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Commit a6e2c39a authored by Piotr Gawron's avatar Piotr Gawron
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gene variant allel frequency support added

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1 merge request!5Frontend refactor
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with 476 additions and 355 deletions
model/src/main/java/lcsb/mapviewer/model/map/layout/GeneVariation.java
+ 39
− 0
View file @ a6e2c39a
......@@ -41,6 +41,9 @@ public class GeneVariation implements Serializable {
*/
private String contig;
private String allelFrequency;
private String variantIdentifier;
/**
* Reference genome type.
*/
......@@ -70,6 +73,8 @@ public class GeneVariation implements Serializable {
this.setReferenceGenomeVersion(original.getReferenceGenomeVersion());
this.addReferences(original.getReferences());
this.setContig(original.getContig());
this.setAllelFrequency(original.getAllelFrequency());
this.setVariantIdentifier(original.getVariantIdentifier());
}
/**
......@@ -235,4 +240,38 @@ public class GeneVariation implements Serializable {
this.position = (long) position;
}
/**
* @return the allelFrequency
* @see #allelFrequency
*/
public String getAllelFrequency() {
return allelFrequency;
}
/**
* @param allelFrequency
* the allelFrequency to set
* @see #allelFrequency
*/
public void setAllelFrequency(String allelFrequency) {
this.allelFrequency = allelFrequency;
}
/**
* @return the variantIdentifier
* @see #variantIdentifier
*/
public String getVariantIdentifier() {
return variantIdentifier;
}
/**
* @param variantIdentifier
* the variantIdentifier to set
* @see #variantIdentifier
*/
public void setVariantIdentifier(String variantIdentifier) {
this.variantIdentifier = variantIdentifier;
}
}
service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaReader.java
+ 8
− 0
View file @ a6e2c39a
......@@ -151,6 +151,8 @@ public class ColorSchemaReader {
Integer contigColumn = schemaColumns.get(ColorSchemaColumn.CONTIG);
Integer nameColumn = schemaColumns.get(ColorSchemaColumn.NAME);
Integer identifierColumn = schemaColumns.get(ColorSchemaColumn.IDENTIFIER);
Integer variantIdentifierColumn = schemaColumns.get(ColorSchemaColumn.VARIANT_IDENTIFIER);
Integer allelFrequencyColumn = schemaColumns.get(ColorSchemaColumn.ALLEL_FREQUENCY);
Integer compartmentColumn = schemaColumns.get(ColorSchemaColumn.COMPARTMENT);
Integer typeColumn = schemaColumns.get(ColorSchemaColumn.TYPE);
Integer positionColumn = schemaColumns.get(ColorSchemaColumn.POSITION);
......@@ -233,6 +235,12 @@ public class ColorSchemaReader {
if (originalDnaColumn != null) {
gv.setOriginalDna(values[originalDnaColumn]);
}
if (allelFrequencyColumn != null) {
gv.setAllelFrequency(values[allelFrequencyColumn]);
}
if (variantIdentifierColumn != null) {
gv.setVariantIdentifier(values[variantIdentifierColumn]);
}
if (alternativeDnaColumn != null) {
gv.setModifiedDna(values[alternativeDnaColumn]);
}
......
service/src/main/java/lcsb/mapviewer/services/utils/data/ColorSchemaColumn.java
+ 4
− 0
View file @ a6e2c39a
......@@ -97,6 +97,10 @@ public enum ColorSchemaColumn {
* Contig where variant was observed.
*/
CONTIG("contig", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }), //
ALLEL_FREQUENCY("allel_frequency", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }), //
VARIANT_IDENTIFIER("variant_identifier", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }), //
/**
* Should the direction of reaction be reversed.
......
service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderTest.java
+ 33
− 0
View file @ a6e2c39a
......@@ -99,6 +99,39 @@ public class ColorSchemaReaderTest extends ServiceTestFunctions {
}
}
@Test
public void testReadGeneVariantsSchemaWithAF() throws Exception {
try {
File f = new File("testFiles/coloring/gene_variants_all_freq.txt");
InputStream in = new FileInputStream(f);
byte[] buff = new byte[8000];
int bytesRead = 0;
ByteArrayOutputStream bao = new ByteArrayOutputStream();
while ((bytesRead = in.read(buff)) != -1) {
bao.write(buff, 0, bytesRead);
}
in.close();
bao.close();
byte[] data = bao.toByteArray();
ByteArrayInputStream bin = new ByteArrayInputStream(data);
ColorSchemaReader reader = new ColorSchemaReader();
Collection<ColorSchema> schemas = reader.readColorSchema(bin, TextFileUtils.getHeaderParametersFromFile(new ByteArrayInputStream(data)));
assertNotNull(schemas);
assertEquals(2, schemas.size());
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
@Test
public void testReadInvalidGeneVariantsSchema() throws Exception {
try {
......
service/testFiles/coloring/gene_variants_all_freq.txt 0 → 100644
+ 8
− 0
View file @ a6e2c39a
#TYPE=GENETIC_VARIANT
#GENOME_TYPE=UCSC
#GENOME_VERSION=hg38
position original_dna alternative_dna name description color contig allel_frequency variant_identifier
10146 AC A DDX11L1 upstream #ff0000 chr1 0.8 identifier_1
10439 AC A DDX11L1;WASH7P upstream;downstream #ff0001 chr1 0.5 identifier_2
10441 AC A DDX11L1;WASH7P upstream;downstream #ff0001 chr1 0.2 identifier_3
10443 AC A DDX11L1;WASH7P upstream;downstream #ff0001 chr1 0.9 identifier_4
web/src/main/webapp/resources/js/AliasInfoWindow.js
+ 366
− 355
View file @ a6e2c39a
/**
* Class representing info window that should be opened when clicking on alias.
*/
function AliasInfoWindow(alias, map) {
// call super constructor
AbstractInfoWindow.call(this, alias, map);
if (alias instanceof AliasMarker) {
this.alias = alias.getAliasData();
} else {
this.alias = alias;
}
var self = this;
if (this.alias != null) {
var point = new google.maps.Point(this.alias.x + this.alias.width / 2,
this.alias.y + this.alias.height / 2);
var latLng = this.customMap.fromPointToLatLng(point);
this.googleInfowindow = new google.maps.InfoWindow({
content : this.content,
position : latLng
});
this.googleInfowindow.open(this.customMap.map, this.getGoogleMarker());
} else {
logger.warn("Opening window without alias specified");
}
this.update(alias);
};
AliasInfoWindow.prototype = Object.create(AbstractInfoWindow.prototype);
AliasInfoWindow.prototype.constructor = AliasInfoWindow;
/**
* Updates content of info window. The content will be automatically obtained
* from {@link CustomMap} instance. The only optional parameter is {@link Alias}
* data.
*
* @param newAlias
* optional {@link Alias} data for which this {@link AliasInfoWindow}
* was created
*/
AliasInfoWindow.prototype.update = function(newAlias) {
if (this.alias == null && newAlias != null) {
this.alias = newAlias;
}
this._updateContent();
};
/**
* Creates and returns chart representing data related to alias on different
* layouts.
*
* @returns {String} html string representing chart with data related to alias
* on different layouts
*/
AliasInfoWindow.prototype.createChartDiv = function() {
var result = document.createElement("div");
for (var i = 0; i < this.layoutAliases.length; i++) {
var rowDiv = document.createElement("div");
if (i % 2 == 0) {
rowDiv.className = "mapChartRowEvenDiv";
} else {
rowDiv.className = "mapChartRowOddDiv";
}
var data = this.layoutAliases[i];
var nameDiv = document.createElement("div");
nameDiv.className = "mapChartNameDiv";
nameDiv.innerHTML = this.layoutNames[i];
rowDiv.appendChild(nameDiv);
if (data != null) {
var value = parseFloat(data.value);
var color = intToColorString(data.color.value);
var leftMarginDiv = document.createElement("div");
leftMarginDiv.innerHTML = "&nbsp;";
leftMarginDiv.style.float = "left";
var centerBarDiv = document.createElement("div");
centerBarDiv.style.width = "1px";
centerBarDiv.style.float = "left";
centerBarDiv.style.background = "#000000";
centerBarDiv.innerHTML = "&nbsp;";
var rightBarDiv = document.createElement("div");
rightBarDiv.innerHTML = "&nbsp;";
rightBarDiv.style.float = "left";
rightBarDiv.style.background = color;
rightBarDiv.style.width = Math.abs(value * 100) + "px";
if (!isNaN(value)) {
rightBarDiv.innerHTML = value.toFixed(2);
if (value > 0) {
var offset = 100;
leftMarginDiv.style.width = offset + "px";
rightBarDiv.style.textAlign = "right";
rowDiv.appendChild(leftMarginDiv);
rowDiv.appendChild(centerBarDiv);
rowDiv.appendChild(rightBarDiv);
} else {
var offset = 100 + (value * 100);
leftMarginDiv.style.width = offset + "px";
rowDiv.appendChild(leftMarginDiv);
rowDiv.appendChild(rightBarDiv);
rowDiv.appendChild(centerBarDiv);
}
} else {
var offset = 100;
leftMarginDiv.style.width = offset + "px";
leftMarginDiv.style.background = color;
rightBarDiv.style.width = offset + "px";
rightBarDiv.style.background = color;
rowDiv.appendChild(leftMarginDiv);
rowDiv.appendChild(centerBarDiv);
rowDiv.appendChild(rightBarDiv);
}
} else {
var emptyDiv = document.createElement("div");
emptyDiv.innerHTML = "&nbsp;";
emptyDiv.style.float = "left";
emptyDiv.style.width = "201px";
rowDiv.appendChild(emptyDiv);
}
result.appendChild(rowDiv);
}
return result;
};
/**
* Methods that creates and return DOM object with the content of the window.
*
* @returns DOM object representing html code for content of the info window
*/
AliasInfoWindow.prototype.createContentDiv = function() {
if (this.alias != null && this.alias.completness == 'FULL') {
var result = document.createElement("div");
var title = document.createElement("h3");
title.innerHTML = this.alias.type + ": " + this.alias.name;
result.appendChild(title);
this.layoutAliases = this.customMap
.getAliasVisibleLayoutsData(this.alias.id);
this.layoutNames = this.customMap.getVisibleLayoutNames();
var selectedLayouts = this.customMap.getTopMap().getSelectedLayouts();
for (var i = 0; i < this.layoutAliases.length; i++) {
if (this.layoutAliases[i] != null) {
if (this.layoutAliases[i].getType() == LayoutAlias.LIGTH) {
if (!ServerConnector.isWaitingForFullAliasLayoutData(
parseInt(selectedLayouts[i]), parseInt(this.alias.getId()))) {
ServerConnector.retreiveFullAliasesForLayout(selectedLayouts[i],
this.alias.getId(), this.alias.getModelId());
}
}
}
}
var chartDiv = this.createChartDiv();
if (chartDiv !== null) {
result.appendChild(chartDiv);
}
var genomicDiv = this.createGenomicDiv();
if (genomicDiv !== null) {
result.appendChild(genomicDiv);
}
return result;
} else {
return null;
}
};
/**
* Returns array with data taken from all known {@link OverlayCollection}.
*
* @returns array with data from {@link OverlayCollection}
*/
AliasInfoWindow.prototype.getOverlaysData = function(general) {
if (this.alias != null) {
return this.getCustomMap().getTopMap().getOverlayDataForAlias(this.alias,
general);
} else {
return null;
}
};
/**
* Method returning identifier of the object for which this window was created.
*/
AliasInfoWindow.prototype.getElementId = function() {
if (this.alias != null) {
return this.alias.getId();
} else {
return null;
}
}
/**
* Method returning type of the object for which this window was created.
*/
AliasInfoWindow.prototype.getElementType = function() {
return "ALIAS";
};
AliasInfoWindow.prototype.createGenomicDiv = function() {
var result = document.createElement("div");
result.style.width = '640px';
var titleElement = document.createElement("h3");
titleElement.innerHTML = "Gene variants";
result.appendChild(titleElement);
var contentElement = document.createElement("div");
result.appendChild(contentElement);
var geneticInformation = false;
var genomes = [];
var pileupSource = [ {
viz : pileup.viz.scale(),
name : 'Scale'
}, {
viz : pileup.viz.location(),
name : 'Location'
} ];
var pileupRange = {
contig : 'chr1',
start : 3000000000,
stop : 0
};
var globalGeneVariants = [];
var missingGeneVariantsData = false;
for (var i = 0; i < this.layoutAliases.length; i++) {
var data = this.layoutAliases[i];
globalGeneVariants.push([]);
if (data != null && !missingGeneVariantsData) {
if (data.getType() == LayoutAlias.LIGHT || data.getType() == null) {
missingGeneVariantsData = true;
} else if (data.getType() == LayoutAlias.GENETIC_VARIANT) {
var geneVariants = data.getGeneVariants();
for (var j = 0; j < geneVariants.length; j++) {
if (!missingGeneVariantsData) {
var variant = geneVariants[j];
globalGeneVariants[i].push(variant);
var genome = this.getCustomMap().getReferenceGenome(
variant.getReferenceGenomeType(),
variant.getReferenceGenomeVersion());
if (variant.getContig() != null) {
pileupRange.contig = variant.getContig();
}
pileupRange.start = Math.min(pileupRange.start, variant
.getPosition());
var length = Math.max(variant.getModifiedDna().length, variant
.getOriginalDna().length);
pileupRange.stop = Math.max(pileupRange.stop, variant.getPosition()
+ length);
if (genome != null && genome.getUrl() != null) {
if (genomes[genome.getUrl()] == null) {
geneticInformation = true;
genomes[genome.getUrl()] = true;
pileupSource.splice(0, 0, {
viz : pileup.viz.genome(),
isReference : pileupSource.length == 2,
data : pileup.formats.twoBit({
url : genome.getUrl()
}),
name : 'Reference ' + variant.getReferenceGenomeVersion()
});
for (var k = 0; k < genome.getGeneMappings().length; k++) {
var mapping = genome.getGeneMappings()[k];
pileupSource.push({
viz : pileup.viz.genes(),
data : pileup.formats.bigBed({
url : mapping.getUrl()
}),
name : 'Genes ' + mapping.getName()
});
}
}
} else {
logger.debug("Genome for " + variant.getReferenceGenomeType()
+ "," + variant.getReferenceGenomeVersion() + " not loaded");
missingGeneVariantsData = true;
}
}
}
}
}
}
if (missingGeneVariantsData) {
geneticInformation = false;
}
if (geneticInformation) {
for (var i = 0; i < this.layoutAliases.length; i++) {
if (globalGeneVariants[i].length > 0) {
var vcfContent = this.createVcfString(globalGeneVariants[i]);
pileupSource.push({
viz : pileup.viz.variants(),
data : pileup.formats.vcf({
content : vcfContent
}),
name : this.layoutNames[i] + ' - Variants'
});
}
}
pileupRange.stop = Math.max(pileupRange.stop, pileupRange.start + 50);
pileupRange.start--;
pileupRange.stop++;
if (this.pileup != null) {
logger.debug("Destroy pileup");
this.pileup.destroy();
logger.debug("Pileup destroyed");
}
this.pileup = pileup.create(contentElement, {
range : pileupRange,
tracks : pileupSource
});
return result;
} else {
return null;
}
};
AliasInfoWindow.prototype.createVcfString = function(geneVariants) {
var result = "";
result += "##fileformat=VCFv4.0\n";
result += "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\n";
for (var i = 0; i < geneVariants.length; i++) {
var variant = geneVariants[i];
result += variant.getContig() + "\t" + //
variant.getPosition() + "\t" + //
".\t" + //
variant.getOriginalDna() + "\t" + //
variant.getModifiedDna() + "\t" + //
"100.0\t" + //
"PASS\t" + //
"\n";
}
return result;
};
/**
* Class representing info window that should be opened when clicking on alias.
*/
function AliasInfoWindow(alias, map) {
// call super constructor
AbstractInfoWindow.call(this, alias, map);
if (alias instanceof AliasMarker) {
this.alias = alias.getAliasData();
} else {
this.alias = alias;
}
var self = this;
if (this.alias != null) {
var point = new google.maps.Point(this.alias.x + this.alias.width / 2,
this.alias.y + this.alias.height / 2);
var latLng = this.customMap.fromPointToLatLng(point);
this.googleInfowindow = new google.maps.InfoWindow({
content : this.content,
position : latLng
});
this.googleInfowindow.open(this.customMap.map, this.getGoogleMarker());
} else {
logger.warn("Opening window without alias specified");
}
this.update(alias);
};
AliasInfoWindow.prototype = Object.create(AbstractInfoWindow.prototype);
AliasInfoWindow.prototype.constructor = AliasInfoWindow;
/**
* Updates content of info window. The content will be automatically obtained
* from {@link CustomMap} instance. The only optional parameter is {@link Alias}
* data.
*
* @param newAlias
* optional {@link Alias} data for which this {@link AliasInfoWindow}
* was created
*/
AliasInfoWindow.prototype.update = function(newAlias) {
if (this.alias == null && newAlias != null) {
this.alias = newAlias;
}
this._updateContent();
};
/**
* Creates and returns chart representing data related to alias on different
* layouts.
*
* @returns {String} html string representing chart with data related to alias
* on different layouts
*/
AliasInfoWindow.prototype.createChartDiv = function() {
var result = document.createElement("div");
for (var i = 0; i < this.layoutAliases.length; i++) {
var rowDiv = document.createElement("div");
if (i % 2 == 0) {
rowDiv.className = "mapChartRowEvenDiv";
} else {
rowDiv.className = "mapChartRowOddDiv";
}
var data = this.layoutAliases[i];
var nameDiv = document.createElement("div");
nameDiv.className = "mapChartNameDiv";
nameDiv.innerHTML = this.layoutNames[i];
rowDiv.appendChild(nameDiv);
if (data != null) {
var value = parseFloat(data.value);
var color = intToColorString(data.color.value);
var leftMarginDiv = document.createElement("div");
leftMarginDiv.innerHTML = "&nbsp;";
leftMarginDiv.style.float = "left";
var centerBarDiv = document.createElement("div");
centerBarDiv.style.width = "1px";
centerBarDiv.style.float = "left";
centerBarDiv.style.background = "#000000";
centerBarDiv.innerHTML = "&nbsp;";
var rightBarDiv = document.createElement("div");
rightBarDiv.innerHTML = "&nbsp;";
rightBarDiv.style.float = "left";
rightBarDiv.style.background = color;
rightBarDiv.style.width = Math.abs(value * 100) + "px";
if (!isNaN(value)) {
rightBarDiv.innerHTML = value.toFixed(2);
if (value > 0) {
var offset = 100;
leftMarginDiv.style.width = offset + "px";
rightBarDiv.style.textAlign = "right";
rowDiv.appendChild(leftMarginDiv);
rowDiv.appendChild(centerBarDiv);
rowDiv.appendChild(rightBarDiv);
} else {
var offset = 100 + (value * 100);
leftMarginDiv.style.width = offset + "px";
rowDiv.appendChild(leftMarginDiv);
rowDiv.appendChild(rightBarDiv);
rowDiv.appendChild(centerBarDiv);
}
} else {
var offset = 100;
leftMarginDiv.style.width = offset + "px";
leftMarginDiv.style.background = color;
rightBarDiv.style.width = offset + "px";
rightBarDiv.style.background = color;
rowDiv.appendChild(leftMarginDiv);
rowDiv.appendChild(centerBarDiv);
rowDiv.appendChild(rightBarDiv);
}
} else {
var emptyDiv = document.createElement("div");
emptyDiv.innerHTML = "&nbsp;";
emptyDiv.style.float = "left";
emptyDiv.style.width = "201px";
rowDiv.appendChild(emptyDiv);
}
result.appendChild(rowDiv);
}
return result;
};
/**
* Methods that creates and return DOM object with the content of the window.
*
* @returns DOM object representing html code for content of the info window
*/
AliasInfoWindow.prototype.createContentDiv = function() {
if (this.alias != null && this.alias.completness == 'FULL') {
var result = document.createElement("div");
var title = document.createElement("h3");
title.innerHTML = this.alias.type + ": " + this.alias.name;
result.appendChild(title);
this.layoutAliases = this.customMap
.getAliasVisibleLayoutsData(this.alias.id);
this.layoutNames = this.customMap.getVisibleLayoutNames();
var selectedLayouts = this.customMap.getTopMap().getSelectedLayouts();
for (var i = 0; i < this.layoutAliases.length; i++) {
if (this.layoutAliases[i] != null) {
if (this.layoutAliases[i].getType() == LayoutAlias.LIGTH) {
if (!ServerConnector.isWaitingForFullAliasLayoutData(
parseInt(selectedLayouts[i]), parseInt(this.alias.getId()))) {
ServerConnector.retreiveFullAliasesForLayout(selectedLayouts[i],
this.alias.getId(), this.alias.getModelId());
}
}
}
}
var chartDiv = this.createChartDiv();
if (chartDiv !== null) {
result.appendChild(chartDiv);
}
var genomicDiv = this.createGenomicDiv();
if (genomicDiv !== null) {
result.appendChild(genomicDiv);
}
return result;
} else {
return null;
}
};
/**
* Returns array with data taken from all known {@link OverlayCollection}.
*
* @returns array with data from {@link OverlayCollection}
*/
AliasInfoWindow.prototype.getOverlaysData = function(general) {
if (this.alias != null) {
return this.getCustomMap().getTopMap().getOverlayDataForAlias(this.alias,
general);
} else {
return null;
}
};
/**
* Method returning identifier of the object for which this window was created.
*/
AliasInfoWindow.prototype.getElementId = function() {
if (this.alias != null) {
return this.alias.getId();
} else {
return null;
}
}
/**
* Method returning type of the object for which this window was created.
*/
AliasInfoWindow.prototype.getElementType = function() {
return "ALIAS";
};
AliasInfoWindow.prototype.createGenomicDiv = function() {
var result = document.createElement("div");
result.style.width = '640px';
var titleElement = document.createElement("h3");
titleElement.innerHTML = "Gene variants";
result.appendChild(titleElement);
var contentElement = document.createElement("div");
result.appendChild(contentElement);
var geneticInformation = false;
var genomes = [];
var pileupSource = [ {
viz : pileup.viz.scale(),
name : 'Scale'
}, {
viz : pileup.viz.location(),
name : 'Location'
} ];
var pileupRange = {
contig : 'chr1',
start : 3000000000,
stop : 0
};
var globalGeneVariants = [];
var missingGeneVariantsData = false;
for (var i = 0; i < this.layoutAliases.length; i++) {
var data = this.layoutAliases[i];
globalGeneVariants.push([]);
if (data != null && !missingGeneVariantsData) {
if (data.getType() == LayoutAlias.LIGHT || data.getType() == null) {
missingGeneVariantsData = true;
} else if (data.getType() == LayoutAlias.GENETIC_VARIANT) {
var geneVariants = data.getGeneVariants();
for (var j = 0; j < geneVariants.length; j++) {
if (!missingGeneVariantsData) {
var variant = geneVariants[j];
globalGeneVariants[i].push(variant);
var genome = this.getCustomMap().getReferenceGenome(
variant.getReferenceGenomeType(),
variant.getReferenceGenomeVersion());
if (variant.getContig() != null) {
pileupRange.contig = variant.getContig();
}
pileupRange.start = Math.min(pileupRange.start, variant
.getPosition());
var length = Math.max(variant.getModifiedDna().length, variant
.getOriginalDna().length);
pileupRange.stop = Math.max(pileupRange.stop, variant.getPosition()
+ length);
if (genome != null && genome.getUrl() != null) {
if (genomes[genome.getUrl()] == null) {
geneticInformation = true;
genomes[genome.getUrl()] = true;
pileupSource.splice(0, 0, {
viz : pileup.viz.genome(),
isReference : pileupSource.length == 2,
data : pileup.formats.twoBit({
url : genome.getUrl()
}),
name : 'Reference ' + variant.getReferenceGenomeVersion()
});
for (var k = 0; k < genome.getGeneMappings().length; k++) {
var mapping = genome.getGeneMappings()[k];
pileupSource.push({
viz : pileup.viz.genes(),
data : pileup.formats.bigBed({
url : mapping.getUrl()
}),
name : 'Genes ' + mapping.getName()
});
}
}
} else {
logger.debug("Genome for " + variant.getReferenceGenomeType()
+ "," + variant.getReferenceGenomeVersion() + " not loaded");
missingGeneVariantsData = true;
}
}
}
}
}
}
if (missingGeneVariantsData) {
geneticInformation = false;
}
if (geneticInformation) {
for (var i = 0; i < this.layoutAliases.length; i++) {
if (globalGeneVariants[i].length > 0) {
var vcfContent = this.createVcfString(globalGeneVariants[i]);
pileupSource.push({
viz : pileup.viz.variants(),
data : pileup.formats.vcf({
content : vcfContent
}),
name : this.layoutNames[i] + ' - Variants',
options : {
variantHeightByFrequency : true
},
});
}
}
pileupRange.stop = Math.max(pileupRange.stop, pileupRange.start + 50);
pileupRange.start--;
pileupRange.stop++;
if (this.pileup != null) {
logger.debug("Destroy pileup");
this.pileup.destroy();
logger.debug("Pileup destroyed");
}
this.pileup = pileup.create(contentElement, {
range : pileupRange,
tracks : pileupSource
});
return result;
} else {
return null;
}
};
AliasInfoWindow.prototype.createVcfString = function(geneVariants) {
var result = "";
result += "##fileformat=VCFv4.0\n";
result += "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\n";
for (var i = 0; i < geneVariants.length; i++) {
var variant = geneVariants[i];
var additionalInfo = "";
if (variant.getAllelFrequency() != null) {
additionalInfo = "AF=" + variant.getAllelFrequency();
}
var variantId = ".";
if (variant.getVariantIdentifier() != null) {
variantId = variant.getVariantIdentifier();
}
result += variant.getContig() + "\t" + //
variant.getPosition() + "\t" + //
variantId + "\t" + //
variant.getOriginalDna() + "\t" + //
variant.getModifiedDna() + "\t" + //
"100.0\t" + //
"PASS\t" + //
additionalInfo + "\n";
}
return result;
};
web/src/main/webapp/resources/js/GeneVariant.js
+ 18
− 0
View file @ a6e2c39a
......@@ -5,6 +5,8 @@ function GeneVariant(javaObject) {
this.setReferenceGenomeType(javaObject.referenceGenomeType);
this.setReferenceGenomeVersion(javaObject.referenceGenomeVersion);
this.setContig(javaObject.contig);
this.setAllelFrequency(javaObject.allelFrequency);
this.setVariantIdentifier(javaObject.variantIdentifier);
};
GeneVariant.prototype.setPosition = function(position) {
......@@ -39,6 +41,22 @@ GeneVariant.prototype.getContig = function() {
return this._contig;
};
GeneVariant.prototype.setAllelFrequency = function(allelFrequency) {
this._allelFrequency = allelFrequency;
};
GeneVariant.prototype.getAllelFrequency = function() {
return this._allelFrequency;
};
GeneVariant.prototype.setVariantIdentifier = function(variantIdentifier) {
this._variantIdentifier = variantIdentifier;
};
GeneVariant.prototype.getVariantIdentifier = function() {
return this._variantIdentifier;
};
GeneVariant.prototype.setReferenceGenomeType = function(referenceGenomeType) {
this._referenceGenomeType = referenceGenomeType;
};
......
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