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updating mapAnnotationsToRows to handle overlapsSelf flag
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@tnrich
tnrich committed Aug 11, 2021
1 parent b85c918 commit 6e34bd6
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Showing 2 changed files with 145 additions and 67 deletions.
134 changes: 68 additions & 66 deletions src/mapAnnotationsToRows.js
View file
Original file line number Diff line number Diff line change
@@ -1,7 +1,10 @@
// const ac = require('ve-api-check');
// ac.throw([ac.string,ac.bool],arguments);
const {
each
each,
forEach,
startsWith,
filter
// some, sortBy, uniq
} = require("lodash");
// const areNonNegativeIntegers = require('validate.io-nonnegative-integer-array');
Expand All @@ -25,12 +28,35 @@ module.exports = function mapAnnotationsToRows(

const annotationsToRowsMap = {};
const yOffsetLevelMap = {};
const wrappedAnnotations = {};

each(annotations, function(annotation) {
const containsLocations = !!(
annotation.locations && annotation.locations.length
);
if (annotation.overlapsSelf) {
//if the annotation overlaps itself, first send a fake full spanning annotation thru the mapping function
if (!wrappedAnnotations[annotation.id]) {
mapAnnotationToRows({
wrappedAnnotations,
annotation: {
start: 0,
end: sequenceLength - 1,
id: `__tempAnnRemoveMe__${annotation.id}`
},
sequenceLength,
bpsPerRow,
annotationsToRowsMap,
yOffsetLevelMap,
containsLocations
});
wrappedAnnotations[annotation.id] = true;
// annotation.yOffset = wrappedAnnotations[annotation.id];
}
}

mapAnnotationToRows({
wrappedAnnotations,
annotation,
sequenceLength,
bpsPerRow,
Expand All @@ -41,6 +67,7 @@ module.exports = function mapAnnotationsToRows(
if (containsLocations) {
annotation.locations.forEach(location => {
mapAnnotationToRows({
wrappedAnnotations,
annotation,
sequenceLength,
bpsPerRow,
Expand All @@ -51,10 +78,17 @@ module.exports = function mapAnnotationsToRows(
});
}
});
forEach(annotationsToRowsMap, (annotationsForRow, i) => {
annotationsToRowsMap[i] = filter(
annotationsForRow,
ann => !startsWith(ann.id, "__tempAnnRemoveMe__")
);
});
return annotationsToRowsMap;
};

function mapAnnotationToRows({
wrappedAnnotations,
annotation,
sequenceLength,
bpsPerRow,
Expand Down Expand Up @@ -89,39 +123,46 @@ function mapAnnotationToRows({
rowNumber === endingRow
? range.end
: rowNumber * bpsPerRow + bpsPerRow - 1;

if (location) {
//if there's a location then we will just use the previous yOffset for its parent annotation
if (annotation.overlapsSelf) {
annotationsForRow.forEach(ann => {
if (ann.id === annotation.id) {
if (ann.id === `__tempAnnRemoveMe__${annotation.id}`) {
yOffset = ann.yOffset;
}
});
} else {
//we need to pass both ranges into this function so that we can correctly
//get the y-offset for circular features that start and end on the same row
//we pass the entire annotation range here and compare it only with ranges that have already been added to the row
if (
index > 0 && //second half of an annotation range
annotationsForRow.length && //there are already annotations within the row
annotationsForRow[annotationsForRow.length - 1].annotation ===
annotation
) {
//the first chunk of the annotation has already been pushed into the row,
//so set the yOffset for the range chunk to the already calculated yOffset
yOffset = annotationsForRow[annotationsForRow.length - 1].yOffset;
if (location) {
//if there's a location then we will just use the previous yOffset for its parent annotation
annotationsForRow.forEach(ann => {
if (ann.id === annotation.id) {
yOffset = ann.yOffset;
}
});
} else {
yOffset = getYOffsetForPotentiallyCircularRange(
annotation,
yOffsetsForRow
);
//we need to pass both ranges into this function so that we can correctly
//get the y-offset for circular features that start and end on the same row
//we pass the entire annotation range here and compare it only with ranges that have already been added to the row
if (
index > 0 && //second half of an annotation range
annotationsForRow.length && //there are already annotations within the row
annotationsForRow[annotationsForRow.length - 1].annotation ===
annotation
) {
//the first chunk of the annotation has already been pushed into the row,
//so set the yOffset for the range chunk to the already calculated yOffset
yOffset = annotationsForRow[annotationsForRow.length - 1].yOffset;
} else {
yOffset = getYOffsetForPotentiallyCircularRange(
annotation,
yOffsetsForRow
);
}
//add the new yOffset to the yOffset array
if (!yOffsetsForRow[yOffset]) yOffsetsForRow[yOffset] = [];
yOffsetsForRow[yOffset].push({
start: start,
end: end
});
}
//add the new yOffset to the yOffset array
if (!yOffsetsForRow[yOffset]) yOffsetsForRow[yOffset] = [];
yOffsetsForRow[yOffset].push({
start: start,
end: end
});
}

annotationsForRow.push({
Expand All @@ -138,42 +179,3 @@ function mapAnnotationToRows({
});
// return annotationsToRowsMap;
}

//
// function calculateNecessaryYOffsetForAnnotationInRow(annotationsAlreadyAddedToRow, ranges) {
// const blockedYOffsets = [];
// //adjust the yOffset of the range being pushed in by checking its range against other ranges already in the row
// each(annotationsAlreadyAddedToRow, function(comparisonRange) {
// //check for overlap with other annotations
// ranges.forEach(function(range){
// if (checkIfNonCircularRangesOverlap(range, comparisonRange)) {
// blockedYOffsets.push(comparisonRange.yOffset);
// return true //break the some loop so we only add the blocked offset once
// }
// });
// });

// const newYOffset = 0;
// //sort and remove duplicates from the blockedYOffsets array
// //then starting with newYOffset = 1, see if there is space for the location
// if (blockedYOffsets.length > 0) {
// const sortedBlockedYOffsets = sortBy(blockedYOffsets, function(n) {
// return n;
// });
// const sortedUniqueBlockedYOffsets = uniq(sortedBlockedYOffsets, true); //true here specifies that the array has already been sorted
// const stillPotentiallyBlocked = true;
// while (stillPotentiallyBlocked) {
// //sortedUniqueBlockedYOffsets is an array starting with 1 eg. [1,2,4,5,6]
// //so we loop through it using the index of newYOffset-1, and if there is a gap
// //in the array, we break the loop and that becomes our final newYOffset
// if (sortedUniqueBlockedYOffsets[newYOffset] !== newYOffset) {
// //the newYOffset isn't blocked
// stillPotentiallyBlocked = false;
// } else {
// //it is blocked
// newYOffset++;
// }
// }
// }
// return newYOffset;
// }
78 changes: 77 additions & 1 deletion src/mapAnnotationsToRows.test.js
View file
Original file line number Diff line number Diff line change
Expand Up @@ -6,11 +6,87 @@ const chaiSubset = require("chai-subset");
chai.use(chaiSubset);
const mapAnnotationsToRows = require("./mapAnnotationsToRows.js");
describe("mapAnnotationsToRows", function() {
it("maps overlapsSelf=true annotations to the same y-offset correctly", function() {
const annotation1 = {
start: 1,
end: 3,
id: "a"
};

const annotationWraps = {
start: 1,
end: 3,
overlapsSelf: true,
id: "overlaps self"
};
const annotationWrapsAddon = {
start: 4,
end: 0,
overlapsSelf: true,
isWrappedAddon: true,
id: "overlaps self"
};
const annotation3 = {
start: 0,
end: 0,
id: "b"
};

const annotation4 = {
start: 0,
end: 0,
id: "c"
};

const annotations = [
annotation1,
annotationWraps,
annotationWrapsAddon,
annotation3,
annotation4
];
const sequenceLength = 10;
const bpsPerRow = 5;
const annotationsToRowsMap = mapAnnotationsToRows(
annotations,
sequenceLength,
bpsPerRow
);
expect(annotationsToRowsMap[0]).to.containSubset([
{
annotation: annotationWraps,
start: 1,
end: 3,
id: annotationWraps.id,
yOffset: 1,
enclosingRangeType: "beginningAndEnd"
},
{
annotation: annotationWrapsAddon,
start: 0,
end: 0,
id: annotationWrapsAddon.id,
yOffset: 1,
enclosingRangeType: "end"
},
{
annotation: annotationWrapsAddon,
start: 4,
end: 4,
id: annotationWrapsAddon.id,
yOffset: 1,
enclosingRangeType: "beginning"
}
]);
});
it("maps overlapping annotations with joined locations to rows correctly", function() {
const annotation1 = {
start: 0,
end: 9,
locations: [{ start: 0, end: 1 }, { start: 7, end: 9 }],
locations: [
{ start: 0, end: 1 },
{ start: 7, end: 9 }
],
id: "a"
};
const annotation2 = {
Expand Down

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