This is the new method for building the COMPND and SOURCE records. Now each method is self-contained.
@author Jules Jacobsen
@param  compoundList
@param  sourceList
439271
private void makeCompounds(List<String> compoundList,
			List<String> sourceList) {
		//		System.out.println("[makeCompounds] making compounds from compoundLines");

		for (String line : compoundList) {
			if (compoundList.indexOf(line) + 1 == compoundList.size()) {
				//				System.out.println("[makeCompounds] Final line in compoundLines.");
				isLastCompndLine = true;
			}
			pdb_COMPND_Handler(line);

		}
		//		System.out.println("[makeCompounds] adding sources to compounds from sourceLines");
		// since we're starting again from the first compound, reset it here
		if ( entities.size() == 0){
			current_compound = new EntityInfo();
		} else {
			current_compound = entities.get(0);
		}
		for (String line : sourceList) {
			if (sourceList.indexOf(line) + 1 == sourceList.size()) {
				//				System.out.println("[makeCompounds] Final line in sourceLines.");
				isLastSourceLine = true;
			}
			pdb_SOURCE_Handler(line);
		}

	}
206973
public final hqlParser.inList_return inList() throws RecognitionException {
		hqlParser.inList_return retval = new hqlParser.inList_return();
		retval.start = input.LT(1);

		CommonTree root_0 = null;

		ParserRuleReturnScope compoundExpr180 =null;

		RewriteRuleSubtreeStream stream_compoundExpr=new RewriteRuleSubtreeStream(adaptor,"rule compoundExpr");

		try {
			// hql.g:487:2: ( compoundExpr -> ^( IN_LIST[\"inList\"] compoundExpr ) )
			// hql.g:487:4: compoundExpr
			{
			pushFollow(FOLLOW_compoundExpr_in_inList2244);
			compoundExpr180=compoundExpr();
			state._fsp--;

			stream_compoundExpr.add(compoundExpr180.getTree());
			// AST REWRITE
			// elements: compoundExpr
			// token labels:
			// rule labels: retval
			// token list labels:
			// rule list labels:
			// wildcard labels:
			retval.tree = root_0;
			RewriteRuleSubtreeStream stream_retval=new RewriteRuleSubtreeStream(adaptor,"rule retval",retval!=null?retval.getTree():null);

			root_0 = (CommonTree)adaptor.nil();
			// 488:2: -> ^( IN_LIST[\"inList\"] compoundExpr )
			{
				// hql.g:488:5: ^( IN_LIST[\"inList\"] compoundExpr )
				{
				CommonTree root_1 = (CommonTree)adaptor.nil();
				root_1 = (CommonTree)adaptor.becomeRoot(adaptor.create(IN_LIST, "inList"), root_1);
				adaptor.addChild(root_1, stream_compoundExpr.nextTree());
				adaptor.addChild(root_0, root_1);
				}

			}


			retval.tree = root_0;

			}

			retval.stop = input.LT(-1);

			retval.tree = (CommonTree)adaptor.rulePostProcessing(root_0);
			adaptor.setTokenBoundaries(retval.tree, retval.start, retval.stop);

		}
		catch (RecognitionException re) {
			reportError(re);
			recover(input,re);
			retval.tree = (CommonTree)adaptor.errorNode(input, retval.start, input.LT(-1), re);
		}
		finally {
			// do for sure before leaving
		}
		return retval;
	}
851828
protected void visit(CompoundConstraint compoundConstraint) {
		Iterator it = compoundConstraint.iterator();
        String compoundMessage = getMessageCode(compoundConstraint);
		while (it.hasNext()) {
			Constraint p = (Constraint) it.next();
			visitorSupport.invokeVisit(this, p);
			if (it.hasNext()) {
				add(compoundMessage, null, compoundMessage);
			}
		}
	}
621677
public void addSubscribedSource(Source source) {
        String sourceId = CollectorManagerUtils.getSourceId(source);
        //If present in pending subscription list remove it.
        pendingSubscriptions.remove(sourceId);
        subscribedSources.add(sourceId);
    }
1278116
@Override
    public <Y> CompoundSelection<Y> construct(Class<Y> arg0, Selection<?>... arg1)
    {
        return new DefaultCompoundSelection<Y>(Arrays.asList(arg1), arg0);
    }
1291394
public void addSource(ISource source) {
		if (sourceList == null) {
			sourceList = new ArrayList<ISource>();
		}
		sourceList.add(source);
	}
1308366
public void setBackupPlanTemplatesList(java.util.Collection<BackupPlanTemplatesListMember> backupPlanTemplatesList) {
        if (backupPlanTemplatesList == null) {
            this.backupPlanTemplatesList = null;
            return;
        }

        this.backupPlanTemplatesList = new java.util.ArrayList<BackupPlanTemplatesListMember>(backupPlanTemplatesList);
    }
378723
public void init(Record record, Object source, boolean bReceiveAllAdds)
    {
        m_htBookmarks = new BookmarkList();
        m_bReceiveAllAdds = bReceiveAllAdds;
        super.init(record, null, source);
        if (record != null)
            record.addListener(new GridSyncRecordMessageFilterHandler(this, true));
    }
699268
public void setPrefixLists(java.util.Collection<PrefixList> prefixLists) {
        if (prefixLists == null) {
            this.prefixLists = null;
            return;
        }

        this.prefixLists = new com.amazonaws.internal.SdkInternalList<PrefixList>(prefixLists);
    }
1141991
@Override
	protected void postProcessCompoundLists(
			List<List<AminoAcidCompound>> compoundLists) {
		for (List<AminoAcidCompound> compounds : compoundLists) {
			if (trimStops) {
				trimStop(compounds);
			}
		}
	}
203472
def p_compound_list(p):
    ''''''
    if len(p) == 2:
        p[0] = p[1]
    else:
        parts = p[2]
        if len(parts) > 1:
            p[0] = ast.node(kind='list', parts=parts, pos=_partsspan(parts))
        else:
            p[0] = parts[0]
1144714
public void initBasedOnOptions() {
    inputSourceMaps.putAll(options.inputSourceMaps);
    // Create the source map if necessary.
    if (options.sourceMapOutputPath != null) {
      sourceMap = options.sourceMapFormat.getInstance();
      sourceMap.setPrefixMappings(options.sourceMapLocationMappings);
      if (options.applyInputSourceMaps) {
        sourceMap.setSourceFileMapping(this);
        if (options.sourceMapIncludeSourcesContent) {
          for (SourceMapInput inputSourceMap : inputSourceMaps.values()) {
            addSourceMapSourceFiles(inputSourceMap);
          }
        }
      }
    }
  }
950390
public void setResourceTypeList(java.util.Collection<String> resourceTypeList) {
        if (resourceTypeList == null) {
            this.resourceTypeList = null;
            return;
        }

        this.resourceTypeList = new java.util.ArrayList<String>(resourceTypeList);
    }
104109
public void setSourceInfo(java.util.Collection<CloudFormationStackRecordSourceInfo> sourceInfo) {
        if (sourceInfo == null) {
            this.sourceInfo = null;
            return;
        }

        this.sourceInfo = new java.util.ArrayList<CloudFormationStackRecordSourceInfo>(sourceInfo);
    }
804146
public void init(SharedBaseRecordTable sharedTable, RecordOwnerParent parent, FieldList recordMain, Map<String, Object> properties)
    {
        m_sharedTable = sharedTable;
        super.init(parent, recordMain, properties);
    }
681296
private void composeDeprecatedList(List<Doc> list, MemberDoc[] members) {
        for (int i = 0; i < members.length; i++) {
            if (Util.isDeprecated(members[i])) {
                list.add(members[i]);
            }
        }
    }
484931
public void init(RecordOwnerParent taskParent, Record recordMain, Map<String, Object> properties)
    {
        m_properties = properties;

        m_strFileName = null;
        m_strPackage = null;
        m_strProjectID = null;
        
        m_ClassNameList = null;     // List of all classes written so far
    
    // Open the source files
        super.init(taskParent, recordMain, properties);
    }