gene variant allel frequency support added

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;
+	}
+
 }

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]);
 					}

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.

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 {

service/testFiles/coloring/gene_variants_all_freq.txt

+#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/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;
 };