Commit 56b8ba58 authored by Piotr Gawron's avatar Piotr Gawron
Browse files

redundant references field in gene variants data overlay is now deprecated

parent 346254c0
......@@ -17,6 +17,8 @@ minerva (14.0.0~alpha.0) unstable; urgency=low
* Small improvement: overlay name is obligatory (#698)
* Small improvement: target gene in search panel contains also information
about type of database that identifies the target (#66)
* Small improvement: redundant 'references' field in gene variants data
overlay is now deprecated (#850)
* Bug fix: export to CellDesigner of reaction with two modifiers connected
with boolean operator resulted was skipping some layout information
* Bug fix: reaction in SBGNML file containing two products was improperly
......
......@@ -74,11 +74,6 @@ public class GeneVariation implements Serializable {
*/
private String referenceGenomeVersion;
/**
* List of references connected to this variant.
*/
private List<MiriamData> references = new ArrayList<>();
/**
* Constructor that creates copy of the {@link GeneVariation}.
*
......@@ -91,7 +86,6 @@ public class GeneVariation implements Serializable {
this.setModifiedDna(original.getModifiedDna());
this.setReferenceGenomeType(original.getReferenceGenomeType());
this.setReferenceGenomeVersion(original.getReferenceGenomeVersion());
this.addReferences(original.getReferences());
this.setContig(original.getContig());
this.setAllelFrequency(original.getAllelFrequency());
this.setVariantIdentifier(original.getVariantIdentifier());
......@@ -104,19 +98,6 @@ public class GeneVariation implements Serializable {
public GeneVariation() {
}
/**
* Adds references.
*
* @param references
* references to add
* @see #references
*/
private void addReferences(Collection<MiriamData> references) {
for (MiriamData reference : references) {
addReference(reference);
}
}
/**
* @return the position
* @see #position
......@@ -185,14 +166,6 @@ public class GeneVariation implements Serializable {
this.referenceGenomeType = referenceGenomeType;
}
/**
* @return the references
* @see #references
*/
public List<MiriamData> getReferences() {
return references;
}
/**
* @return the referenceGenomeVersion
* @see #referenceGenomeVersion
......@@ -210,17 +183,6 @@ public class GeneVariation implements Serializable {
this.referenceGenomeVersion = referenceGenomeVersion;
}
/**
* Adds reference.
*
* @param reference
* reference to add
* @see #references
*/
public void addReference(MiriamData reference) {
this.references.add(reference);
}
/**
* Creates copy of the object.
*
......
......@@ -46,18 +46,6 @@ public class GeneVariationTest {
}
}
@Test
public void testAddReference() throws Exception {
try {
GeneVariation gv = new GeneVariation();
gv.addReference(new MiriamData());
assertEquals(1, gv.getReferences().size());
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
@Test
public void testCopy() throws Exception {
try {
......@@ -66,12 +54,10 @@ public class GeneVariationTest {
GeneVariation gv = new GeneVariation();
gv.setModifiedDna(modifiedDna);
gv.addReference(new MiriamData());
GeneVariation copy = gv.copy();
assertEquals(gv.getModifiedDna(), copy.getModifiedDna());
assertEquals(1, copy.getReferences().size());
} catch (Exception e) {
e.printStackTrace();
throw e;
......
......@@ -655,11 +655,6 @@ public class LayoutService implements ILayoutService {
sb.append(schema.getGeneVariations().get(0).getReferenceGenomeVersion() + "\t");
} else if (column.equals(ColorSchemaColumn.CONTIG)) {
sb.append(schema.getGeneVariations().get(0).getContig() + "\t");
} else if (column.equals(ColorSchemaColumn.REFERENCES)) {
MiriamConnector mc = new MiriamConnector();
for (MiriamData md : schema.getGeneVariations().get(0).getReferences()) {
sb.append(mc.miriamDataToUri(md) + "\t");
}
} else {
throw new InvalidArgumentException("Unknown column type: " + column + " for schema type: " + schema.getClass());
}
......
......@@ -177,7 +177,6 @@ public class ColorSchemaReader {
Integer originalDnaColumn = schemaColumns.get(ColorSchemaColumn.ORIGINAL_DNA);
Integer alternativeDnaColumn = schemaColumns.get(ColorSchemaColumn.ALTERNATIVE_DNA);
Integer descriptionColumn = schemaColumns.get(ColorSchemaColumn.DESCRIPTION);
Integer referencesColumn = schemaColumns.get(ColorSchemaColumn.REFERENCES);
Integer referenceGenomeTypeColumn = schemaColumns.get(ColorSchemaColumn.REFERENCE_GENOME_TYPE);
Integer referenceGenomeVersionColumn = schemaColumns.get(ColorSchemaColumn.REFERENCE_GENOME_VERSION);
Integer aminoAcidChangeColumn = schemaColumns.get(ColorSchemaColumn.AMINO_ACID_CHANGE);
......@@ -273,16 +272,6 @@ public class ColorSchemaReader {
if (aminoAcidChangeColumn != null) {
gv.setAminoAcidChange(values[aminoAcidChangeColumn]);
}
if (referencesColumn != null) {
String[] references = values[referencesColumn].split(";");
for (String string : references) {
try {
gv.addReference(MiriamType.getMiriamByUri(string));
} catch (InvalidArgumentException e) {
throw new InvalidColorSchemaException("[Line " + lineIndex + "] Invalid reference: " + string, e);
}
}
}
if (referenceGenomeTypeColumn != null) {
gv.setReferenceGenomeType(extractReferenceGenomeType(values[referenceGenomeTypeColumn]));
} else {
......
......@@ -53,7 +53,7 @@ public enum ColorSchemaColumn {
/**
* Identifier of the element.
*/
IDENTIFIER(new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }),
IDENTIFIER("references",new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }),
/**
* Element identifier.
......@@ -91,11 +91,6 @@ public enum ColorSchemaColumn {
*/
DESCRIPTION(new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT, ColorSchemaType.GENERIC }),
/**
* Variant references.
*/
REFERENCES(new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }),
/**
* What's the {@link ReferenceGenomeType}.
*/
......
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