
  padding: 6px;
  font-size: 14px;
  border: 1px solid #555;
  border-radius: 4px;
  background-color: #222;
  color: #e0e0e0;
  outline: none;
}

.arCOG-table-container {
  width: 100%;
  max-height: 60vh;
  overflow-y: auto;
  margin-bottom: 20px;
  border: 1px solid #444;
}

#arcog_resultsTable {
  display: none;
}

.arCOG-results-table {
  width: 100%;
  border-collapse: collapse;
  margin-top: 10px;
}

.arCOG-results-table th,
.arCOG-results-table td {
  border: 1px solid #555;
  padding: 8px;
  text-align: center;
  font-size: 8px;
}

.arCOG-results-table th .header-text {
  display: block;
  padding: 8px;
  padding-right: 25px;
  white-space: nowrap;
  overflow: auto;
  text-align: inherit;
}

.arCOG-results-table th {
  background-color: #2e2e2e;
}

.arCOG-results-table th {
  position: sticky;
  top: 0;
  background-color: #2e2e2e;
  z-index: 10;
  cursor: pointer;
  padding-right: 25px;
  padding: 8px;
}

.arCOG-results-table td {
  text-align: center;
}

.arCOG-message {
  text-align: center;
  margin-top: 5px;
  color: #ffb74d;
}

#helpButton {
  background-color: #2e2e2e;
  /* Primary blue */
  color: #fff;
  font-size: 14px;
  font-weight: bold;
  text-align: center;
  cursor: pointer;
  transition: background 0.3s ease;
}

#helpButton:hover {
  background-color: #000000;
}

#legendTableContainer table {
  width: 100%;
  border-collapse: collapse;
  font-family: Arial, sans-serif;
}

#legendTableContainer thead {
  background-color: #2e2e2e;
  color: #fff;
}

#legendTableContainer th,
#legendTableContainer td {
  border: 1px solid #ddd;
  padding: 8px;
  text-align: left;
}

#legendTableContainer tbody tr:nth-child(even) {
  background-color: #f9f9f9;
}

#legendTableContainer tbody tr:hover {
  background-color: #f1f1f1;
}

/* Bubble chart container */
#arcog_barChart {
  width: 100%;
  height: 40vh;
  margin-top: 20px;
  background-color: #f5efef;
  border: 2px solid #555;
  border-radius: 4px;
  padding: 10px;
}

#tableControls {
  display: flex;
  gap: 10px;
  margin: 10px 0;
  background-color: #1e1e1e;
  padding: 10px;
  border: 1px solid #555;
  border-radius: 4px;
}

#tableList input[type="checkbox"] {
  transform: scale(1.5);
  display: block;
  margin: 0 auto;
}

#plotButton {
  position: relative;
  left: 0px;
  top: 5px;
}

#prevGene,
#nextGene {
  width: 150px;
}

/* Modal styles for legend table */
.modal {
  display: none;
  position: fixed;
  z-index: 1000;
  left: 0;
  top: 0;
  width: 100%;
  height: 100%;
  overflow: auto;
  background-color: rgba(0, 0, 0, 0.4);
}

.modal-content {
  background-color: #fefefe;
  margin: 5% auto;
  padding: 20px;
  border: 1px solid #888;
  width: 80%;
  max-width: 800px;
  text-align: left;
  color: #000;
}

.modal-body {
  font-size: 15px;
  line-height: 1.5;
}

.modal-body p {
  margin-top: 0;
}

.modal-guidelines {
  margin: 10px 0 16px 20px;
  padding: 0;
  list-style: disc;
}

.modal-guidelines li {
  margin-bottom: 8px;
}

.close {
  color: #aaa;
  float: right;
  font-size: 28px;
  font-weight: bold;
}

.close:hover,
.close:focus {
  color: black;
  text-decoration: none;
  cursor: pointer;
}

.condition-group {
  margin-bottom: 20px;
}

.condition-group h3 {
  margin: 0 0 8px 0;
  color: #222;
}

.condition-list {
  list-style: none;
  margin: 0;
  padding: 0;
}

.condition-list li {
  margin-bottom: 6px;
  line-height: 1.4;
  color: #222;
}

.condition-label {
  font-weight: 600;
  color: #111;
}

/* Resources styling */
#resourcesTab {
  max-width: 64%;
  margin: auto;
  background-color: #1e1e1e;
  padding: 10px 20px 20px 20px;
  border-radius: 8px;
  box-shadow: 0 4px 12px rgba(0, 0, 0, 0.5);
}

.resources-heading {
  margin-bottom: 20px;
  text-align: left;
}

.resource-list {
  list-style: none;
  padding-left: 0;
  text-align: left;
  font-size: 1.05em;
  line-height: 1.8;
}

.resource-list li {
  margin-bottom: 10px;
  color: #ccc;
  display: flex;
  align-items: flex-start;
}

.resource-list .dash {
  margin-right: 10px;
  color: #888;
  font-weight: bold;
  width: 10px;
  display: inline-block;
}

.resource-list a {
  color: #4db8ff;
  text-decoration: none;
  font-weight: 500;
}

.resource-list a:hover {
  color: #ffffff;
  text-decoration: underline;
}

/* Footer styling */
.footer {
  margin-top: 40px;
  padding: 20px;
  font-size: 0.9em;
  color: #888;
  text-align: center;
}

.footer a {
  color: #aaa;
  text-decoration: none;
}

.footer a:hover {
  color: #fff;
}