/* ========================================================= 
   GLOBAL CSS — Shared Across All Pages 
   ========================================================= */

body.analyzer #formSectionContainer {
    flex: 0 0 50%;
    max-width: 520px;
    margin-right: 0;
    margin-left: 0;
}

body.analyzer #formContainer {
    float: none;
    width: 100%;
}

body.analyzer .flex-container {
    position: relative;
}

body.analyzer .sidebar {
    flex-basis: 200px;
    background-color: #fad366c0;
    padding: 20px;
    box-shadow: 0 0 8px rgba(213, 127, 127, 0.723);
}

body.analyzer .pairing,
body.analyzer .match-lines,
body.analyzer .miRNA-seq,
body.analyzer .target-seq,
body.analyzer .base-pattern {
    font-family: 'Courier New', Courier, monospace;
    white-space: pre;
    color: #000;
}

body.analyzer section {
    display: flex;
    align-items: center;
    margin-bottom: 10px;
}

body.analyzer label {
    display: inline-block;
    margin-right: 20px;
    width: 200px;
}

body.analyzer select.uniform-width,
body.analyzer input.uniform-width {
    width: 260px;  
    height: 36px;
    box-sizing: border-box;
    padding: 5px 10px;
    margin-top: 5px;
    margin-bottom: 10px;
    border: 1px solid #ccc;
    border-radius: 4px;
    font-size: 14px;
}

body.analyzer nav.horizontal-menu {
    margin: 0;
    padding: 0;
}

body.analyzer main {
    margin-top: 0;
    display: flex;
    flex-direction: row;
    flex-wrap: nowrap;
    justify-content: flex-start;
    align-items: flex-start;
    gap: 20px;
    padding: 20px;
}

body.analyzer #leftMenu {
    width: 100%; 
    max-width: none;
    background-color: #ffffff;
    padding: 0;
    border: 1px solid #cccccc;
    border-radius: 5px;
    box-shadow: 2px 2px 5px rgba(0, 0, 0, 0.1);
    flex-shrink: 0;
}

body.analyzer #leftMenu ul {
    list-style-type: none;
    padding: 0;
    margin: 0;
}

body.analyzer #leftMenu li {
    padding: 12px 16px;
    cursor: pointer;
    transition: background-color 0.3s, color 0.3s;
    border-bottom: 1px solid #eeeeee;
}

body.analyzer #leftMenu li:last-child {
    border-bottom: none;
}

body.analyzer #leftMenu li:hover {
    background-color: #f0f0f0;
    color: #333;
}

body.analyzer #leftMenu li.selected,
body.analyzer #leftMenu li.current {
    background-color: #e67e22;
    color: #ffffff;
    font-weight: bold;
}

body.analyzer #formAndImageContainer {
    display: flex;
    flex-direction: row;
    gap: 10px;
    flex: 1;
    margin: 0;
}

body.analyzer #formSectionContainer,
body.analyzer #imageContainer {
    flex: 1;
}

body.analyzer #imageContainer {
    display: flex;
    flex-direction: column;
    align-items: flex-start;
    justify-content: flex-start;
}

body.analyzer .image-section img {
    background-color: rgba(233, 232, 232, 0.064);
    display: block;
    width: 100%;
    max-width: 700px;
    min-width: 400px;
    height: auto;
    border-radius: 10px;
    padding: 5px;
}

.form-section {
    display: none;
}

.form-section.active {
    display: block;
}

.selected-menu-item {
    background-color: #e67e22;
    color: #ffffff;
    font-weight: bold;
}

body.analyzer #formAndImageContainer.default-layout {
    display: flex !important;
    margin-left: 0 !important;
}

body.analyzer #default_imageContainer {
    display: none;  
}

body.analyzer #imageContainer {
    margin-left: 0 !important;
    flex: 1 !important;
}

.default-layout {
    display: flex;
}

.default-layout #formSectionContainer {
    display: none;
}

.default-layout #imageContainer {
    flex: 1;
    display: flex;
    flex-direction: column;
    justify-content: flex-start;
    align-items: center;
    padding-top: 20px;
}

body.analyzer #formAndImageContainer.default-layout #default_imageContainer {
    display: block !important;
}

.default-layout #default_image {
    max-width: 900px;
    min-width: 600px;
    width: 100%;
    height: auto;
    margin: 0 auto;
}

#aqseq_fastqUpload section,
#aqseq_fastaUpload section {
    display: block;
    margin-bottom: 10px;
}

.small-text {
    font-size: smaller;
}

#searchForm {
    display: none;
}

#addAqseq_PairedEndSampleButton {
    display: block;
}

#addAqseq_SingleEndSampleButton {
    display: none;
}

#CumulativeCurve {
    display: block;
}

#CumulativeCurveUploadForm section,
#AQseqUploadForm section {
    margin-bottom: 10px;
}

.custom-file-input {
    display: flex;
    align-items: center;
    gap: 10px;
}

.custom-file-input button {
    padding: 5px 10px;
    cursor: pointer;
    background-color: #007BFF;
    color: #FFFFFF;
    border: none;
    border-radius: 4px;
}

.custom-file-input button:hover {
    background-color: #0056b3;
}

.custom-file-input span {
    font-size: 14px;
    color: #333333;
}

.template-download a {
    display: inline-block;
    padding: 8px 12px;
    background-color: rgba(172, 255, 47, 0.356);
    color: #000000;
    text-decoration: none;
    border-radius: 4px;
}

.template-download p {
    margin-top: 10px;
}

.search-title {
    font-size: 24px;
}

.job-status-panel {
    background: #f9f9f9;
    border: 1px solid #ddd;
    border-radius: 8px;
    padding: 20px;
    width: 480px;
    max-width: 500px;
    min-width: 400px;
    margin-top: 20px;
    position: relative;
    z-index: 100;
}

.job-status-panel h2 {
    margin-top: 0;
    font-size: 1.5em;
    color: #333;
    border-bottom: 2px solid #e67e22;
    padding-bottom: 5px;
}

.job-status-content .status-line {
    margin: 10px 0;
    font-size: 1.1em;
    color: #555;
}

.job-status-content label {
    display: block;
    font-weight: bold;
    margin-bottom: 5px;
}

.job-status-content input[type="text"] {
    width: calc(100% - 110px);
    padding: 6px;
    border: 1px solid #ccc;
    border-radius: 4px;
}

.job-status-content button {
    padding: 6px 12px;
    margin-left: 10px;
    background-color: #e67e22;
    color: #fff;
    border: none;
    border-radius: 4px;
    cursor: pointer;
}

.job-status-content button:hover {
    background-color: #cf711f;
}

.job-status-content #jobResult {
    margin-top: 15px;
    font-size: 1em;
    color: #333;
}

body.analyzer .eisa-options {
    display: flex;
    flex-direction: column;
    gap: 8px; 
    padding-top: 3px; 
}

body.analyzer .radio-label {
    width: auto !important; 
    display: flex;
    align-items: center;
    cursor: pointer;
    margin-right: 0 !important;
    font-weight: normal;
}

body.analyzer .radio-label input[type="radio"] {
    margin-right: 8px;
    margin-top: 0;
    margin-bottom: 0;
}

body.analyzer .eisa-desc {
    font-size: 0.85em;
    color: #888;
    margin-left: 24px; 
    margin-top: -2px;  
    line-height: 1.3;
}

/* =========================================
   Sidebar Layout & Help Section
   ========================================= */

.sidebar-wrapper {
    width: 200px;
    min-width: 200px;
    display: flex;
    flex-direction: column;
    gap: 30px;
    flex-shrink: 0;
}

.help-section {
    padding-left: 10px;
}

.help-title {
    font-weight: bold;
    color: #333;
    font-size: 1rem;
    margin-top: 0;
    margin-bottom: 10px;
}

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

.help-section .help-list a {
    display: block;
    text-decoration: none;
    color: #0066cc;
    font-size: 0.95rem;
    padding: 5px 0;
    transition: color 0.2s;
}

.help-section .help-list a:hover {
    text-decoration: underline;
    color: #004499;
}