Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Provide a dialog to add extra genomic context for linear read vs. ref visualization #1560

Merged
merged 3 commits into from
Jan 8, 2021
Merged

Provide a dialog to add extra genomic context for linear read vs. ref visualization #1560

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
f7cbeab
Provide genomic context for linear vs. ref
elliothershberg Dec 14, 2020
1b6c40c
Add window size dialog
cmdcolin Jan 8, 2021
8e10f28
Add explainer and form to increase window size
cmdcolin Jan 8, 2021
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
65 changes: 30 additions & 35 deletions plugins/alignments/src/LinearPileupDisplay/components/ColorByTag.tsx
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -55,41 +55,36 @@ export default function ColorByTagDlg(props: {
for minimap2 read strand, HP for haplotype, RG for read group, etc.
</Typography>

<form>
<TextField
value={tag}
onChange={event => {
setTag(event.target.value)
}}
placeholder="Enter tag name"
inputProps={{
maxLength: 2,
'data-testid': 'color-tag-name-input',
}}
error={tag.length === 2 && !validTag}
helperText={
tag.length === 2 && !validTag ? 'Not a valid tag' : ''
}
autoComplete="off"
data-testid="color-tag-name"
/>
<Button
variant="contained"
color="primary"
type="submit"
style={{ marginLeft: 20 }}
onClick={() => {
display.setColorScheme({
type: 'tag',
tag,
})
handleClose()
}}
disabled={!validTag}
>
Submit
</Button>
</form>
<TextField
value={tag}
onChange={event => {
setTag(event.target.value)
}}
placeholder="Enter tag name"
inputProps={{
maxLength: 2,
'data-testid': 'color-tag-name-input',
}}
error={tag.length === 2 && !validTag}
helperText={tag.length === 2 && !validTag ? 'Not a valid tag' : ''}
autoComplete="off"
data-testid="color-tag-name"
/>
<Button
variant="contained"
color="primary"
style={{ marginLeft: 20 }}
onClick={() => {
display.setColorScheme({
type: 'tag',
tag,
})
handleClose()
}}
disabled={!validTag}
>
Submit
</Button>
</div>
</DialogContent>
</Dialog>
Expand Down
166 changes: 82 additions & 84 deletions plugins/alignments/src/LinearPileupDisplay/components/FilterByTag.tsx
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -128,92 +128,90 @@ export default observer(
for details
</Typography>
<div className={classes.root}>
<form>
<Paper className={classes.paper} variant="outlined">
<div style={{ display: 'flex' }}>
<div>
<Typography>Read must have ALL these flags</Typography>
<Bitmask flag={flagInclude} setFlag={setFlagInclude} />
</div>
<div>
<Typography>Read must have NONE of these flags</Typography>
<Bitmask flag={flagExclude} setFlag={setFlagExclude} />
</div>
<Paper className={classes.paper} variant="outlined">
<div style={{ display: 'flex' }}>
<div>
<Typography>Read must have ALL these flags</Typography>
<Bitmask flag={flagInclude} setFlag={setFlagInclude} />
</div>
</Paper>
<Paper className={classes.paper} variant="outlined">
<Typography>
Filter by tag name and value. Use * in the value field to get
all reads containing any value for that tag. Example: filter
tag name SA with value * to get all split/supplementary reads
</Typography>
<TextField
className={classes.field}
value={tag}
onChange={event => {
setTag(event.target.value)
}}
placeholder="Enter tag name"
inputProps={{
maxLength: 2,
'data-testid': 'color-tag-name-input',
}}
error={tag.length === 2 && !validTag}
helperText={
tag.length === 2 && !validTag ? 'Not a valid tag' : ''
}
data-testid="color-tag-name"
/>
<TextField
className={classes.field}
value={tagValue}
onChange={event => {
setTagValue(event.target.value)
}}
placeholder="Enter tag value"
inputProps={{
'data-testid': 'color-tag-name-input',
}}
data-testid="color-tag-value"
/>
</Paper>
<Paper className={classes.paper} variant="outlined">
<Typography>Filter by read name</Typography>
<TextField
className={classes.field}
value={readName}
onChange={event => {
setReadName(event.target.value)
}}
placeholder="Enter read name"
inputProps={{
'data-testid': 'color-tag-readname-input',
}}
data-testid="color-tag-readname"
/>
</Paper>
<Button
variant="contained"
color="primary"
onClick={() => {
display.setFilterBy({
flagInclude,
flagExclude,
readName,
tagFilter:
tag !== ''
? {
tag,
value: tagValue,
}
: undefined,
})
handleClose()
<div>
<Typography>Read must have NONE of these flags</Typography>
<Bitmask flag={flagExclude} setFlag={setFlagExclude} />
</div>
</div>
</Paper>
<Paper className={classes.paper} variant="outlined">
<Typography>
Filter by tag name and value. Use * in the value field to get
all reads containing any value for that tag. Example: filter tag
name SA with value * to get all split/supplementary reads
</Typography>
<TextField
className={classes.field}
value={tag}
onChange={event => {
setTag(event.target.value)
}}
placeholder="Enter tag name"
inputProps={{
maxLength: 2,
'data-testid': 'color-tag-name-input',
}}
error={tag.length === 2 && !validTag}
helperText={
tag.length === 2 && !validTag ? 'Not a valid tag' : ''
}
data-testid="color-tag-name"
/>
<TextField
className={classes.field}
value={tagValue}
onChange={event => {
setTagValue(event.target.value)
}}
>
Submit
</Button>
</form>
placeholder="Enter tag value"
inputProps={{
'data-testid': 'color-tag-name-input',
}}
data-testid="color-tag-value"
/>
</Paper>
<Paper className={classes.paper} variant="outlined">
<Typography>Filter by read name</Typography>
<TextField
className={classes.field}
value={readName}
onChange={event => {
setReadName(event.target.value)
}}
placeholder="Enter read name"
inputProps={{
'data-testid': 'color-tag-readname-input',
}}
data-testid="color-tag-readname"
/>
</Paper>
<Button
variant="contained"
color="primary"
onClick={() => {
display.setFilterBy({
flagInclude,
flagExclude,
readName,
tagFilter:
tag !== ''
? {
tag,
value: tagValue,
}
: undefined,
})
handleClose()
}}
>
Submit
</Button>
</div>
</DialogContent>
</Dialog>
Expand Down
54 changes: 25 additions & 29 deletions plugins/alignments/src/LinearPileupDisplay/components/SortByTag.tsx
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -50,35 +50,31 @@ export default function ColorByTagDlg(props: {
<DialogContent>
<div>
<Typography>Set the tag to sort by</Typography>
<form>
<TextField
value={tag}
onChange={event => {
setTag(event.target.value)
}}
placeholder="Enter tag name"
inputProps={{
maxLength: 2,
'data-testid': 'sort-tag-name-input',
}}
error={tag.length === 2 && !validTag}
helperText={
tag.length === 2 && !validTag ? 'Not a valid tag' : ''
}
autoComplete="off"
data-testid="sort-tag-name"
/>
<Button
variant="contained"
color="primary"
onClick={() => {
display.setSortedBy('tag', tag)
handleClose()
}}
>
Submit
</Button>
</form>
<TextField
value={tag}
onChange={event => {
setTag(event.target.value)
}}
placeholder="Enter tag name"
inputProps={{
maxLength: 2,
'data-testid': 'sort-tag-name-input',
}}
error={tag.length === 2 && !validTag}
helperText={tag.length === 2 && !validTag ? 'Not a valid tag' : ''}
autoComplete="off"
data-testid="sort-tag-name"
/>
<Button
variant="contained"
color="primary"
onClick={() => {
display.setSortedBy('tag', tag)
handleClose()
}}
>
Submit
</Button>
</div>
</DialogContent>
</Dialog>
Expand Down
4 changes: 2 additions & 2 deletions plugins/linear-comparative-view/package.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -16,8 +16,8 @@
},
"author": "JBrowse Team",
"distMain": "dist/index.js",
"srcMain": "src/index.ts",
"main": "src/index.ts",
"srcMain": "src/index.tsx",
"main": "src/index.tsx",
"distModule": "dist/plugin-linear-comparative-view.esm.js",
"module": "",
"files": [
Expand Down
Loading