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Formalize system of using 'none' in bedFile to fix left and right buttons without BED #402

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merged 1 commit into from
Mar 13, 2024
Merged

Formalize system of using 'none' in bedFile to fix left and right buttons without BED #402

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40 changes: 24 additions & 16 deletions src/components/HeaderForm.js
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Original file line number Diff line number Diff line change
Expand Up @@ -68,6 +68,8 @@ const CLEAR_STATE = {
pathNames: [],

tracks: {},
// BED file of regions to jump between. Regions may have pre-extracted chunks in the last column.
// If not used, may be undefined or may have the sting value "none".
bedFile: undefined,
region: "",
name: undefined,
Expand All @@ -94,6 +96,12 @@ const EMPTY_STATE = {
bedSelectOptions: [],
};

// Return true if file is set to a string file name or URL, and false if it is
// falsey or the "none" sentinel.
function isSet(file) {
return (file !== "none" && file);
}

// Creates track to be stored in ViewTarget
// Modify as the track system changes
// INPUT: file structure, see Types.ts
Expand Down Expand Up @@ -289,7 +297,7 @@ class HeaderForm extends Component {
initState = () => {
// Populate state with either viewTarget or the first example
let ds = this.props.defaultViewTarget ?? DATA_SOURCES[0];
const bedSelect = ds.bedFile ? ds.bedFile : "none";
const bedSelect = isSet(ds.bedFile) ? ds.bedFile : "none";
if (bedSelect !== "none") {
this.getBedRegions(bedSelect);
}
Expand Down Expand Up @@ -317,7 +325,7 @@ class HeaderForm extends Component {
setTrackFile = (type, index, file) => {
// Set the nth track of the given type to the given file.
// If there is no nth track of that type, create one.
// If the file is "none", remove that track.
// If the file is unset, remove that track.
this.setState((state) => {
console.log(
"Set file " +
Expand All @@ -340,13 +348,13 @@ class HeaderForm extends Component {
let track = state.tracks[key];
if (track.trackType === type) {
if (seenTracksOfType === index) {
if (file !== "none") {
if (isSet(file)) {
// We want to adjust it, so keep a modified copy of it
let newTrack = JSON.parse(JSON.stringify(track));
newTrack.trackFile = file;
newTracks[key] = newTrack;
}
// If the file is "none" we drop the track.
// If the file is unset we drop the track.
} else {
// We want to keep it as is
newTracks[key] = track;
Expand All @@ -364,7 +372,7 @@ class HeaderForm extends Component {
console.log(
"Saw " + seenTracksOfType + " tracks of type vs index " + index
);
if (seenTracksOfType === index && file !== "none") {
if (seenTracksOfType === index && isSet(file)) {
// We need to add this track
console.log("Create track at index " + (maxKey + 1));
newTracks[maxKey + 1] = createTrack({ type: type, name: file });
Expand All @@ -379,8 +387,8 @@ class HeaderForm extends Component {
};

getTrackFile = (tracks, type, index) => {
// Get the file used in the nth track of the gicen type, or "none" if no
// such track exists.
// Get the file used in the nth track of the given type, or the unset
// "none" sentinel if no such track exists.
let seenTracksOfType = 0;
for (const key in tracks) {
let track = tracks[key];
Expand Down Expand Up @@ -416,7 +424,7 @@ class HeaderForm extends Component {
const bedSelect = json.bedFiles.includes(state.bedSelect)
? state.bedSelect
: "none";
if (bedSelect !== "none") {
if (isSet(bedSelect)) {
this.getBedRegions(bedSelect);
}
for (const key in state.tracks) {
Expand Down Expand Up @@ -515,7 +523,7 @@ class HeaderForm extends Component {
DATA_SOURCES.forEach((ds) => {
if (ds.name === value) {
let bedSelect = "none";
if (ds.bedFile) {
if (isSet(ds.bedFile)) {
this.getBedRegions(ds.bedFile);
bedSelect = ds.bedFile;
} else {
Expand Down Expand Up @@ -648,7 +656,7 @@ class HeaderForm extends Component {
if (tracks) {
this.setState({ tracks: this.convertArrayToObject(tracks) });
console.log("New tracks have been applied");
} else if (this.state.bedFile && chunk) {
} else if (isSet(this.state.bedFile) && chunk) {
// Try to retrieve tracks from the server
const json = await this.api.getChunkTracks(
this.state.bedFile,
Expand Down Expand Up @@ -681,7 +689,7 @@ class HeaderForm extends Component {

// update path names
const graphFile = this.getTrackFile(newTracks, fileTypes.GRAPH, 0);
if (graphFile && graphFile !== "none") {
if (isSet(graphFile)) {
this.getPathNames(graphFile);
}
};
Expand All @@ -691,7 +699,7 @@ class HeaderForm extends Component {
const value = event.target.value;
this.setState({ [id]: value });

if (value !== "none") {
if (isSet(value)) {
this.getBedRegions(value);
}
this.setState({ bedFile: value });
Expand Down Expand Up @@ -737,15 +745,15 @@ class HeaderForm extends Component {
}

canGoLeft = (regionIndex) => {
if (this.state.bedFile){
if (isSet(this.state.bedFile)){
return (regionIndex > 0);
} else {
return true;
}
}

canGoRight = (regionIndex) => {
if (this.state.bedFile){
if (isSet(this.state.bedFile)){
if (!this.state.regionInfo["chr"]){
return false;
}
Expand All @@ -757,15 +765,15 @@ class HeaderForm extends Component {


handleGoRight = () => {
if (this.state.bedFile){
if (isSet(this.state.bedFile)){
this.jumpRegion(1);
} else {
this.budgeRegion(0.5);
}
};

handleGoLeft = () => {
if (this.state.bedFile){
if (isSet(this.state.bedFile)){
this.jumpRegion(-1);
} else {
this.budgeRegion(-0.5);
Expand Down
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