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feat: update vanilla mode navigation and support highlight SV from clinical panel #155

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feat: update vanilla mode navigation and support highlight SV from clinical panel #155

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7ce301a
-feat: add navigation buttons
crfmc Jan 30, 2025
0ee0058
style: update thumbnail generation styles
crfmc Jan 30, 2025
8deace7
-feat: placeholder for getting started guide
crfmc Feb 13, 2025
69025ee
-feat: update instructions modal with getting started and other views
crfmc Mar 11, 2025
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21 changes: 15 additions & 6 deletions src/App.tsx
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Original file line number Diff line number Diff line change
Expand Up @@ -29,6 +29,7 @@ import { VariantViewModal } from './ui/VariantViewModal';
import { NavigationButtons } from './ui/NavigationButtons';
import { Track, getTrackDocData } from './ui/getTrackDocData.js';
import { NavigationBar } from './ui/NavigationBar';
import { InstructionsModal } from './ui/InstructionsModal';
import { ClinicalPanel } from './ui/ClinicalPanel';

import 'bootstrap/dist/css/bootstrap.min.css';
Expand Down Expand Up @@ -65,7 +66,7 @@ function App(props: RouteComponentProps) {
top: isMinimalMode ? 0 : 60,
right: isMinimalMode ? 0 : 60,
bottom: isMinimalMode ? 0 : 60,
left: isMinimalMode ? 0 : 60
left: isMinimalMode ? 0 : 100
};

// !! instead of using `urlParams.get('external')`, we directly parse the external URL in order to include
Expand Down Expand Up @@ -614,6 +615,7 @@ function App(props: RouteComponentProps) {
return (
<a
key={i}
id={`track-tooltip-${d.type}`}
tabIndex={showSamples ? -1 : 0}
role="button"
className="track-tooltip"
Expand Down Expand Up @@ -993,7 +995,7 @@ function App(props: RouteComponentProps) {
{!isMinimalMode && (
<div
style={{
width: '100%',
width: `calc(100% - ${0}px)`,
height: '100%',
boxShadow: `inset 0 0 0 3px ${
interactiveMode && mouseOnVis
Expand All @@ -1012,7 +1014,7 @@ function App(props: RouteComponentProps) {
}}
/>
)}
<NavigationButtons showSamples={!isMinimalMode && showSamples} isMinimalMode={isMinimalMode} />
<NavigationButtons isMinimalMode={isMinimalMode} selectedSvId={selectedSvId} />
{
// External links and export buttons
isMinimalMode ? (
Expand Down Expand Up @@ -1489,9 +1491,15 @@ function App(props: RouteComponentProps) {
</svg>
</button>
<div id="hidden-gosling" style={{ visibility: 'collapse', position: 'fixed' }} />
<div className="instructions-modals-container">
<GenomeViewModal />
<VariantViewModal />
<div className={`instructions-modals-container ${isMinimalMode ? 'minimal' : 'vanilla'}`}>
{isMinimalMode ? (
<>
<GenomeViewModal />
<VariantViewModal />
</>
) : (
<InstructionsModal />
)}
</div>
{!isMinimalMode && !!demo?.clinicalInfo && (
<ClinicalPanel
Expand All @@ -1502,6 +1510,7 @@ function App(props: RouteComponentProps) {
isClinicalPanelOpen={isClinicalPanelOpen}
setIsClinicalPanelOpen={setIsClinicalPanelOpen}
setInteractiveMode={setInteractiveMode}
setSelectedSvId={setSelectedSvId}
/>
)}
</div>
Expand Down
264 changes: 158 additions & 106 deletions src/css/App.css
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Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
/* Import component-level CSS files */
@import url('./NavigationBar.css');
@import url('./ClinicalPanel.css');
@import url('./InstructionsModal.css');

/* Overwrite Bootstrap's default box-sizing */
*,
Expand Down Expand Up @@ -548,11 +549,16 @@ a:hover {
}

.thumbnail-generate-button {
margin-left: 400px;
line-height: 30px;
border-radius: 0px;
border: 1px solid grey;
border: 1px solid lightgray;
background-color: transparent;
cursor: pointer;
border-radius: 4px;
font-size: 1rem;
}
.thumbnail-generate-button:hover {
background-color: #eaeaea;
}

.thumbnail-loading-message {
Expand Down Expand Up @@ -833,6 +839,155 @@ a:hover {
outline-offset: 2px;
}

/* Styles for the navigation panel */

.navigation-panel {
position: fixed;
z-index: 998;
display: flex;
flex-direction: column;
top: 60px;
left: 0px;
width: 100px;
height: min-content;
padding: 20px 10px;
box-sizing: border-box !important;

.navigation-buttons {
position: relative;
display: flex;
flex-direction: column;
left: 0px;
top: 0px;
background-color: #ffffff;
border: 1px solid #e5e5e5;
border-radius: 10px;
padding: 4px 4px;
gap: 15px;
box-shadow: -1px 1px 4px 1px #e5e5e5;

.active-backdrop {
background-color: #e4eeff;
width: 70px;
height: 70px;
border-radius: 8px;
position: absolute;
transition: top 100ms linear;
z-index: -1;
}
.active-backdrop.genome {
top: 5px;
}
.active-backdrop.variant {
top: 90px;
}
.active-backdrop.read {
top: 174px;
}

.navigation-button-container {
display: flex;
margin: auto;

.navigation-button {
margin: auto;
width: 70px;
height: 70px;
border-radius: 8px;
border: 1px solid;
padding: 5px 0px;
background-color: transparent;
border: none;

.navigation-button-content {
display: flex;
flex-direction: column;
color: #5e5e5e;
justify-content: center;
font-size: 0.875rem;

.section-icon {
margin: auto;
width: 30px;
}
}
}
.navigation-button:hover {
background-color: #f8f8f8;
transition: background-color 50ms ease-out;
.navigation-button-content {
font-weight: 500;
color: #5e5e5e;
}
}
.navigation-button:active {
background-color: #f4f4f4;
}
.navigation-button.active {
.navigation-button-content {
font-weight: 500;
color: #5286c9;
/* transition-delay: 250ms; */
/* transition-property: color; */
transition: color 50ms ease-out;
}
}
.navigation-button.active:hover {
background-color: transparent;
}
.navigation-button:disabled {
.navigation-button-content {
color: #c3c3c3;
}
}
.navigation-button:disabled:hover {
background-color: #ffffff;
}
}
}

.help-button-container {
padding: 20px 5px;
display: flex;
justify-content: center;

.help-button {
background-color: white;
border: 1px solid #5e5e5e;
border-radius: 100%;
height: 20px;
width: 20px;
display: flex;
justify-content: center;
padding: 5px;
box-shadow: -1px 1px 4px 1px #5e5e5e33;

.help-button-icon {
width: 15px;
height: 15px;
margin: auto;

path {
fill: #5e5e5e;
}
}
}
.help-button:hover {
background-color: #5e5e5e;
transition: background-color 150ms ease-out, box-shadow 150ms ease-out;
.help-button-icon {
path {
fill: white;
transition: fill 150ms ease-out;
}
}
}
.help-button:active {
box-shadow: none;
}
}
}

.navigation-buttons {
box-sizing: border-box;
position: fixed;
Expand Down Expand Up @@ -903,6 +1058,7 @@ a:hover {
.gosling-panel {
overflow-y: scroll;
overflow-x: hidden;
padding: 60px 300px 60px 100px;
}

.sample-label {
Expand Down Expand Up @@ -974,8 +1130,6 @@ a:hover {

.open-in-chromoscope-link:hover {
text-decoration: none;
cursor: pointer;
background-color: #ebebeb;
}

.open-in-chromoscope-link:active {
Expand Down Expand Up @@ -1145,108 +1299,6 @@ a:hover {
}
}

.instructions-modals-container {
.modal {
.modal-dialog {
width: 100%;
}
.modal-body {
box-sizing: border-box !important;
max-height: 80vh;
overflow-y: scroll;
display: flex;
justify-content: start;
padding: 24px 36px;
width: 100%;

.modal-body-content {
display: flex;
flex-direction: column;
width: 100%;
}
.section {
display: flex;
flex-direction: column;
/* margin-bottom: 20px; */

.section-content {
padding: 0px 55px;
}

h3 {
font-size: 1.25rem;
font-weight: 600;
margin-bottom: 4px;
}

hr {
color: #cdcdcd;
border-width: 1px;
margin: 0px;
}
hr.header {
color: #b0b0b0;
border-width: 2px;
}

.block {
flex: 1;
display: flex;
margin: 32px 0px;
min-height: 120px;
}
.block.with-image {
justify-content: center;
height: auto;

.image-container.two-image {
display: flex;
flex-direction: column;
}

img {
width: 250px;
height: fit-content;
margin: auto 0px;
border: 2px solid #ebebeb;
object-fit: contain;
}

.text {
display: flex;
width: 300px;
flex-direction: column;
justify-content: space-evenly;
margin-left: 60px;

p {
margin-bottom: 0px;

span.text-button-example {
display: inline-flex;
justify-content: center;
background-color: #efefef;
width: 25px;
height: 25px;
border-radius: 10px 0px 0px 10px;
border: 2px solid lightgray;

b {
line-height: 20px;
margin: auto auto 5px;
}
}
span.text-button-example.right {
border-radius: 0px 10px 10px 0px;
}
}
}
}
}
}
}
}

.popover.track-tooltip-popover {
max-width: none;
box-shadow: 0px 0px 10px 0px #22252954;
Expand Down
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