getter for geneSymbolList - gets GeneSymbolList in PubMed
@generated
@return value of the feature
186055
public StringArray getGeneSymbolList() {
    if (ManualDescriptor_Type.featOkTst && ((ManualDescriptor_Type)jcasType).casFeat_geneSymbolList == null)
      jcasType.jcas.throwFeatMissing("geneSymbolList", "de.julielab.jules.types.pubmed.ManualDescriptor");
    return (StringArray)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefValue(addr, ((ManualDescriptor_Type)jcasType).casFeatCode_geneSymbolList)));}
1353221
protected Object[] getSourceValues() {
		Object[] values = new Object[sourceValueModels.length];
		for (int i = 0; i < values.length; i++) {
			values[i] = sourceValueModels[i].getValue();
		}
		return values;
	}
227593
public void setGeneSymbolList(int i, String v) { 
    if (ManualDescriptor_Type.featOkTst && ((ManualDescriptor_Type)jcasType).casFeat_geneSymbolList == null)
      jcasType.jcas.throwFeatMissing("geneSymbolList", "de.julielab.jules.types.pubmed.ManualDescriptor");
    jcasType.jcas.checkArrayBounds(jcasType.ll_cas.ll_getRefValue(addr, ((ManualDescriptor_Type)jcasType).casFeatCode_geneSymbolList), i);
    jcasType.ll_cas.ll_setStringArrayValue(jcasType.ll_cas.ll_getRefValue(addr, ((ManualDescriptor_Type)jcasType).casFeatCode_geneSymbolList), i, v);}
266442
public FSArray getMeSHList() {
    if (ManualDescriptor_Type.featOkTst && ((ManualDescriptor_Type)jcasType).casFeat_meSHList == null)
      jcasType.jcas.throwFeatMissing("meSHList", "de.julielab.jules.types.pubmed.ManualDescriptor");
    return (FSArray)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefValue(addr, ((ManualDescriptor_Type)jcasType).casFeatCode_meSHList)));}
721450
@SuppressWarnings({"unchecked", "rawtypes"})
    public List<E> getValueAsList() {

        final Object fieldValue = getValue();
        final Class<?> fieldType = getType();

        if(Collection.class.isAssignableFrom(fieldType)) {
            final Collection<Object> value = (fieldValue == null ? new ArrayList<Object>() : (Collection<Object>) fieldValue);
            final List<Object> list = Utils.convertCollectionToList(value);
            return (List)list;

        } else if(fieldType.isArray()) {
            Class<?> componentType = fieldType.getComponentType();
            final List<Object> list = Utils.asList(fieldValue, componentType);
            return (List)list;

        } else {
            throw new IllegalStateException(MessageBuilder.create("validation.notSupportType")
                    .var("property", getFieldPath())
                    .varWithClass("type", fieldType)
                    .format());
        }

    }
208457
public FSArray getThemes_protein() {
    if (Event_Type.featOkTst && ((Event_Type)jcasType).casFeat_themes_protein == null)
      jcasType.jcas.throwFeatMissing("themes_protein", "ch.epfl.bbp.uima.genia.Event");
    return (FSArray)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefValue(addr, ((Event_Type)jcasType).casFeatCode_themes_protein)));}
1329269
public java.util.List<? extends org.tensorflow.framework.Summary.ValueOrBuilder> 
      getValueOrBuilderList() {
    return value_;
  }
392580
public AnnotationTypeElementDoc[] elements() {
        List<AnnotationTypeElementDoc> elements = List.nil();
        for (Symbol sym : tsym.members().getSymbols(NON_RECURSIVE)) {
            if (sym != null && sym.kind == MTH) {
                MethodSymbol s = (MethodSymbol)sym;
                elements = elements.prepend(env.getAnnotationTypeElementDoc(s));
            }
        }
        return
            elements.toArray(new AnnotationTypeElementDoc[elements.length()]);
    }
1263922
public static List<GeneName> getGeneNames(InputStream inStream) throws IOException{

		ArrayList<GeneName> geneNames = new ArrayList<GeneName>();
		BufferedReader reader = new BufferedReader(new InputStreamReader(inStream));

		// skip reading first line (it is the legend)
		String line = reader.readLine();

		while ((line = reader.readLine()) != null) {
			// process line...
			//System.out.println(Arrays.toString(line.split("\t")));

			GeneName  geneName = getGeneName(line);
			if ( geneName != null)
				geneNames.add(geneName);
				//System.out.println(geneName);

		}

		// since this is a large list, let's free up unused space...
		geneNames.trimToSize();
		return geneNames;
	}
1258212
public StringArray getTokens() {
    if (FeatureTokens_Type.featOkTst && ((FeatureTokens_Type)jcasType).casFeat_tokens == null)
      jcasType.jcas.throwFeatMissing("tokens", "ch.epfl.bbp.uima.types.FeatureTokens");
    return (StringArray)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefValue(addr, ((FeatureTokens_Type)jcasType).casFeatCode_tokens)));}
1024705
public Coref getRef() {
    if (Coref_Type.featOkTst && ((Coref_Type)jcasType).casFeat_ref == null)
      jcasType.jcas.throwFeatMissing("ref", "de.julielab.jules.types.muc7.Coref");
    return (Coref)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefValue(addr, ((Coref_Type)jcasType).casFeatCode_ref)));}
209028
public List<GetterType<BeanType<T>>> getAllGetter()
   {
      List<GetterType<BeanType<T>>> list = new ArrayList<GetterType<BeanType<T>>>();
      List<Node> nodeList = childNode.get("getter");
      for(Node node: nodeList)
      {
         GetterType<BeanType<T>>  type = new GetterTypeImpl<BeanType<T>>(this, "getter", childNode, node);
         list.add(type);
      }
      return list;
   }
1275414
def get_ncbi_id_from_symbol(gene_symbol):
        
        monarch_url = 'https://solr.monarchinitiative.org/solr/search/select'
        params = DipperUtil._get_solr_weight_settings()
        params["q"] = "{0} \"{0}\"".format(gene_symbol)
        params["fq"] = ["taxon:\"NCBITaxon:9606\"", "category:\"gene\""]
        gene_id = None
        try:
            monarch_request = requests.get(monarch_url, params=params)
            response = monarch_request.json()
            count = response['response']['numFound']
            if count > 0:
                gene_id = response['response']['docs'][0]['id']
        except requests.ConnectionError:
            print("error fetching {0}".format(monarch_url))

        return gene_id
304673
@JsonIgnore
    @Override
    public Collection<Object> getValues() {
        ReportConnector reportConnector = report.getReportConnector();
        reportConnector.run(extra);
        if (reportConnector.getRows() == null) return new ArrayList<Object>();
        return CollectionUtils.collect(reportConnector.getRows(), new Transformer() {
            @Override
            public Object transform(Object input) {
                Map<String, Object> map = (Map<String, Object>) input;
                if (map.size() == 1)
                    return map.values().iterator().next();
                else
                    return map.get(selectedColumn);
            }
        });
    }
150569
public FSArray getPointerList() {
    if (MMAXAnnotation_Type.featOkTst && ((MMAXAnnotation_Type)jcasType).casFeat_pointerList == null)
      jcasType.jcas.throwFeatMissing("pointerList", "de.julielab.jules.types.mmax.MMAXAnnotation");
    return (FSArray)(jcasType.ll_cas.ll_getFSForRef(jcasType.ll_cas.ll_getRefValue(addr, ((MMAXAnnotation_Type)jcasType).casFeatCode_pointerList)));}
919986
def get_proteins_psms_for_map(self):
        """"""
        fields = ['p.gene_acc', 'sets.set_name',
                  'pep.sequence', 'psm.psm_id']
        firstjoin = ('protein_psm', 'pp', 'protein_acc')
        genetable = 'genes'
        return self.get_unique_gene_psms(genetable, fields, firstjoin)
466448
public java.util.List<String> getStringListValues() {
        if (stringListValues == null) {
            stringListValues = new com.amazonaws.internal.SdkInternalList<String>();
        }
        return stringListValues;
    }