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index.html
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<!doctype html>
<html lang="en">
<head>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1">
<meta name="description" content="Graphical User Interface for phastDNA">
<meta name="author" content="Maciej Michalczyk">
<title>phastDNA</title>
<link href="https://cdn.jsdelivr.net/npm/bootstrap@5.3.0-alpha1/dist/css/bootstrap.min.css" rel="stylesheet"
integrity="sha384-GLhlTQ8iRABdZLl6O3oVMWSktQOp6b7In1Zl3/Jr59b6EGGoI1aFkw7cmDA6j6gD" crossorigin="anonymous">
<script src="https://cdn.jsdelivr.net/npm/bootstrap@5.3.0-alpha1/dist/js/bootstrap.bundle.min.js"
integrity="sha384-w76AqPfDkMBDXo30jS1Sgez6pr3x5MlQ1ZAGC+nuZB+EYdgRZgiwxhTBTkF7CXvN"
crossorigin="anonymous"></script>
<link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/bootstrap-icons@1.10.3/font/bootstrap-icons.css">
<script src="https://ajax.googleapis.com/ajax/libs/jquery/3.6.3/jquery.min.js"></script>
<script src="https://cdn.jsdelivr.net/npm/choices.js/public/assets/scripts/choices.min.js"></script>
<link rel="stylesheet"href="https://cdn.jsdelivr.net/npm/choices.js/public/assets/styles/choices.min.css"/>
<!-- Custom styles for this template -->
<link href="{{ url_for('static', filename='phastDNA_ui.css') }}" rel="stylesheet">
<link rel="preconnect" href="https://fonts.googleapis.com">
<link rel="preconnect" href="https://fonts.gstatic.com" crossorigin>
<link href="https://fonts.googleapis.com/css2?family=Signika:wght@300;400;500;600;700&display=swap"
rel="stylesheet">
<link rel="preconnect" href="https://fonts.googleapis.com">
<link rel="preconnect" href="https://fonts.gstatic.com" crossorigin>
<link
href="https://fonts.googleapis.com/css2?family=Jost:ital,wght@0,100;0,200;0,300;0,400;0,500;0,600;0,700;0,800;0,900;1,100;1,200;1,300;1,400;1,500;1,600;1,700;1,800;1,900&display=swap"
rel="stylesheet">
</head>
<body>
<!-- main container -->
<div class="container-fluid contrast-bg">
<div class="container-xl p-4 py-md-5">
<!-- header menu -->
<header class="viewport-header d-flex align-items-center pb-3 mb-5">
<div class="d-flex me-auto align-items-start">
<h1 class="me-auto display-1">phastDNA</h1><p class="d-inline-flex lead">1.2.0</p>
</div>
<div class="d-flex p-4">
<ul class="nav nav-pills mb-3" id="pills-tab" role="tablist">
<li class="nav-item" role="presentation">
<button class="nav-link active" id="pills-home-tab" data-bs-toggle="pill"
data-bs-target="#pills-home" type="button" role="tab" aria-controls="pills-home"
aria-selected="true">Home</button>
</li>
<li class="nav-item" role="presentation">
<button class="nav-link" id="pills-predict-tab" data-bs-toggle="pill"
data-bs-target="#pills-predict" type="button" role="tab" aria-controls="pills-predict"
aria-selected="false">Predict</button>
</li>
<li class="nav-item" role="presentation">
<button class="nav-link" id="pills-train-tab" data-bs-toggle="pill"
data-bs-target="#pills-train" type="button" role="tab" aria-controls="pills-train"
aria-selected="false">Train</button>
</li>
<!-- <li class="nav-item" role="presentation">
<button class="nav-link" id="pills-task-tab" data-bs-toggle="pill"
data-bs-target="#pills-task" type="button" role="tab" aria-controls="pills-task"
aria-selected="false">Tasks</button>
</li> -->
</ul>
</div>
</header>
<!-- main content -->
<main>
<div class="tab-content" id="pills-tabContent">
<!-- Home tab -->
<div class="tab-pane fade show active" id="pills-home" role="tabpanel"
aria-labelledby="pills-home-tab" tabindex="0">First release. This is some placeholder content the Home tab. There will be nice things in the future.
<!-- <button type="button" class="btn btn-primary" id="liveToastBtn">Show live toast</button> -->
<!-- <div class="toast-container position-fixed bottom-0 start-0 p-3">
<div id="liveToast" class="toast" role="alert" aria-live="assertive" aria-atomic="true">
<div class="toast-header">
<img src="..." class="rounded me-2" alt="...">
<strong class="me-auto">Bootstrap</strong>
<small>11 mins ago</small>
<button type="button" class="btn-close" data-bs-dismiss="toast" aria-label="Close"></button>
</div>
<div class="toast-body">
Hello, world! This is a toast message.
</div>
</div>
</div> -->
</div>
<!-- Predict tab -->
<div class="tab-pane fade" id="pills-predict" role="tabpanel" aria-labelledby="pills-predict-tab"
tabindex="0">
<div class="row">
<!-- <div id="predict-toasts" class="toast-container position-fixed bottom-0 start-0 p-3"></div> -->
<form action="/task" method="post" class="was-validated" id="predict-form" target="_blank">
<!-- <button id="post-button" type="submit" class="btn btn-primary">Post</button> -->
<div class="accordion accordion-flush" id="accordionPredict">
<div class="accordion-item">
<h2 class="accordion-header" id="predict-headingSettingsPath">
<button class="accordion-button" type="button" data-bs-toggle="collapse"
data-bs-target="#predict-collapseSettingsPath" aria-expanded="true"
aria-controls="predict-collapseSettingsPath">
<div class="d-flex">
Path settings
</div>
<div class="d-flex flavor-active align-self-center accordion-button-desc mx-3 fs-5">
| Settings related to the required data paths.
</div>
</button>
</h2>
<div id="predict-collapseSettingsPath" class="accordion-collapse collapse show"
aria-labelledby="predict-headingSettingsPath"
data-bs-parent="#accordionPredict">
<div class="accordion-body">
<div class="glass p-5 mb-4 rounded-3">
<!-- style="background-image:linear-gradient(
rgba(0, 0, 0, 0.35),
rgba(0, 0, 0, 0.35));
background-position: center;
background-size: cover;" -->
<div class="container-fluid">
<!-- <div class="d-flex align-content-between flex-wrap flex-column">
<p class="flavor-7 mt-auto col-md-8 fs-6">Settings related
to required data paths.</p>
</div> -->
<div
class="d-flex justify-content-between flex-wrap mb-3 flex-column">
<div class="d-flex">
<!-- <h3 class="flavor-5">Output path</h3> -->
<h3>
<label class="flavor-5"
for="predict-path-output">Output path</label>
</h3>
<button id="predict-info-output"
class="btn-icon keep-top" type="button"
data-bs-toggle="collapse"
data-bs-target="#predict-outputInfo"
aria-expanded="false"
aria-controls="predict-outputInfo">
<i class="bi bi-info-circle-fill btn btn-icon info-icon"></i>
</button>
</div>
<div class="collapse mb-3 flex-grow-1"
id="predict-outputInfo">
<div class="glass-card flavor-visibility card card-body" id="predict-outputInfoText">
Path to directory with result files.
</div>
</div>
<!-- new ^([A-Z]:\\)?(\.[\\/])?([\w\s.\-]+[\\/])*[\w\s.\-]+$ -->
<!-- old ^([A-Z]:\\)?(\.[\\/])?([\w\s.-]+[\\/])*[\w\s.-]+$ -->
<input type="text" pattern="^([A-Z]:\\)?(\.[\\/])?([\w\s.\-]+[\\/])*[\w\s.\-]+$" class="form-control"
id="predict-path-output" aria-describedby="emailHelp"
name="--output" required>
<div class="invalid-feedback">Please fill out this field
with a valid path.</div>
</div>
<div
class="d-flex justify-content-between flex-wrap mb-3 flex-column">
<div class="d-flex">
<h3>
<label class="flavor-5"
for="predict-path-classifier">Classfier
path</label>
</h3>
<button class="btn-icon" type="button"
data-bs-toggle="collapse"
data-bs-target="#predict-classifierInfo"
aria-expanded="false"
aria-controls="predict-classifierInfo">
<i class="bi bi-info-circle-fill btn btn-icon info-icon"></i>
</button>
</div>
<div class="collapse mb-3 flex-grow-1"
id="predict-classifierInfo">
<div class="glass-card flavor-visibility card card-body">
Path to pre-trained phastDNA classifier.
</div>
</div>
<input type="text" pattern="^([A-Z]:\\)?(\.[\\/])?([\w\s.-]+[\\/])*[\w\s.-]+$" class="form-control"
id="predict-path-classifier"
aria-describedby="emailHelp" name="--classifier"
required>
<div class="invalid-feedback">Please fill out this field
with a valid path.</div>
</div>
<div
class="d-flex justify-content-between flex-wrap mb-3 flex-column">
<div class="d-flex">
<h3>
<label class="flavor-5"
for="predict-path-virus">Viruses path</label>
</h3>
<button class="btn-icon" type="button"
data-bs-toggle="collapse"
data-bs-target="#predict-virusInfo"
aria-expanded="false"
aria-controls="predict-virusInfo">
<i class="bi bi-info-circle-fill btn btn-icon info-icon"></i>
</button>
</div>
<div class="collapse mb-3 flex-grow-1"
id="predict-virusInfo">
<div class="glass-card flavor-visibility card card-body">
Path to directory with viral genomes.
</div>
</div>
<input type="text" pattern="^([A-Z]:\\)?(\.[\\/])?([\w\s.-]+[\\/])*[\w\s.-]+$" class="form-control"
id="predict-path-virus" aria-describedby="emailHelp"
name="--viruses" required>
<div class="invalid-feedback">Please fill out this field
with a valid path.</div>
</div>
<div class="d-flex justify-content-between flex-wrap mb-3">
<!-- setting name + info -->
<div class="d-flex">
<h3 class="flavor-5">fastDNA path</h3>
<button class="btn-icon" type="button"
data-bs-toggle="collapse"
data-bs-target="#predict-fastdnaInfo"
aria-expanded="false"
aria-controls="predict-fastdnaInfo">
<i class="bi bi-info-circle-fill btn btn-icon info-icon"></i>
</button>
</div>
<!-- info content -->
<div class="collapse glass mb-3" id="predict-fastdnaInfo">
<div class="glass-card flavor-visibility card card-body">
Path to fastDNA executables.
<div class="alert alert-warning d-flex align-items-center mt-3"
role="alert">
<i
class="bi bi-exclamation-triangle-fill flex-shrink-0 me-2"></i>
<div>
It is not advised to change fastDNA path,
since the default one points into specially
modified version of fastDNA which is
required for correct phastDNA execution.
</div>
</div>
</div>
</div>
<!-- setting value -->
<input type="text" value="./fastDNA/fastdna" class="form-control"
id="predict-fastdna-path" aria-describedby="emailHelp"
name="--fastdna" required>
<div class="invalid-feedback">Please fill out this field
with a valid path.</div>
</div>
</div>
</div>
</div>
</div>
</div>
<div class="accordion-item">
<h2 class="accordion-header" id="predict-headingSettingsPrediction">
<button class="accordion-button collapsed" type="button"
data-bs-toggle="collapse"
data-bs-target="#predict-collapseSettingsPrediction"
aria-expanded="false"
aria-controls="predict-collapseSettingsPrediction">
<div class="d-flex">
Run settings
</div>
<div class="d-flex flavor-active align-self-center accordion-button-desc mx-3 fs-5">
| Settings related to the overall run parameters.
</div>
</button>
</h2>
<div id="predict-collapseSettingsPrediction" class="accordion-collapse collapse"
aria-labelledby="predict-headingSettingsPrediction"
data-bs-parent="#accordionPredict">
<div class="accordion-body">
<div class="glass p-5 mb-4 rounded-3">
<!-- style="background-image:linear-gradient(
rgba(0, 0, 0, 0.35),
rgba(0, 0, 0, 0.35));
background-position: center;
background-size: cover;"> -->
<!-- <form action="/" method="post" class="was-validated"> -->
<!-- <button type="submit" class="btn btn-primary">Post</button> -->
<div class="container-fluid">
<div class="d-flex align-content-between flex-wrap flex-column">
<p class="flavor-7 mt-auto col-md-8 fs-6">Settings related
to the results of virus-host pair prediction.</p>
</div>
<div class="d-flex justify-content-between flex-wrap mb-3">
<!-- <div class="d-flex mb-3"> -->
<div class="d-flex">
<h3 class="flavor-5">Considered hits</h3>
<button class="btn-icon" type="button"
data-bs-toggle="collapse"
data-bs-target="#predict-hitsInfo"
aria-expanded="false"
aria-controls="predict-hitsInfo">
<i class="bi bi-info-circle-fill btn btn-icon info-icon"></i>
</button>
</div>
<div class="collapse mb-3 flex-grow-1"
id="predict-hitsInfo">
<div class="glass-card flavor-visibility card card-body">
Maximum number of host hits to include in fastDNA
prediction step.
</div>
</div>
<input type="number" value="50" min="1" class="form-control"
id="predict-fastdna-hits" aria-describedby="emailHelp"
name="--considered" required>
<div class="invalid-feedback">Please fill out this field
with a positive value.</div>
</div>
<div class="d-flex">
<h3 class="flavor-5">Threads</h3>
<button class="btn-icon" type="button"
data-bs-toggle="collapse"
data-bs-target="#predict-threadsInfo"
aria-expanded="false"
aria-controls="predict-threadsInfo">
<i class="bi bi-info-circle-fill btn btn-icon info-icon"></i>
</button>
</div>
<div class="collapse mb-3" id="predict-threadsInfo">
<div class="glass-card flavor-visibility card card-body">
Number of processor threads to be used by phastDNA.
</div>
</div>
<div class="row g-3">
<div class="col-sm">
<h4 id="predict-threads-num" class="flavor-5">4</h4>
</div>
<div class="col-sm-11 pt-1">
<input type="range" class="slider" min="1" max="5"
step="1" id="predict-fastdna-threads"
name="--threads">
</div>
</div>
</div>
<!-- </form> -->
</div>
</div>
</div>
</div>
</div>
</form>
</div>
</div>
<!-- Train tab -->
<div class="tab-pane fade" id="pills-train" role="tabpanel" aria-labelledby="pills-train-tab"
tabindex="1">
<div class="row">
<!-- <div id="train-toasts" class="toast-container position-fixed bottom-0 start-0 p-3"></div> -->
<form action="/task" method="post" class="was-validated" id="train-form" target="_blank">
<!-- <button id="post-button" type="submit" class="btn btn-primary">Post</button> -->
<div class="accordion accordion-flush" id="accordionTrain">
<div class="accordion-item">
<h2 class="accordion-header" id="train-headingSettingsPath">
<button class="accordion-button d-inline-flex justify-content-start flex-wrap flex-row" type="button" data-bs-toggle="collapse"
data-bs-target="#train-collapseSettingsPath" aria-expanded="true"
aria-controls="train-collapseSettingsPath">
<div class="d-flex">
Path settings
</div>
<div class="d-flex flavor-active align-self-center accordion-button-desc mx-3 fs-5">
| Settings related to the required data paths.
</div>
</button>
</h2>
<div id="train-collapseSettingsPath" class="accordion-collapse collapse show"
aria-labelledby="train-headingSettingsPath"
data-bs-parent="#accordionTrain">
<div class="accordion-body">
<div class="glass p-5 mb-4 rounded-3">
<!-- style="background-image:linear-gradient(
rgba(0, 0, 0, 0.35),
rgba(0, 0, 0, 0.35));
background-position: center;
background-size: cover;"> -->
<div class="container-fluid">
<!-- <div class="d-flex align-content-between flex-wrap flex-column">
<p class="flavor-7 mt-auto col-md-8 fs-6">Settings related
to the required data paths.</p>
</div> -->
<div
class="d-flex justify-content-between flex-wrap mb-3 flex-column">
<div class="d-flex">
<!-- <h3 class="flavor-5">Output path</h3> -->
<h3>
<label class="flavor-5"
for="train-path-output">Output path</label>
</h3>
<button id="train-info-output" class="btn-icon keep-top"
type="button" data-bs-toggle="collapse"
data-bs-target="#train-outputInfo"
aria-expanded="false"
aria-controls="train-outputInfo">
<i class="bi bi-info-circle-fill btn btn-icon info-icon"></i>
</button>
</div>
<div class="collapse mb-3 flex-grow-1"
id="train-outputInfo">
<div class="glass-card flavor-visibility card card-body" id="train-outputInfoText">
Path to directory with result files.
</div>
</div>
<!-- new ^([A-Z]:\\)?(\.[\\/])?([\w\s.\-]+[\\/])*[\w\s.\-]+$ -->
<!-- old ^([A-Z]:\\)?(\.[\\/])?([\w\s.-]+[\\/])*[\w\s.-]+$ -->
<input type="text" pattern="^(?:[A-Z]:\\|\/)?(?:\.\.\/|\.\/)?(?:[\w\s.-]+[\\\/])*[\w\s.-]+$" class="form-control"
id="train-path-output" aria-describedby="emailHelp"
name="--output" required>
<div class="invalid-feedback">Please fill out this field
with a valid path.</div>
</div>
<div
class="d-flex justify-content-between flex-wrap mb-3 flex-column">
<div class="d-flex">
<h3>
<label class="flavor-5" for="train-path-host">Hosts
path</label>
</h3>
<button class="btn-icon" type="button"
data-bs-toggle="collapse"
data-bs-target="#train-hostInfo"
aria-expanded="false"
aria-controls="train-hostInfo">
<i class="bi bi-info-circle-fill btn btn-icon info-icon"></i>
</button>
</div>
<div class="collapse mb-3 flex-grow-1" id="train-hostInfo">
<div class="glass-card flavor-visibility card card-body">
Path to directory with host genomes.
</div>
</div>
<input type="text" pattern="^([A-Z]:\\)?(\.[\\/])?([\w\s.-]+[\\/])*[\w\s.-]+$" class="form-control" id="train-path-host"
aria-describedby="emailHelp" name="--hosts" required>
<div class="invalid-feedback">Please fill out this field
with a valid path.</div>
</div>
<div
class="d-flex justify-content-between flex-wrap mb-3 flex-column">
<div class="d-flex">
<h3>
<label class="flavor-5"
for="train-path-virus">Viruses path</label>
</h3>
<button class="btn-icon" type="button"
data-bs-toggle="collapse"
data-bs-target="#train-virusInfo"
aria-expanded="false"
aria-controls="train-virusInfo">
<i class="bi bi-info-circle-fill btn btn-icon info-icon"></i>
</button>
</div>
<div class="collapse mb-3 flex-grow-1" id="train-virusInfo">
<div class="glass-card flavor-visibility card card-body">
Path to directory with viral genomes.
</div>
</div>
<input type="text" pattern="^([A-Z]:\\)?(\.[\\/])?([\w\s.-]+[\\/])*[\w\s.-]+$" class="form-control" id="train-path-virus"
aria-describedby="emailHelp" name="--trainvir" required>
<div class="invalid-feedback">Please fill out this field
with a valid path.</div>
</div>
<div class="d-flex justify-content-between flex-wrap mb-3">
<!-- setting name + info -->
<div class="d-flex">
<h3 class="flavor-5">fastDNA path</h3>
<button class="btn-icon" type="button"
data-bs-toggle="collapse"
data-bs-target="#train-fastdnaInfo"
aria-expanded="false"
aria-controls="train-fastdnaInfo">
<i class="bi bi-info-circle-fill btn btn-icon info-icon"></i>
</button>
</div>
<!-- info content -->
<div class="collapse mb-3" id="train-fastdnaInfo">
<div class="glass-card flavor-visibility card card-body">
Path to fastDNA executables.
<div class="alert alert-warning d-flex align-items-center mt-3"
role="alert">
<i
class="bi bi-exclamation-triangle-fill flex-shrink-0 me-2"></i>
<div>
It is not advised to change fastDNA path,
since the default one points into specially
modified version of fastDNA which is
required for correct phastDNA execution.
</div>
</div>
</div>
</div>
<!-- setting value -->
<input type="text" value="./fastDNA/fastdna" class="form-control"
id="train-fastdna-path" aria-describedby="emailHelp"
name="--fastdna" required>
<div class="invalid-feedback">Please fill out this field
with a valid path.</div>
</div>
</div>
</div>
</div>
</div>
</div>
<!-- <div class="accordion-item">
<h2 class="accordion-header" id="train-headingSettingsFastdna">
<button class="accordion-button collapsed" type="button"
data-bs-toggle="collapse"
data-bs-target="#train-collapseSettingsFastdna" aria-expanded="false"
aria-controls="train-collapseSettingsFastdna">
fastDNA settings
</button>
</h2>
<div id="train-collapseSettingsFastdna" class="accordion-collapse collapse"
aria-labelledby="train-headingSettingsFastdna"
data-bs-parent="#accordionTrain">
<div class="accordion-body">
<div class="glass p-5 mb-4 rounded-3">
<div class="container-fluid">
<div class="d-flex align-content-between flex-wrap flex-column">
<p class="flavor-7 mt-auto col-md-8 fs-6"> Settings related
to fastDNA</p>
</div>
<div class="d-flex">
<h3 class="flavor-5">Threads</h3>
<button class="btn-icon" type="button"
data-bs-toggle="collapse"
data-bs-target="#train-threadsInfo"
aria-expanded="false" aria-controls="train-threadsInfo">
<i class="bi bi-info-circle-fill btn btn-icon info-icon"></i>
</button>
</div>
<div class="collapse mb-3" id="train-threadsInfo">
<div class="glass-card flavor-visibility card card-body">
Number of processor threads to be used by phastDNA.
</div>
</div>
<div class="row g-3">
<div class="col-sm">
<h4 id="train-threads-num" class="flavor-5">4</h4>
</div>
<div class="col-sm-11 pt-1">
<input type="range" class="slider" min="1" max="5"
step="1" id="train-fastdna-threads" name="--threads">
</div>
</div>
</div>
</div>
</div>
</div>
</div> -->
<div class="accordion-item">
<h2 class="accordion-header" id="train-headingSettingsTraining">
<button class="accordion-button collapsed d-inline-flex justify-content-start flex-wrap" type="button"
data-bs-toggle="collapse"
data-bs-target="#train-collapseSettingsTraining" aria-expanded="false"
aria-controls="train-collapseSettingsTraining">
<div class="d-flex">
Hyperparameter settings
</div>
<div class="d-flex flavor-active align-self-center accordion-button-desc mx-3 fs-5">
| Settings related to the training and optimisation.
</div>
</button>
</h2>
<div id="train-collapseSettingsTraining" class="accordion-collapse collapse"
aria-labelledby="train-headingSettingsTraining"
data-bs-parent="#accordionTrain">
<div class="accordion-body">
<div class="glass p-5 mb-4 rounded-3">
<!-- style="background-image:linear-gradient(
rgba(0, 0, 0, 0.35),
rgba(0, 0, 0, 0.35));
background-position: center;
background-size: cover;"> -->
<!-- <form action="/" method="post" class="was-validated"> -->
<!-- <button type="submit" class="btn btn-primary">Post</button> -->
<div class="container-fluid">
<!-- <div class="d-flex align-content-between flex-wrap flex-column">
<p class="flavor-7 mt-auto col-md-8 fs-6">Settings related
to the training process of the fastDNA classifier.</p>
</div> -->
<div
class="d-flex justify-content-between flex-wrap mb-3 flex-column">
<!-- <div class="d-flex mb-3"> -->
<div class="d-flex justify-content-between">
<div class="d-flex">
<h3 class="flavor-5">Word vector size</h3>
<button class="btn-icon" type="button"
data-bs-toggle="collapse"
data-bs-target="#train-dimInfo"
aria-expanded="false" aria-controls="train-dimInfo">
<i class="bi bi-info-circle-fill btn btn-icon info-icon"></i>
</button>
</div>
<div class="d-flex fs-5" id="train-training-dim-opt" style="visibility: hidden;" data-bs-toggle="popover" data-bs-placement="top" data-bs-content="This setting will be optimised." data-bs-trigger="hover">
<!-- <p class="flavor-7 fs-6 mx-3">Subject to optimisation</p> -->
<i class="bi bi-wrench-adjustable-circle-fill opt-icon"></i>
</div>
</div>
<div class="collapse mb-3 flex-grow-1" id="train-dimInfo">
<div class="glass-card flavor-visibility card card-body">
Dimensionality (size) of k-mer embedding.
<div class="alert alert-warning d-flex align-items-center mt-3"
role="alert">
<i
class="bi bi-exclamation-triangle-fill flex-shrink-0 me-2"></i>
<div>
The higher dimensionality, the more time the
embedding will take.
</div>
</div>
</div>
</div>
<!-- <input type="checkbox" id="rangeCheckbox">
<label for="rangeCheckbox">Specify a range of dimensionality</label>
<div id="rangeInput" style="display: none;">
<label for="minDimInput">Minimum Dimensionality:</label>
<input type="number" id="minDimInput" class="form-control" min="1" name="--dim" required>
<label for="maxDimInput">Maximum Dimensionality:</label>
<input type="number" id="maxDimInput" class="form-control" min="1" name="--dim" required>
</div> -->
<!-- <input type="number" value="100" min="1"
class="form-control" id="train-training-dim"
aria-describedby="emailHelp" name="--dim" required> -->
<div class="d-flex justify-content-around flex-wrap flex-row">
<div class="d-flex flex-column flex-fill mx-3">
<label for="train-training-dim-lower" class="flavor-5">Lower bound</label>
<input type="number" value="100" min="1" class="form-control lower-bound-input" id="train-training-dim-lower" name="--dim-lower" required>
</div>
<div class="d-flex flex-column flex-fill mx-3">
<label for="train-training-dim-upper" class="flavor-5">Upper bound</label>
<input type="number" value="100" min="1" class="form-control upper-bound-input" id="train-training-dim-upper" name="--dim-upper" required>
</div>
</div>
<div class="invalid-feedback">Please fill out this field
with a positive value.</div>
</div>
<div
class="d-flex justify-content-between flex-wrap mb-3 flex-column">
<!-- <div class="d-flex mb-3"> -->
<div class="d-flex justify-content-between">
<div class="d-flex">
<h3 class="flavor-5">Minimum k-mer size</h3>
<button class="btn-icon" type="button"
data-bs-toggle="collapse"
data-bs-target="#train-minnInfo"
aria-expanded="false"
aria-controls="train-minnInfo">
<i class="bi bi-info-circle-fill btn btn-icon info-icon"></i>
</button>
</div>
<div class="d-flex fs-5" id="train-training-minn-opt" style="visibility: hidden;" data-bs-toggle="popover" data-bs-placement="top" data-bs-content="This setting will be optimised." data-bs-trigger="hover">
<!-- <p class="flavor-7 fs-6 mx-3">Subject to optimisation</p> -->
<i class="bi bi-wrench-adjustable-circle-fill opt-icon"></i>
</div>
</div>
<div class="collapse mb-3 flex-grow-1" id="train-minnInfo">
<div class="glass-card flavor-visibility card card-body">
Minimum k-mer size that is used to create n-grams.
<div class="alert alert-warning d-flex align-items-center mt-3"
role="alert">
<i
class="bi bi-exclamation-triangle-fill flex-shrink-0 me-2"></i>
<div>
The longer k-mers, the more memory will be
used.
</div>
</div>
</div>
</div>
<div class="d-flex justify-content-between flex-wrap flex-row">
<!-- <div class="d-flex"> -->
<!-- <div class="d-flex flex-column"> -->
<!-- <div class="col-sm-2"> -->
<!-- <h4 id="minn-num" class="flavor-5">7</h4> -->
<!-- </div> -->
<!-- <div class="d-flex flex-column flex-grow-1 me-auto"> -->
<!-- <div class="d-flex"> -->
<!-- <div class="col-sm-10 pt-1"> -->
<div class="container-sm mb-1">
<!-- <div class="d-flex flex-column flex-fill"> -->
<!-- <input id="ex2" type="text" class="span2" value="" data-slider-min="10" data-slider-max="1000" data-slider-step="5" data-slider-value="[250,450]"/> -->
<label for="train-training-minn-lower" class="flavor-5 fs-4" id="minn-num">7</label>
<div class="range-slider">
<input type="range" value="7" min="1" max="15"
step="1" class="slider"
id="train-training-minn-lower"
aria-describedby="emailHelp" name="--minn-lower"
required>
<input type="range" value="7" min="1" max="15"
step="1" class="slider"
id="train-training-minn-upper"
aria-describedby="emailHelp" name="--minn-upper"
required>
</div>
</div>
<!-- </div> -->
<!-- </div> -->
</div>
</div>
<div
class="d-flex justify-content-between flex-wrap mb-3 flex-column">
<!-- <div class="d-flex mb-3"> -->
<div class="d-flex justify-content-between">
<div class="d-flex">
<h3 class="flavor-5">Maximum k-mer size</h3>
<button class="btn-icon" type="button"
data-bs-toggle="collapse"
data-bs-target="#train-maxnInfo"
aria-expanded="false"
aria-controls="train-maxnInfo">
<i class="bi bi-info-circle-fill btn btn-icon info-icon"></i>
</button>
</div>
<div class="d-flex fs-5" id="train-training-maxn-opt" style="visibility: hidden;" data-bs-toggle="popover" data-bs-placement="top" data-bs-content="This setting will be optimised." data-bs-trigger="hover">
<!-- <p class="flavor-7 fs-6 mx-3">Subject to optimisation</p> -->
<i class="bi bi-wrench-adjustable-circle-fill opt-icon"></i>
</div>
</div>
<div class="collapse mb-3 flex-grow-1" id="train-maxnInfo">
<div class="glass-card flavor-visibility card card-body">
Maximum k-mer size that is used to create n-grams.
<div class="alert alert-warning d-flex align-items-center mt-3"
role="alert">
<i
class="bi bi-exclamation-triangle-fill flex-shrink-0 me-2"></i>
<div>
The longer k-mers, the more memory will be
used.
</div>
</div>
</div>
</div>
<div class="d-flex justify-content-between flex-wrap flex-row">
<!-- <div class="row g-3"> -->
<!-- <div class="col-sm">
<h4 id="maxn-num" class="flavor-5">8</h4>
</div> -->
<!-- <div class="col-sm-11 pt-1"> -->
<div class="container-sm mb-1">
<label for="train-training-maxn-lower" class="flavor-5 fs-4" id="maxn-num">8</label>
<div class="range-slider">
<input type="range" value="8" min="1" max="15"
step="1" class="slider"
id="train-training-maxn-lower"
aria-describedby="emailHelp" name="--maxn-lower"
required>
<input type="range" value="8" min="1" max="15"
step="1" class="slider"
id="train-training-maxn-upper"
aria-describedby="emailHelp" name="--maxn-upper"
required>
</div>
</div>
<!-- </div> -->
</div>
</div>
<div
class="d-flex justify-content-between flex-wrap mb-3 flex-column">
<!-- <div class="d-flex mb-3"> -->
<div class="d-flex justify-content-between">
<div class="d-flex">
<h3 class="flavor-5">Read length</h3>
<button class="btn-icon" type="button"
data-bs-toggle="collapse"
data-bs-target="#train-readlenInfo"
aria-expanded="false"
aria-controls="train-readlenInfo">
<i class="bi bi-info-circle-fill btn btn-icon info-icon"></i>
</button>
</div>
<div class="d-flex fs-5" id="train-training-readlen-opt" style="visibility: hidden;" data-bs-toggle="popover" data-bs-placement="top" data-bs-content="This setting will be optimised." data-bs-trigger="hover">
<!-- <p class="flavor-7 fs-6 mx-3">Subject to optimisation</p> -->
<i class="bi bi-wrench-adjustable-circle-fill opt-icon"></i>
</div>
</div>
<div class="collapse mb-3 flex-grow-1"
id="train-readlenInfo">
<div class="glass-card flavor-visibility card card-body">
Length of sampled reads from sequences.
</div>
</div>
<!-- <input type="number" value="200" min="1"
class="form-control" id="train-training-readlen"
aria-describedby="emailHelp" name="--fraglen" required> -->
<div class="d-flex justify-content-around flex-wrap flex-row">
<div class="d-flex flex-column flex-fill mx-3">
<label for="train-training-dim-lower" class="flavor-5">Lower bound</label>
<input type="number" value="200" min="1" class="form-control lower-bound-input" id="train-training-readlen-lower" name="--fraglen-lower" required>
</div>
<div class="d-flex flex-column flex-fill mx-3">
<label for="train-training-dim-upper" class="flavor-5">Upper bound</label>
<input type="number" value="200" min="1" class="form-control upper-bound-input" id="train-training-readlen-upper" name="--fraglen-upper" required>
</div>
</div>
<div class="invalid-feedback">Please fill out this field
with a positive value.</div>
</div>
<div
class="d-flex justify-content-between flex-wrap mb-3 flex-column">
<!-- <div class="d-flex mb-3"> -->
<div class="d-flex justify-content-between">
<div class="d-flex">
<h3 class="flavor-5">Read samples number</h3>
<button class="btn-icon" type="button"
data-bs-toggle="collapse"
data-bs-target="#train-readnumInfo"
aria-expanded="false"
aria-controls="train-readnumInfo">
<i class="bi bi-info-circle-fill btn btn-icon info-icon"></i>
</button>
</div>
<div class="d-flex fs-5" id="train-training-readnum-opt" style="visibility: hidden;" data-bs-toggle="popover" data-bs-placement="top" data-bs-content="This setting will be optimised." data-bs-trigger="hover">
<!-- <p class="flavor-7 fs-6 mx-3">Subject to optimisation</p> -->
<i class="bi bi-wrench-adjustable-circle-fill opt-icon"></i>
</div>
</div>
<div class="collapse mb-3 flex-grow-1"
id="train-readnumInfo">
<div class="glass-card flavor-visibility card card-body">
Number of sampled reads from sequences.
<div class="alert alert-warning d-flex align-items-center mt-3"
role="alert">
<i
class="bi bi-exclamation-triangle-fill flex-shrink-0 me-2"></i>
<div>
The more samples, the more time the overall
training will take.
</div>
</div>
</div>
</div>
<div class="d-flex justify-content-around flex-wrap flex-row">
<div class="d-flex flex-column flex-fill mx-3">
<label for="train-training-readnum-lower" class="flavor-5">Lower bound</label>
<input type="number" value="100" min="1"
class="form-control lower-bound-input" id="train-training-readnum-lower"
aria-describedby="emailHelp" name="--samples-lower" required>
</div>
<div class="d-flex flex-column flex-fill mx-3">
<label for="train-training-readnum-upper" class="flavor-5">Upper bound</label>
<input type="number" value="100" min="1"
class="form-control upper-bound-input" id="train-training-readnum-upper"
aria-describedby="emailHelp" name="--samples-upper" required>
</div>
</div>
<div class="invalid-feedback">Please fill out this field
with a positive value.</div>
</div>
<div
class="d-flex justify-content-between flex-wrap mb-3 flex-column">
<!-- <div class="d-flex mb-3"> -->
<div class="d-flex justify-content-between">
<div class="d-flex">
<h3 class="flavor-5">Learning rate</h3>
<button class="btn-icon" type="button"
data-bs-toggle="collapse"
data-bs-target="#train-lrInfo" aria-expanded="false"
aria-controls="train-lrInfo">
<i class="bi bi-info-circle-fill btn btn-icon info-icon"></i>
</button>
</div>
<div class="d-flex fs-5" id="train-training-lr-opt" style="visibility: hidden;" data-bs-toggle="popover" data-bs-placement="top" data-bs-content="This setting will be optimised." data-bs-trigger="hover">
<!-- <p class="flavor-7 fs-6 mx-3">Subject to optimisation</p> -->
<i class="bi bi-wrench-adjustable-circle-fill opt-icon"></i>
</div>
</div>
<div class="collapse mb-3 flex-grow-1" id="train-lrInfo">
<div class="glass-card flavor-visibility card card-body">
Training learning rate.
</div>
</div>
<div class="d-flex justify-content-around flex-wrap flex-row">
<div class="d-flex flex-column flex-fill mx-3">
<label for="train-training-lr-lower" class="flavor-5">Lower bound</label>
<input type="number" value="0.1" min="0" max="1"
step="0.000001" class="form-control lower-bound-input"
id="train-training-lr-lower" aria-describedby="emailHelp"
name="--lrate-lower" required>
</div>
<div class="d-flex flex-column flex-fill mx-3">
<label for="train-training-lr-upper" class="flavor-5">Upper bound</label>
<input type="number" value="0.1" min="0" max="1"
step="0.000001" class="form-control upper-bound-input"
id="train-training-lr-upper" aria-describedby="emailHelp"
name="--lrate-upper" required>
</div>
</div>
<div class="invalid-feedback">Please fill out this field
with value between 0 and 1.</div>
</div>
<div
class="d-flex justify-content-between flex-wrap mb-3 flex-column">
<!-- <div class="d-flex mb-3"> -->
<div class="d-flex justify-content-between">
<div class="d-flex">
<h3 class="flavor-5">Learning rate update rate</h3>
<button class="btn-icon" type="button"
data-bs-toggle="collapse"
data-bs-target="#train-ulrInfo"
aria-expanded="false" aria-controls="train-ulrInfo">
<i class="bi bi-info-circle-fill btn btn-icon info-icon"></i>
</button>
</div>
<div class="d-flex fs-5" id="train-training-ulr-opt" style="visibility: hidden;" data-bs-toggle="popover" data-bs-placement="top" data-bs-content="This setting will be optimised." data-bs-trigger="hover">
<!-- <p class="flavor-7 fs-6 mx-3">Subject to optimisation</p> -->
<i class="bi bi-wrench-adjustable-circle-fill opt-icon"></i>
</div>
</div>
<div class="collapse mb-3 flex-grow-1" id="train-ulrInfo">
<div class="glass-card flavor-visibility card card-body">
Update dynamics of the the learning rate.
</div>
</div>
<div class="d-flex justify-content-around flex-wrap flex-row">
<div class="d-flex flex-column flex-fill mx-3">
<label for="train-training-ulr-lower" class="flavor-5">Lower bound</label>
<input type="number" value="100" min="0"
class="form-control lower-bound-input" id="train-training-ulr-lower"
aria-describedby="emailHelp" name="--ulr-lower" required>
</div>
<div class="d-flex flex-column flex-fill mx-3">
<label for="train-training-ulr-upper" class="flavor-5">Upper bound</label>
<input type="number" value="100" min="0"
class="form-control upper-bound-input" id="train-training-ulr-upper"
aria-describedby="emailHelp" name="--ulr-upper" required>
</div>
</div>
<div class="invalid-feedback">Please fill out this field
with a not negative value.</div>
</div>
<div
class="d-flex justify-content-between flex-wrap mb-3 flex-column">
<!-- <div class="d-flex mb-3"> -->
<div class="d-flex justify-content-between">
<div class="d-flex">
<h3 class="flavor-5">Epochs number</h3>
<button class="btn-icon" type="button"
data-bs-toggle="collapse"
data-bs-target="#train-epochInfo"
aria-expanded="false"
aria-controls="train-epochInfo">
<i class="bi bi-info-circle-fill btn btn-icon info-icon"></i>
</button>
</div>
<div class="d-flex fs-5" id="train-training-epoch-opt" style="visibility: hidden;" data-bs-toggle="popover" data-bs-placement="top" data-bs-content="This setting will be optimised." data-bs-trigger="hover">
<!-- <p class="flavor-7 fs-6 mx-3">Subject to optimisation</p> -->
<i class="bi bi-wrench-adjustable-circle-fill opt-icon"></i>
</div>
</div>
<div class="collapse mb-3 flex-grow-1" id="train-epochInfo">
<div class="glass-card flavor-visibility card card-body">
Number of epochs - how many times the trained model
will be presented with each word.
<div class="alert alert-warning d-flex align-items-center mt-3"
role="alert">
<i
class="bi bi-exclamation-triangle-fill flex-shrink-0 me-2"></i>
<div>
The more epochs, the significantly more time
the overall training will take.
</div>
</div>
</div>
</div>
<div class="d-flex justify-content-around flex-wrap flex-row">
<div class="d-flex flex-column flex-fill mx-3">
<label for="train-training-epoch-lower" class="flavor-5">Lower bound</label>
<input type="number" value="20" min="1" class="form-control lower-bound-input"
id="train-training-epoch-lower" aria-describedby="emailHelp"
name="--epochs-lower" required>
</div>
<div class="d-flex flex-column flex-fill mx-3">
<label for="train-training-epoch-upper" class="flavor-5">Upper bound</label>
<input type="number" value="20" min="1" class="form-control upper-bound-input"
id="train-training-epoch-upper" aria-describedby="emailHelp"
name="--epochs-upper" required>
</div>
</div>
<div class="invalid-feedback">Please fill out this field
with a positive value.</div>
</div>
<div
class="d-flex justify-content-between flex-wrap mb-3 flex-column">
<!-- <div class="d-flex mb-3"> -->