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Valis 8 prevent collision btw annot txts #39

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merged 15 commits into from
Feb 4, 2022
Merged

Valis 8 prevent collision btw annot txts #39

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145caf7
fix overlapping annotation names
leepc12 Dec 14, 2021
24bba5a
fix disappearing (fading out) annotation names at higher LoD (zoomed-…
leepc12 Dec 14, 2021
df12a0f
add gene name check to prevent multiple collision checking on the sam…
leepc12 Dec 15, 2021
ba61f19
linting
leepc12 Dec 16, 2021
bffaa54
max opacity (1.0) for gene name regardless of LoD (zoom level)
leepc12 Dec 16, 2021
7466e8e
better explanation for duplicate collision checking
leepc12 Dec 16, 2021
a02760c
build valis
leepc12 Jan 6, 2022
782b816
strict comparison
leepc12 Jan 12, 2022
79d6f48
rebuild valis
leepc12 Jan 12, 2022
7acb35e
fix typo in comment
leepc12 Jan 13, 2022
0c7af6a
rebuild valis
leepc12 Jan 13, 2022
28198e6
fix typo
leepc12 Jan 13, 2022
cc46a33
rebuild valis
leepc12 Jan 13, 2022
d582281
use correct width for annot label, remove redundant width checking
leepc12 Jan 27, 2022
269fc81
rebuild valis
leepc12 Jan 27, 2022
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76 changes: 60 additions & 16 deletions dist/valis-hpgv.js
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Original file line number Diff line number Diff line change
Expand Up @@ -76672,7 +76672,8 @@ var AnnotationTrack = /** @class */ (function (_super) {
_this.macroLodBlendRange = 2;
_this.macroLodThresholdLow = 7;
_this.macroLodThresholdHigh = _this.macroLodThresholdLow + _this.macroLodBlendRange;
_this.namesLodBlendRange = 1;
//VALIS-8: increased 1->4 to show annotatation names at higher (zoomed out) LoD level
_this.namesLodBlendRange = 4;
_this.namesLodThresholdLow = 6;
_this.namesLodThresholdHigh = _this.namesLodThresholdLow + _this.namesLodBlendRange;
_this.annotationY = (_a = {},
Expand Down Expand Up @@ -76788,6 +76789,8 @@ var AnnotationTrack = /** @class */ (function (_super) {
namesOpacity = 0;
}
var microSamplingDensity = 1;
// VALIS-8: prevent collision between annotation names
var createdAnnotationNames = new Array();
this.getTileLoader().forEachTile(x0, x1, microSamplingDensity, true, function (tile) {
var e_1, _a;
// debug: draw red lines at tile boundaries
Expand All @@ -76805,6 +76808,7 @@ var AnnotationTrack = /** @class */ (function (_super) {
return;
}
var _loop_1 = function (gene) {
var e_2, _a;
// @! temp performance hack, only use node when visible
// (don't need to do this when using instancing)
{
Expand Down Expand Up @@ -76858,9 +76862,49 @@ var AnnotationTrack = /** @class */ (function (_super) {
annotation.gene.relativeX = (gene.startIndex - x0) / span;
annotation.gene.opacity = opacity;
annotation.name.visible = namesOpacity > 0;
annotation.name.opacity = namesOpacity;
// VALIS-8: no blending for gene name
annotation.name.opacity = Math.max(namesOpacity, 1.0);
annotation.name.x = 5;
annotation.name.relativeX = Math.max(annotation.gene.relativeX, 0);
// VALIS-8: prevent collision between annotation names
var annotationNameWidth = annotation.name.getComputedWidth();
if (annotation.name.visible && annotationNameWidth !== 0) {
try {
for (var createdAnnotationNames_1 = __values(createdAnnotationNames), createdAnnotationNames_1_1 = createdAnnotationNames_1.next(); !createdAnnotationNames_1_1.done; createdAnnotationNames_1_1 = createdAnnotationNames_1.next()) {
var name_1 = createdAnnotationNames_1_1.value;
if (annotation.name.y === name_1.y && gene.name !== name_1.geneName) {
// check gene's name to prevent multiple collision checking on the same gene
// this is because if we shift gene's name to the right and if it crosses
// the boundary of the current tile block then the gene is queued to the
// next tile block and then revisited in the next tile loop
if (annotation.name.relativeX >= name_1.relativeX &&
annotation.name.relativeX < name_1.relativeX + name_1.relativeW) {
annotation.name.relativeX = name_1.relativeX + name_1.relativeW;
}
}
}
}
catch (e_2_1) { e_2 = { error: e_2_1 }; }
finally {
try {
if (createdAnnotationNames_1_1 && !createdAnnotationNames_1_1.done && (_a = createdAnnotationNames_1.return)) _a.call(createdAnnotationNames_1);
}
finally { if (e_2) throw e_2.error; }
}
var trackWidth = _this.getComputedWidth();
var spacingFactor = 0.1;
// 10% (based on left name's width) spacing between two overlapping annotation names
createdAnnotationNames.push({
geneName: gene.name,
y: annotation.name.y,
relativeX: annotation.name.relativeX,
relativeW: annotationNameWidth / trackWidth * (1.0 + spacingFactor)
});
}
else {
// hide names with zero width
annotation.name.visible = false;
}
// add to the scene graph (auto removed when unused)
_this._onStageAnnotations.get(annotationKey, function () {
_this.add(annotation.gene);
Expand Down Expand Up @@ -76942,7 +76986,7 @@ var AnnotationTrack = /** @class */ (function (_super) {
}
// Instance Rendering
var tileObject = _this._macroTileCache.get(_this.contig + ':' + tile.key, function () {
var e_2, _a;
var e_3, _a;
// initialize macro gene instances
// create array of gene annotation data
var instanceData = new Array();
Expand Down Expand Up @@ -76991,12 +77035,12 @@ var AnnotationTrack = /** @class */ (function (_super) {
}
}
}
catch (e_2_1) { e_2 = { error: e_2_1 }; }
catch (e_3_1) { e_3 = { error: e_3_1 }; }
finally {
try {
if (_c && !_c.done && (_a = _b.return)) _a.call(_b);
}
finally { if (e_2) throw e_2.error; }
finally { if (e_3) throw e_3.error; }
}
var geneInstances = new IntervalInstances_1.default(instanceData);
geneInstances.y = 0;
Expand Down Expand Up @@ -77074,20 +77118,20 @@ var GeneAnnotation = /** @class */ (function (_super) {
return this._opacity;
},
set: function (v) {
var e_3, _a;
var e_4, _a;
this._opacity = v;
try {
for (var _b = __values(this.children), _c = _b.next(); !_c.done; _c = _b.next()) {
var child = _c.value;
child.opacity = v;
}
}
catch (e_3_1) { e_3 = { error: e_3_1 }; }
catch (e_4_1) { e_4 = { error: e_4_1 }; }
finally {
try {
if (_c && !_c.done && (_a = _b.return)) _a.call(_b);
}
finally { if (e_3) throw e_3.error; }
finally { if (e_4) throw e_4.error; }
}
},
enumerable: true,
Expand All @@ -77098,7 +77142,7 @@ var GeneAnnotation = /** @class */ (function (_super) {
var TranscriptAnnotation = /** @class */ (function (_super) {
__extends(TranscriptAnnotation, _super);
function TranscriptAnnotation(sharedState, transcript, strand, onAnnotationClicked) {
var e_4, _a, e_5, _b;
var e_5, _a, e_6, _b;
var _this = _super.call(this) || this;
_this.transcript = transcript;
_this._opacity = 1;
Expand Down Expand Up @@ -77161,12 +77205,12 @@ var TranscriptAnnotation = /** @class */ (function (_super) {
_this.add(exon);
}
}
catch (e_4_1) { e_4 = { error: e_4_1 }; }
catch (e_5_1) { e_5 = { error: e_5_1 }; }
finally {
try {
if (_d && !_d.done && (_a = _c.return)) _a.call(_c);
}
finally { if (e_4) throw e_4.error; }
finally { if (e_5) throw e_5.error; }
}
try {
// create untranslated regions
Expand All @@ -77180,12 +77224,12 @@ var TranscriptAnnotation = /** @class */ (function (_super) {
_this.add(utr);
}
}
catch (e_5_1) { e_5 = { error: e_5_1 }; }
catch (e_6_1) { e_6 = { error: e_6_1 }; }
finally {
try {
if (_f && !_f.done && (_b = _e.return)) _b.call(_e);
}
finally { if (e_5) throw e_5.error; }
finally { if (e_6) throw e_6.error; }
}
// create protein coding sequences
// ! assuming CDS array is sorted from startIndex
Expand All @@ -77210,20 +77254,20 @@ var TranscriptAnnotation = /** @class */ (function (_super) {
return this._opacity;
},
set: function (v) {
var e_6, _a;
var e_7, _a;
this._opacity = v;
try {
for (var _b = __values(this.children), _c = _b.next(); !_c.done; _c = _b.next()) {
var child = _c.value;
child.opacity = v;
}
}
catch (e_6_1) { e_6 = { error: e_6_1 }; }
catch (e_7_1) { e_7 = { error: e_7_1 }; }
finally {
try {
if (_c && !_c.done && (_a = _b.return)) _a.call(_b);
}
finally { if (e_6) throw e_6.error; }
finally { if (e_7) throw e_7.error; }
}
},
enumerable: true,
Expand Down
2 changes: 1 addition & 1 deletion dist/valis-hpgv.js.map
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76 changes: 60 additions & 16 deletions dist/valis-hpgv.react-peer.js
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -48397,7 +48397,8 @@ var AnnotationTrack = /** @class */ (function (_super) {
_this.macroLodBlendRange = 2;
_this.macroLodThresholdLow = 7;
_this.macroLodThresholdHigh = _this.macroLodThresholdLow + _this.macroLodBlendRange;
_this.namesLodBlendRange = 1;
//VALIS-8: increased 1->4 to show annotatation names at higher (zoomed out) LoD level
_this.namesLodBlendRange = 4;
_this.namesLodThresholdLow = 6;
_this.namesLodThresholdHigh = _this.namesLodThresholdLow + _this.namesLodBlendRange;
_this.annotationY = (_a = {},
Expand Down Expand Up @@ -48513,6 +48514,8 @@ var AnnotationTrack = /** @class */ (function (_super) {
namesOpacity = 0;
}
var microSamplingDensity = 1;
// VALIS-8: prevent collision between annotation names
var createdAnnotationNames = new Array();
this.getTileLoader().forEachTile(x0, x1, microSamplingDensity, true, function (tile) {
var e_1, _a;
// debug: draw red lines at tile boundaries
Expand All @@ -48530,6 +48533,7 @@ var AnnotationTrack = /** @class */ (function (_super) {
return;
}
var _loop_1 = function (gene) {
var e_2, _a;
// @! temp performance hack, only use node when visible
// (don't need to do this when using instancing)
{
Expand Down Expand Up @@ -48583,9 +48587,49 @@ var AnnotationTrack = /** @class */ (function (_super) {
annotation.gene.relativeX = (gene.startIndex - x0) / span;
annotation.gene.opacity = opacity;
annotation.name.visible = namesOpacity > 0;
annotation.name.opacity = namesOpacity;
// VALIS-8: no blending for gene name
annotation.name.opacity = Math.max(namesOpacity, 1.0);
annotation.name.x = 5;
annotation.name.relativeX = Math.max(annotation.gene.relativeX, 0);
// VALIS-8: prevent collision between annotation names
var annotationNameWidth = annotation.name.getComputedWidth();
if (annotation.name.visible && annotationNameWidth !== 0) {
try {
for (var createdAnnotationNames_1 = __values(createdAnnotationNames), createdAnnotationNames_1_1 = createdAnnotationNames_1.next(); !createdAnnotationNames_1_1.done; createdAnnotationNames_1_1 = createdAnnotationNames_1.next()) {
var name_1 = createdAnnotationNames_1_1.value;
if (annotation.name.y === name_1.y && gene.name !== name_1.geneName) {
// check gene's name to prevent multiple collision checking on the same gene
// this is because if we shift gene's name to the right and if it crosses
// the boundary of the current tile block then the gene is queued to the
// next tile block and then revisited in the next tile loop
if (annotation.name.relativeX >= name_1.relativeX &&
annotation.name.relativeX < name_1.relativeX + name_1.relativeW) {
annotation.name.relativeX = name_1.relativeX + name_1.relativeW;
}
}
}
}
catch (e_2_1) { e_2 = { error: e_2_1 }; }
finally {
try {
if (createdAnnotationNames_1_1 && !createdAnnotationNames_1_1.done && (_a = createdAnnotationNames_1.return)) _a.call(createdAnnotationNames_1);
}
finally { if (e_2) throw e_2.error; }
}
var trackWidth = _this.getComputedWidth();
var spacingFactor = 0.1;
// 10% (based on left name's width) spacing between two overlapping annotation names
createdAnnotationNames.push({
geneName: gene.name,
y: annotation.name.y,
relativeX: annotation.name.relativeX,
relativeW: annotationNameWidth / trackWidth * (1.0 + spacingFactor)
});
}
else {
// hide names with zero width
annotation.name.visible = false;
}
// add to the scene graph (auto removed when unused)
_this._onStageAnnotations.get(annotationKey, function () {
_this.add(annotation.gene);
Expand Down Expand Up @@ -48667,7 +48711,7 @@ var AnnotationTrack = /** @class */ (function (_super) {
}
// Instance Rendering
var tileObject = _this._macroTileCache.get(_this.contig + ':' + tile.key, function () {
var e_2, _a;
var e_3, _a;
// initialize macro gene instances
// create array of gene annotation data
var instanceData = new Array();
Expand Down Expand Up @@ -48716,12 +48760,12 @@ var AnnotationTrack = /** @class */ (function (_super) {
}
}
}
catch (e_2_1) { e_2 = { error: e_2_1 }; }
catch (e_3_1) { e_3 = { error: e_3_1 }; }
finally {
try {
if (_c && !_c.done && (_a = _b.return)) _a.call(_b);
}
finally { if (e_2) throw e_2.error; }
finally { if (e_3) throw e_3.error; }
}
var geneInstances = new IntervalInstances_1.default(instanceData);
geneInstances.y = 0;
Expand Down Expand Up @@ -48799,20 +48843,20 @@ var GeneAnnotation = /** @class */ (function (_super) {
return this._opacity;
},
set: function (v) {
var e_3, _a;
var e_4, _a;
this._opacity = v;
try {
for (var _b = __values(this.children), _c = _b.next(); !_c.done; _c = _b.next()) {
var child = _c.value;
child.opacity = v;
}
}
catch (e_3_1) { e_3 = { error: e_3_1 }; }
catch (e_4_1) { e_4 = { error: e_4_1 }; }
finally {
try {
if (_c && !_c.done && (_a = _b.return)) _a.call(_b);
}
finally { if (e_3) throw e_3.error; }
finally { if (e_4) throw e_4.error; }
}
},
enumerable: true,
Expand All @@ -48823,7 +48867,7 @@ var GeneAnnotation = /** @class */ (function (_super) {
var TranscriptAnnotation = /** @class */ (function (_super) {
__extends(TranscriptAnnotation, _super);
function TranscriptAnnotation(sharedState, transcript, strand, onAnnotationClicked) {
var e_4, _a, e_5, _b;
var e_5, _a, e_6, _b;
var _this = _super.call(this) || this;
_this.transcript = transcript;
_this._opacity = 1;
Expand Down Expand Up @@ -48886,12 +48930,12 @@ var TranscriptAnnotation = /** @class */ (function (_super) {
_this.add(exon);
}
}
catch (e_4_1) { e_4 = { error: e_4_1 }; }
catch (e_5_1) { e_5 = { error: e_5_1 }; }
finally {
try {
if (_d && !_d.done && (_a = _c.return)) _a.call(_c);
}
finally { if (e_4) throw e_4.error; }
finally { if (e_5) throw e_5.error; }
}
try {
// create untranslated regions
Expand All @@ -48905,12 +48949,12 @@ var TranscriptAnnotation = /** @class */ (function (_super) {
_this.add(utr);
}
}
catch (e_5_1) { e_5 = { error: e_5_1 }; }
catch (e_6_1) { e_6 = { error: e_6_1 }; }
finally {
try {
if (_f && !_f.done && (_b = _e.return)) _b.call(_e);
}
finally { if (e_5) throw e_5.error; }
finally { if (e_6) throw e_6.error; }
}
// create protein coding sequences
// ! assuming CDS array is sorted from startIndex
Expand All @@ -48935,20 +48979,20 @@ var TranscriptAnnotation = /** @class */ (function (_super) {
return this._opacity;
},
set: function (v) {
var e_6, _a;
var e_7, _a;
this._opacity = v;
try {
for (var _b = __values(this.children), _c = _b.next(); !_c.done; _c = _b.next()) {
var child = _c.value;
child.opacity = v;
}
}
catch (e_6_1) { e_6 = { error: e_6_1 }; }
catch (e_7_1) { e_7 = { error: e_7_1 }; }
finally {
try {
if (_c && !_c.done && (_a = _b.return)) _a.call(_b);
}
finally { if (e_6) throw e_6.error; }
finally { if (e_7) throw e_7.error; }
}
},
enumerable: true,
Expand Down
2 changes: 1 addition & 1 deletion dist/valis-hpgv.react-peer.js.map
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