method to get all blob polymers given a list of PolymerNotation objects

@param polymers List of PolymerNotation objects
@return list of blob polymers
488587
public final static List<PolymerNotation> getBLOBPolymers(List<PolymerNotation> polymers) {
    List<PolymerNotation> blobPolymers = new ArrayList<PolymerNotation>();
    for (PolymerNotation polymer : polymers) {
      if (polymer.getPolymerID() instanceof BlobEntity) {
        blobPolymers.add(polymer);
      }
    }
    return blobPolymers;
  }
343755
public static List<EntityInfo> findPolyEntities(List<List<Chain>> polyModels) {
		TreeMap<String,EntityInfo> chainIds2entities = findEntitiesFromAlignment(polyModels);

		List<EntityInfo> entities = findUniqueEntities(chainIds2entities);

		return entities;
	}
480407
protected List<Node> getTransformableNodes(final List<Node> childNodes) {
        final List<Node> nodes = new LinkedList<Node>();
        for (final Node childNode : childNodes) {
            if (isTransformableNode(childNode)) {
                nodes.add(childNode);
            }
        }

        return nodes;
    }
356438
public static List<MonomerNotation> getListOfMonomerNotation(List<PolymerNotation> polymers) {
    List<MonomerNotation> items = new ArrayList<MonomerNotation>();
    for (PolymerNotation polymer : polymers) {
      items.addAll(polymer.getListMonomers());
    }

    return items;

  }
371897
public List<Blob> batchGet(String bucketName, String blobName1, String blobName2) {
    // [START batchGet]
    BlobId firstBlob = BlobId.of(bucketName, blobName1);
    BlobId secondBlob = BlobId.of(bucketName, blobName2);
    List<Blob> blobs = storage.get(firstBlob, secondBlob);
    // [END batchGet]
    return blobs;
  }
971665
public static List<Object> getAllNodes(TreeModel treeModel)
    {
        List<Object> result = new ArrayList<Object>();
        getAllDescendants(treeModel, treeModel.getRoot(), result);
        result.add(0, treeModel.getRoot());
        return result;
    }
1372400
public java.util.List<DBSnapshotAttribute> getDBSnapshotAttributes() {
        if (dBSnapshotAttributes == null) {
            dBSnapshotAttributes = new com.amazonaws.internal.SdkInternalList<DBSnapshotAttribute>();
        }
        return dBSnapshotAttributes;
    }
595966
public List<Monomer> getAllMonomersList() {
    List<Monomer> monomers = new ArrayList<Monomer>();
    for (String polymerType : getPolymerTypeSet()) {
      Map<String, Monomer> map = getMonomers(polymerType);
      monomers.addAll(map.values());
    }
    return monomers;

  }
37765
private static PbDocument [] getPbDocs(final NodeList nl) {
		List    list   = new ArrayList();
		Element prevpb = null;

		for (int i = 0; i < nl.getLength(); i++) {
			Element    pb    = (Element) nl.item(i);
			PbDocument pbdoc = new PbDocument(prevpb, pb);
			list.add(pbdoc);
			prevpb = pb;

			if (i == (nl.getLength() - 1)) {
				pbdoc = new PbDocument(pb, null);
				list.add(pbdoc);
			} // end if
		} // end for

		PbDocument array[] = new PbDocument[list.size()];

		for (int i = 0; i < list.size(); i++) {
			array[i] = (PbDocument) list.get(i);
		} // end for

		return array;
	}
662609
public static final int getTotalMonomerCount(HELM2Notation helm2notation) {
    int result = 0;
    for (PolymerNotation polymer : helm2notation.getListOfPolymers()) {
      result += PolymerUtils.getTotalMonomerCount(polymer);
    }
    return result;
  }
120858
public static String generateFastaFromRNAPolymer(List<PolymerNotation> polymers)
			throws FastaFormatException, ChemistryException {
		StringBuilder fasta = new StringBuilder();
		for (PolymerNotation polymer : polymers) {
			String header = polymer.getPolymerID().getId();
			if (polymer.getAnnotation() != null) {
				header = polymer.getAnnotation();
			}

			fasta.append(">" + header + "\n");
			try {
				fasta.append(
						generateFastaFromRNA(MethodsMonomerUtils.getListOfHandledMonomers(polymer.getListMonomers()))
								+ "\n");
			} catch (HELM2HandledException e) {
				e.printStackTrace();
				throw new FastaFormatException(e.getMessage());
			}
		}
		return fasta.toString();
	}
238346
function getBlockNodes(nodes) {
  // TODO(perf): update `nodes` instead of creating a new object?
  var node = nodes[0];
  var endNode = nodes[nodes.length - 1];
  var blockNodes;

  for (var i = 1; node !== endNode && (node = node.nextSibling); i++) {
    if (blockNodes || nodes[i] !== node) {
      if (!blockNodes) {
        blockNodes = jqLite(slice.call(nodes, 0, i));
      }
      blockNodes.push(node);
    }
  }

  return blockNodes || nodes;
}
124732
public static Set<Label> getLabels(final Collection<Annotation> annotations) {
        return annotations.stream()
                .flatMap(AnnotationUtils::extractRepeatable)
                .map(AnnotationUtils::getMarks)
                .flatMap(Collection::stream)
                .collect(Collectors.toSet());
    }
1254615
public final static List<PolymerNotation> getRNAPolymers(List<PolymerNotation> polymers) {
    List<PolymerNotation> rnaPolymers = new ArrayList<PolymerNotation>();
    for (PolymerNotation polymer : polymers) {
      if (polymer.getPolymerID() instanceof RNAEntity) {
        rnaPolymers.add(polymer);
      }
    }
    return rnaPolymers;
  }
385155
public Monomer getMonomer(String polymerType, String alternateId) {
	Map<String, Monomer> map1 = monomerDB.get(polymerType);
	//alternateId = alternateId.toUpperCase();
    return monomerDB.get(polymerType).get(alternateId);
  }
1040089
public List<T> getChildren(T payload) {
    List<T> children = new ArrayList<>();
    if (!mIndex.containsKey(payload)) {
      return children;
    }
    DirectedAcyclicGraphNode<T> node = mIndex.get(payload);
    for (DirectedAcyclicGraphNode<T> child : node.getChildren()) {
      children.add(child.getPayload());
    }
    return children;
  }
1005506
public final static List<PolymerNotation> getPeptidePolymers(List<PolymerNotation> polymers) {
    List<PolymerNotation> peptidePolymers = new ArrayList<PolymerNotation>();
    for (PolymerNotation polymer : polymers) {
      if (polymer.getPolymerID() instanceof PeptideEntity) {
        peptidePolymers.add(polymer);
      }
    }
    return peptidePolymers;
  }