diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/GeneVariation.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/GeneVariation.java
index 9239fc6c7542b72e9e46c918eab82dee5f5e9e4f..76eeee8ea91697cc6d490192ec827a4b0f58e405 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/GeneVariation.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/GeneVariation.java
@@ -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;
+ }
+
}
diff --git a/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaReader.java b/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaReader.java
index d06c19183f1019116142d54131801dac457b6f4c..1d59bc9127d17416136204f696e6601f3fad8afe 100644
--- a/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaReader.java
+++ b/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaReader.java
@@ -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]);
}
diff --git a/service/src/main/java/lcsb/mapviewer/services/utils/data/ColorSchemaColumn.java b/service/src/main/java/lcsb/mapviewer/services/utils/data/ColorSchemaColumn.java
index 2dfd6d892c2747ef8845b72a605357cab7d35ad5..a7f6ed47414cfab0c7d833e2575cee3013659371 100644
--- a/service/src/main/java/lcsb/mapviewer/services/utils/data/ColorSchemaColumn.java
+++ b/service/src/main/java/lcsb/mapviewer/services/utils/data/ColorSchemaColumn.java
@@ -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.
diff --git a/service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderTest.java b/service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderTest.java
index 4cb1a9685bf767d2ca8bd5c15997f7577282b9e5..4b86da5e966329268caaae83de02578a4f4f3278 100644
--- a/service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderTest.java
@@ -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 {
diff --git a/service/testFiles/coloring/gene_variants_all_freq.txt b/service/testFiles/coloring/gene_variants_all_freq.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c63af80978611c50da87d3a47836dcfc4dd740be
--- /dev/null
+++ b/service/testFiles/coloring/gene_variants_all_freq.txt
@@ -0,0 +1,8 @@
+#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
diff --git a/web/src/main/webapp/resources/js/AliasInfoWindow.js b/web/src/main/webapp/resources/js/AliasInfoWindow.js
index 63b01c02abb4654df9238615b09ce6d067b910e1..858dfbed15eb50a129e31eed7199e143c7f16449 100644
--- a/web/src/main/webapp/resources/js/AliasInfoWindow.js
+++ b/web/src/main/webapp/resources/js/AliasInfoWindow.js
@@ -1,355 +1,366 @@
-/**
- * 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 = " ";
- leftMarginDiv.style.float = "left";
- var centerBarDiv = document.createElement("div");
- centerBarDiv.style.width = "1px";
- centerBarDiv.style.float = "left";
- centerBarDiv.style.background = "#000000";
- centerBarDiv.innerHTML = " ";
-
- var rightBarDiv = document.createElement("div");
- rightBarDiv.innerHTML = " ";
- 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 = " ";
- 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 = " ";
+ leftMarginDiv.style.float = "left";
+ var centerBarDiv = document.createElement("div");
+ centerBarDiv.style.width = "1px";
+ centerBarDiv.style.float = "left";
+ centerBarDiv.style.background = "#000000";
+ centerBarDiv.innerHTML = " ";
+
+ var rightBarDiv = document.createElement("div");
+ rightBarDiv.innerHTML = " ";
+ 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 = " ";
+ 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;
+};
diff --git a/web/src/main/webapp/resources/js/GeneVariant.js b/web/src/main/webapp/resources/js/GeneVariant.js
index 5c62e0b6caa2b2257a7c7b29c96d8bf994f34548..5500d57c928ebf0ed0934816514f9294fffb6678 100644
--- a/web/src/main/webapp/resources/js/GeneVariant.js
+++ b/web/src/main/webapp/resources/js/GeneVariant.js
@@ -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;
};