Set the list of variants for variant resources

@param variantSets
494369
@Override
	public void setVariants(Map<String, VariantSet> variantSets) {

		if (variantSets != null) {
			this.variants = new TreeMap<>(variantSets);
			variantKeys = VariantUtils.getAllVariantKeys(this.variants);
		}
	}
1160937
public void setResourceShareArns(java.util.Collection<String> resourceShareArns) {
        if (resourceShareArns == null) {
            this.resourceShareArns = null;
            return;
        }

        this.resourceShareArns = new java.util.ArrayList<String>(resourceShareArns);
    }
212503
public void setReplicationTasks(java.util.Collection<ReplicationTask> replicationTasks) {
        if (replicationTasks == null) {
            this.replicationTasks = null;
            return;
        }

        this.replicationTasks = new java.util.ArrayList<ReplicationTask>(replicationTasks);
    }
209674
public function setVariants(Collection $variants)
    {
        foreach ($variants as $variant) {
            $this->addVariant($variant);
        }

        return $this;
    }
414317
private static String serializeVariantSets(Map<String, VariantSet> map) {
		StringBuilder result = new StringBuilder();

		for (Entry<String, VariantSet> entry : map.entrySet()) {
			result.append(entry.getKey()).append(":");
			VariantSet variantSet = (VariantSet) entry.getValue();
			result.append(variantSet.getDefaultVariant()).append(":");
			result.append(getCommaSeparatedString(variantSet));
			result.append(";");
		}

		return result.toString();
	}
338965
public void setServiceSpecificCredentials(java.util.Collection<ServiceSpecificCredentialMetadata> serviceSpecificCredentials) {
        if (serviceSpecificCredentials == null) {
            this.serviceSpecificCredentials = null;
            return;
        }

        this.serviceSpecificCredentials = new com.amazonaws.internal.SdkInternalList<ServiceSpecificCredentialMetadata>(serviceSpecificCredentials);
    }
329640
def insertVariantSet(self, variantSet):
        
        # We cheat a little here with the VariantSetMetadata, and encode these
        # within the table as a JSON dump. These should really be stored in
        # their own table
        metadataJson = json.dumps(
            [protocol.toJsonDict(metadata) for metadata in
             variantSet.getMetadata()])
        urlMapJson = json.dumps(variantSet.getReferenceToDataUrlIndexMap())
        try:
            models.Variantset.create(
                id=variantSet.getId(),
                datasetid=variantSet.getParentContainer().getId(),
                referencesetid=variantSet.getReferenceSet().getId(),
                name=variantSet.getLocalId(),
                created=datetime.datetime.now(),
                updated=datetime.datetime.now(),
                metadata=metadataJson,
                dataurlindexmap=urlMapJson,
                attributes=json.dumps(variantSet.getAttributes()))
        except Exception as e:
            raise exceptions.RepoManagerException(e)
        for callSet in variantSet.getCallSets():
            self.insertCallSet(callSet)
1102576
def removeVariantSet(self, variantSet):
        
        for variantSetRecord in models.Variantset.select().where(
                        models.Variantset.id == variantSet.getId()):
            variantSetRecord.delete_instance(recursive=True)
1177011
public void setFailures(java.util.Collection<String> failures) {
        if (failures == null) {
            this.failures = null;
            return;
        }

        this.failures = new java.util.ArrayList<String>(failures);
    }
982701
public static String getVariantKey(Map<String, String> variants) {

		String variantKey = "";
		if (variants != null) {
			variantKey = getVariantKey(variants, variants.keySet());
		}

		return variantKey;
	}
1181623
public void addUniqueFields(Set<FieldSet> uniqueFieldSets) {
		if (this.uniqueFields == null) {
			this.uniqueFields = new HashSet<FieldSet>();
		}
		this.uniqueFields.addAll(uniqueFieldSets);
	}
922480
public void setSubResources(java.util.Collection<SubResourceSummary> subResources) {
        if (subResources == null) {
            this.subResources = null;
            return;
        }

        this.subResources = new java.util.ArrayList<SubResourceSummary>(subResources);
    }
456220
private static List<String> getVariantKeys(String variantKeyPrefix, Collection<String> variants) {

		List<String> variantKeys = new ArrayList<>();
		for (String variant : variants) {
			if (variant == null) {
				variant = "";
			}
			if (variantKeyPrefix == null) {
				variantKeys.add(variant);
			} else {
				variantKeys.add(variantKeyPrefix + variant);
			}
		}

		return variantKeys;
	}
1221530
public void run(List<Variant> variantList) {
        for (int i = 0; i < variantList.size(); i++) {
            Map<String, AdditionalAttribute> customAnnotation = getCustomAnnotation(variantList.get(i));
            // Update only if there are annotations for this variant. customAnnotation may be empty if the variant
            // exists in the vcf but the info field does not contain any of the required attributes
            if (customAnnotation != null && customAnnotation.get(fileId).getAttribute().size() > 0) {
                VariantAnnotation variantAnnotation = variantList.get(i).getAnnotation();
                if (variantAnnotation != null) {
                    Map<String, AdditionalAttribute> additionalAttributes = variantAnnotation.getAdditionalAttributes();
                    if (additionalAttributes == null) {
                        // variantList and variantAnnotationList must contain variants in the SAME order: variantAnnotation
                        // at position i must correspond to variant i
                        variantAnnotation.setAdditionalAttributes(customAnnotation);
                    } else {
                        additionalAttributes.putAll(customAnnotation);
                        // variantList and variantAnnotationList must contain variants in the SAME order: variantAnnotation
                        // at position i must correspond to variant i
//                        variantAnnotation.setAdditionalAttributes(additionalAttributes);
                    }
                }
            }
        }
    }
189046
public void setPresets(java.util.Collection<Preset> presets) {
        if (presets == null) {
            this.presets = null;
            return;
        }

        this.presets = new java.util.ArrayList<Preset>(presets);
    }
501558
public void setValueSet(java.util.Collection<String> valueSet) {
        if (valueSet == null) {
            this.valueSet = null;
            return;
        }

        this.valueSet = new com.amazonaws.internal.SdkInternalList<String>(valueSet);
    }
735562
@Override
	public List<BundlePath> getItemPathList(Map<String, String> variants) {
		return getItemPathList(bundlePathMapping.getItemPathList(), variants);
	}