This adds a dense feature to a vector, setting the appropriate component of the given vector to the passed in
value.
@param vector the vector
@param featureName the feature whose value to set
@param value the value we want to set this vector to
505203
public void setDenseFeature(ConcatVector vector, String featureName, double[] value) {
        vector.setDenseComponent(ensureFeature(featureName), value);
    }
786000
public void incrementFeature(Assignment featureAssignment, double amount) {
    if (isDense) {
      statistics.incrementEntry(amount, statisticNames.assignmentToIntArray(featureAssignment));
    } else {
      Tensor increment = SparseTensor.singleElement(getTensorDimensions(), getTensorSizes(),
          statisticNames.assignmentToIntArray(featureAssignment), amount);
      statisticsTensor = statisticsTensor.elementwiseAddition(increment);
    }
  }
635033
public void setFeature(Feature feature) {
		if (feature != null) {
			this.feature = feature;
			copyToForm(this.feature);
		} else {
			this.feature = null;
			featureForm.clear();
		}
	}
410484
private void handleResidueAnnotation(String seqName, String featureName, String value) {

		if (featureName.equals(GR_SURFACE_ACCESSIBILITY)) {
			stockholmStructure.addSurfaceAccessibility(seqName, value);
		} else if (featureName.equals(GR_TRANS_MEMBRANE)) {
			stockholmStructure.addTransMembrane(seqName, value);
		} else if (featureName.equals(GR_POSTERIOR_PROBABILITY)) {
			stockholmStructure.addPosteriorProbability(seqName, value);
		} else if (featureName.equals(GR_LIGAND_BINDING)) {
			stockholmStructure.addLigandBinding(seqName, value);
		} else if (featureName.equals(GR_ACTIVE_SITE)) {
			stockholmStructure.addActiveSite(seqName, value);
		} else if (featureName.equals(GR_AS_PFAM_PREDICTED)) {
			stockholmStructure.addASPFamPredicted(seqName, value);
		} else if (featureName.equals(GR_AS_SWISSPROT)) {
			stockholmStructure.addASSwissProt(seqName, value);
		} else if (featureName.equals(GR_INTRON)) {
			stockholmStructure.addIntron(seqName, value);
		} else if (featureName.equals(GR_SECONDARY_STRUCTURE)) {
			stockholmStructure.addSecondaryStructure(seqName, value);
		} else {
			// unknown feature
			logger.warn("Unknown Residue Feature [{}].\nPlease contact the Biojava team.", featureName);
		}
	}
921171
void addValue(String columnName, String value)
    {
        addValue(columnNames.indexOf(columnName), value);
    }
1255279
void update(Object feature) throws LayerException {
		SimpleFeatureSource source = getFeatureSource();
		if (source instanceof SimpleFeatureStore) {
			SimpleFeatureStore store = (SimpleFeatureStore) source;
			String featureId = getFeatureModel().getId(feature);
			Filter filter = filterService.createFidFilter(new String[] { featureId });
			transactionSynchronization.synchTransaction(store);
			List<Name> names = new ArrayList<Name>();
			Map<String, Attribute> attrMap = getFeatureModel().getAttributes(feature);
			List<Object> values = new ArrayList<Object>();
			for (Map.Entry<String, Attribute> entry : attrMap.entrySet()) {
				String name = entry.getKey();
				names.add(store.getSchema().getDescriptor(name).getName());
				values.add(entry.getValue().getValue());
			}

			try {
				store.modifyFeatures(names.toArray(new Name[names.size()]), values.toArray(), filter);
				store.modifyFeatures(store.getSchema().getGeometryDescriptor().getName(), getFeatureModel()
						.getGeometry(feature), filter);
				log.debug("Updated feature {} in {}", featureId, getFeatureSourceName());
			} catch (IOException ioe) {
				featureModelUsable = false;
				throw new LayerException(ioe, ExceptionCode.LAYER_MODEL_IO_EXCEPTION);
			}
		} else {
			log.error("Don't know how to create or update " + getFeatureSourceName() + ", class "
					+ source.getClass().getName() + " does not implement SimpleFeatureStore");
			throw new LayerException(ExceptionCode.CREATE_OR_UPDATE_NOT_IMPLEMENTED, getFeatureSourceName(), source
					.getClass().getName());
		}
	}
1045802
public void setColumn(int j, double value) {
        VectorIterator it = iteratorOfColumn(j);

        while (it.hasNext()) {
            it.next();
            it.set(value);
        }
    }
998539
public void addProperty(final String propertyName, final String value) {
        Preconditions.checkNotNull(propertyName);
        Preconditions.checkNotNull(value);
        List<String> values = properties.get(propertyName);
        if (values == null) {
            values = new ArrayList<>();
            values.add(value);
            properties.put(propertyName, values);
        } else {
            values.add(value);
        }
    }
1326218
public void setComponentId(String v) {
    if (Annotation_Type.featOkTst && ((Annotation_Type)jcasType).casFeat_componentId == null)
      jcasType.jcas.throwFeatMissing("componentId", "de.julielab.jules.types.Annotation");
    jcasType.ll_cas.ll_setStringValue(addr, ((Annotation_Type)jcasType).casFeatCode_componentId, v);}
1280224
public void setVariable(String name, Object value) {
        if (variables == null)
            variables = new LinkedHashMap();
        variables.put(name, value);
    }
1079466
@Override
    public void set(String propName, Object value) {
        if (propName.equals(PROP_C)) {
            setC(((String) value));
        }
        if (propName.equals(PROP_COUNTRY_NAME)) {
            setCountryName(((String) value));
        }
        if (propName.equals(PROP_DESCRIPTION)) {
            getDescription().add(((String) value));
        }
        super.set(propName, value);
    }
928699
public void setValues(FSArray v) {
    if (Document_Type.featOkTst && ((Document_Type)jcasType).casFeat_values == null)
      jcasType.jcas.throwFeatMissing("values", "de.julielab.jules.types.ace.Document");
    jcasType.ll_cas.ll_setRefValue(addr, ((Document_Type)jcasType).casFeatCode_values, jcasType.ll_cas.ll_getFSRef(v));}
488787
public boolean setFeatureStyle(PolylineOptions polylineOptions, FeatureRow featureRow) {
        return StyleUtils.setFeatureStyle(polylineOptions, featureStyleExtension, featureRow, density);
    }
1114006
private void handleFileAnnotation(String featureName, String value) {
		if (featureName.equals(GF_ACCESSION_NUMBER)) {
			stockholmStructure.getFileAnnotation().setGFAccessionNumber(value);
		} else if (featureName.equals(GF_IDENTIFICATION)) {
			stockholmStructure.getFileAnnotation().setGFIdentification(value);
		} else if (featureName.equals(GF_DB_REFERENCE)) {
			stockholmStructure.getFileAnnotation().addDBReference(value);
		} else if (featureName.equals(GF_DEFINITION)) {
			stockholmStructure.getFileAnnotation().setGFDefinition(value);
		} else if (featureName.equals(GF_AUTHOR)) {
			stockholmStructure.getFileAnnotation().setGFAuthors(value);
		} else if (featureName.equals(GF_ALIGNMENT_METHOD)) {
			stockholmStructure.getFileAnnotation().setAlignmentMethod(value);
		} else if (featureName.equals(GF_BUILD_METHOD)) {
			stockholmStructure.getFileAnnotation().addGFBuildMethod(value);
		} else if (featureName.equals(GF_SEARCH_METHOD)) {
			stockholmStructure.getFileAnnotation().setGFSearchMethod(value);
		} else if (featureName.equals(GF_SOURCE_SEED)) {
			stockholmStructure.getFileAnnotation().setGFSourceSeed(value);
		} else if (featureName.equals(GF_SOURCE_STRUCTURE)) {
			stockholmStructure.getFileAnnotation().setGFSourceStructure(value);
		} else if (featureName.equals(GF_GATHERING_THRESHOLD)) {
			stockholmStructure.getFileAnnotation().setGFGatheringThreshs(value);
		} else if (featureName.equals(GF_TRUSTED_CUTOFF)) {
			stockholmStructure.getFileAnnotation().setGFTrustedCutoffs(value);
		} else if (featureName.equals(GF_NOISE_CUTOFF)) {
			stockholmStructure.getFileAnnotation().setGFNoiseCutoffs(value);
		} else if (featureName.equals(GF_TYPE_FIELD)) {
			stockholmStructure.getFileAnnotation().setGFTypeField(value);
		} else if (featureName.equals(GF_PREVIOUS_IDS)) {
			stockholmStructure.getFileAnnotation().setGFPreviousIDs(value);
		} else if (featureName.equals(GF_SEQUENCE)) {
			// status = STATUS_IN_SEQUENCE;
			stockholmStructure.getFileAnnotation().setGFNumSequences(value);
		} else if (featureName.equals(GF_DB_COMMENT)) {
			stockholmStructure.getFileAnnotation().setGFDBComment(value);
			// } else if (featureName.equals(GF_DB_REFERENCE)) {
			// stockholmStructure.getFileAnnotation().addDBReference(value);
		} else if (featureName.equals(GF_REFERENCE_COMMENT)) {
			stockholmStructure.getFileAnnotation().setGFRefComment(value);
		} else if (featureName.equals(GF_REFERENCE_NUMBER)) {
			StockholmFileAnnotationReference reference = new StockholmFileAnnotationReference();
			stockholmStructure.getFileAnnotation().getReferences().add(reference);
		} else if (featureName.equals(GF_REFERENCE_MEDLINE)) {
			stockholmStructure.getFileAnnotation().getReferences().lastElement().setRefMedline(value);
		} else if (featureName.equals(GF_REFERENCE_TITLE)) {
			stockholmStructure.getFileAnnotation().getReferences().lastElement().addToRefTitle(value);
		} else if (featureName.equals(GF_REFERENCE_AUTHOR)) {
			stockholmStructure.getFileAnnotation().getReferences().lastElement().addToRefAuthor(value);
		} else if (featureName.equals(GF_REFERENCE_LOCALTION)) {
			stockholmStructure.getFileAnnotation().getReferences().lastElement().setRefLocation(value);
		} else if (featureName.equals(GF_KEYWORDS)) {
			stockholmStructure.getFileAnnotation().setGFKeywords(value);
		} else if (featureName.equals(GF_COMMENT)) {
			stockholmStructure.getFileAnnotation().addToGFComment(value);
		} else if (featureName.equals(GF_PFAM_ACCESSION)) {
			stockholmStructure.getFileAnnotation().setGFPfamAccession(value);
		} else if (featureName.equals(GF_LOCATION)) {
			stockholmStructure.getFileAnnotation().setGFLocation(value);
		} else if (featureName.equals(GF_WIKIPEDIA_LINK)) {
			stockholmStructure.getFileAnnotation().setGFWikipediaLink(value);
		} else if (featureName.equals(GF_CLAN)) {
			stockholmStructure.getFileAnnotation().setGFClan(value);
		} else if (featureName.equals(GF_MEMBERSHIP)) {
			stockholmStructure.getFileAnnotation().setGFMembership(value);
		} else if (featureName.equals(GF_NEW_HAMPSHIRE)) {
			stockholmStructure.getFileAnnotation().addGFNewHampshire(value);
		} else if (featureName.equals(GF_TREE_ID)) {
			stockholmStructure.getFileAnnotation().addGFTreeID(value);
		} else if (featureName.equals(GF_FALSE_DISCOVERY_RATE)) {
			stockholmStructure.getFileAnnotation().addGFFalseDiscoveryRate(value);
		} else {
			// unknown feature
			logger.warn("Unknown File Feature [{}].\nPlease contact the Biojava team.", featureName);
		}
	}
1121349
@Override
	public Feature create(org.geomajas.layer.feature.Feature feature, FeaturesSupported layer) {
		Map<String, Attribute<?>> attributes = new HashMap<String, Attribute<?>>();
		for (String key : feature.getAttributes().keySet()) {
			attributes.put(key, new AttributeImpl(feature.getAttributes().get(key)));
		}
		return new FeatureImpl(layer, feature.getId(), attributes, feature.getGeometry(), feature.getLabel());
	}
244448
public void addFeature(com.ibm.websphere.servlet.container.WebContainer.Feature feature) {
        this.features.add(feature);
    }
23977
public void setTokens(StringArray v) {
    if (FeatureTokens_Type.featOkTst && ((FeatureTokens_Type)jcasType).casFeat_tokens == null)
      jcasType.jcas.throwFeatMissing("tokens", "ch.epfl.bbp.uima.types.FeatureTokens");
    jcasType.ll_cas.ll_setRefValue(addr, ((FeatureTokens_Type)jcasType).casFeatCode_tokens, jcasType.ll_cas.ll_getFSRef(v));}