/* (non-Javadoc)
@see org.rcsb.mmtf.decoder.StructureDecoderInterface
#setGroupInfo(java.lang.String, int, char, int, int)
491443
@Override
	public void setGroupInfo(String groupName, int groupNumber,
			char insertionCode, String chemCompType, int atomCount, int bondCount,
			char singleLetterCode, int sequenceIndexId, int secStructType) {
		// Get the polymer type
		ResidueType residueType = ResidueType.getResidueTypeFromString(chemCompType);
		int polymerType = getGroupTypIndicator(residueType.polymerType);
		switch (polymerType) {
		case 1:
			AminoAcid aa = new AminoAcidImpl();
			// Now set the one letter code
			aa.setAminoType(singleLetterCode);
			group = aa;
			break;
		case 2:
			group = new NucleotideImpl();
			break;
		default:
			group = new HetatomImpl();
			break;
		}
		atomsInGroup = new ArrayList<Atom>();
		ChemComp chemComp = new ChemComp();
		chemComp.setOne_letter_code(String.valueOf(singleLetterCode));
		chemComp.setType(chemCompType.toUpperCase());
		chemComp.setResidueType(residueType);
		chemComp.setPolymerType(residueType.polymerType);
		group.setChemComp(chemComp);
		group.setPDBName(groupName);
		if (insertionCode == MmtfStructure.UNAVAILABLE_CHAR_VALUE) {
			group.setResidueNumber(chain.getName().trim(), groupNumber, null);
		} else {
			group.setResidueNumber(chain.getName().trim(),
					groupNumber, insertionCode);
		}
		group.setAtoms(new ArrayList<Atom>(atomCount));
		if (polymerType==1 || polymerType==2) {
			MmtfUtils.insertSeqResGroup(chain, group, sequenceIndexId);
		}
		if (atomCount > 0) {
			chain.addGroup(group);
		}
		MmtfUtils.setSecStructType(group, secStructType);
	}
825960
public void setTypeInfos(java.util.Collection<ActivityTypeInfo> typeInfos) {
        if (typeInfos == null) {
            this.typeInfos = null;
            return;
        }

        this.typeInfos = new java.util.ArrayList<ActivityTypeInfo>(typeInfos);
    }
896022
public void setGroupIds(java.util.Collection<String> groupIds) {
        if (groupIds == null) {
            this.groupIds = null;
            return;
        }

        this.groupIds = new com.amazonaws.internal.SdkInternalList<String>(groupIds);
    }
548669
public void setSutInfo(String sutInfo)
    {
        StringTokenizer stk = new StringTokenizer(sutInfo, "@");
        this.sutProjectName = stk.nextToken();
        this.sutName = stk.nextToken();
    }
585003
public void setKeyAndKeyGroup(@Nonnull K key, @Nonnegative int keyGroupId) {
		try {
			serializeKeyGroupAndKey(key, keyGroupId);
		} catch (IOException shouldNeverHappen) {
			throw new FlinkRuntimeException(shouldNeverHappen);
		}
	}
158206
public void setInfo(SortedMap<String, Object> addInfo) {

        m_addInfoEditable = new TreeMap<String, Object>(addInfo);
    }
579616
public void setGroupName(String name, int id) {
        PreparedStatement statement = null;

        try (Connection sqlConnection = sqlService.getConnection()) {
            statement = sqlConnection.prepareStatement(
                "UPDATE " + Constants.DB_TABLE_SERVER_GROUPS +
                    " SET " + Constants.GENERIC_NAME + " = ?" +
                    " WHERE " + Constants.GENERIC_ID + " = ?"
            );
            statement.setString(1, name);
            statement.setInt(2, id);
            statement.executeUpdate();
            statement.close();
        } catch (Exception e) {
            e.printStackTrace();
        } finally {
            try {
                if (statement != null) {
                    statement.close();
                }
            } catch (Exception e) {
            }
        }
    }
1260718
public void setGroups(java.util.Collection<ReservationUtilizationGroup> groups) {
        if (groups == null) {
            this.groups = null;
            return;
        }

        this.groups = new java.util.ArrayList<ReservationUtilizationGroup>(groups);
    }
1243834
public void setGroupMembers(List<String> membershipInfo) {
        for (String line : membershipInfo) {
            String[] fields = line.split("\\|");
            if (fields.length < 2) {
                continue;
            }
            Set<String> users = StringUtils.commaDelimitedListToSet(fields[1]);
            String groupName = fields[0];
            groups.putIfAbsent(groupName, null);

            boolean groupAdmin = (3 <= fields.length && "write".equalsIgnoreCase(fields[2])) ? true : false;
            if (groupAdmin) {
                groupAdmins.put(groupName, users);
            } else {
                groupMembers.put(groupName, users);
            }
        }
        logger.debug("groups: " + groups);
        logger.debug("admins: " + groupAdmins + ", members: " + groupMembers);
    }
1307866
public void setGroups(java.util.Collection<GroupMetadata> groups) {
        if (groups == null) {
            this.groups = null;
            return;
        }

        this.groups = new java.util.ArrayList<GroupMetadata>(groups);
    }
188446
public MulticastConfig setGroup(String group) {
    try {
      InetAddress address = InetAddress.getByName(group);
      if (!address.isMulticastAddress()) {
        throw new ConfigurationException("Invalid multicast group " + group);
      }
      return setGroup(address);
    } catch (UnknownHostException e) {
      throw new ConfigurationException("Failed to locate multicast group", e);
    }
  }
138234
private void doSelectGroup(final Message<JsonObject> message) {
    final Object key = message.body().getValue("key");
    if (key == null) {
      message.reply(new JsonObject().putString("status", "error").putString("message", "No key specified."));
    } else {
      selectGroup(key, new Handler<AsyncResult<String>>() {
        @Override
        public void handle(AsyncResult<String> result) {
          if (result.failed()) {
            message.reply(new JsonObject().putString("status", "error").putString("message", result.cause().getMessage()));
          } else if (result.result() == null) {
            message.reply(new JsonObject().putString("status", "error").putString("message", "No groups to select."));
          } else {
            message.reply(new JsonObject().putString("status", "ok").putString("result", result.result()));
          }
        }
      });
    }
  }
1356068
public void setRuleGroups(java.util.Collection<RuleGroupSummary> ruleGroups) {
        if (ruleGroups == null) {
            this.ruleGroups = null;
            return;
        }

        this.ruleGroups = new java.util.ArrayList<RuleGroupSummary>(ruleGroups);
    }
265588
public void assignGroup(XEvent event, String group) {
		if (group != null && group.trim().length() > 0) {
			XAttributeLiteral attr = (XAttributeLiteral) ATTR_GROUP.clone();
			attr.setValue(group.trim());
			event.getAttributes().put(KEY_GROUP, attr);
		}
	}
689664
public void setSecurityGroups(java.util.Collection<String> securityGroups) {
        if (securityGroups == null) {
            this.securityGroups = null;
            return;
        }

        this.securityGroups = new java.util.ArrayList<String>(securityGroups);
    }
1221459
public void setGroups(java.util.Collection<SegmentGroup> groups) {
        if (groups == null) {
            this.groups = null;
            return;
        }

        this.groups = new java.util.ArrayList<SegmentGroup>(groups);
    }
231782
public void setDeploymentGroupsInfo(java.util.Collection<DeploymentGroupInfo> deploymentGroupsInfo) {
        if (deploymentGroupsInfo == null) {
            this.deploymentGroupsInfo = null;
            return;
        }

        this.deploymentGroupsInfo = new com.amazonaws.internal.SdkInternalList<DeploymentGroupInfo>(deploymentGroupsInfo);
    }