private CMLReactionList cdkReactionSetToCMLReactionList(IReactionSet reactionSet, boolean setIDs) { CMLReactionList reactionList = new CMLReactionList(); if (useCMLIDs && setIDs) { IDCreator.createIDs(reactionSet); } if (reactionSet.getID() != null && !reactionSet.getID().equals("")) reactionList.setId(reactionSet.getID()); Iterator<IReaction> reactionIter = reactionSet.reactions().iterator(); while (reactionIter.hasNext()) { reactionList.appendChild(cdkReactionToCMLReaction(reactionIter.next(), false)); } return reactionList; }
private CMLReactionList cdkReactionSetToCMLReactionList(IReactionSet reactionSet, boolean setIDs) { CMLReactionList reactionList = new CMLReactionList(); if (useCMLIDs && setIDs) { IDCreator.createIDs(reactionSet); } if (reactionSet.getID() != null && !reactionSet.getID().equals("")) reactionList.setId(reactionSet.getID()); Iterator<IReaction> reactionIter = reactionSet.reactions().iterator(); while (reactionIter.hasNext()) { reactionList.appendChild(cdkReactionToCMLReaction(reactionIter.next(), false)); } return reactionList; }
private static void createIDsForReactionSet(IReactionSet reactionSet, List<String> tabuList) { if (tabuList == null) tabuList = ReactionSetManipulator.getAllIDs(reactionSet); if (null == reactionSet.getID()) { // generate new ID for the set reactionSetCount = setID(REACTIONSET_PREFIX, reactionSetCount, reactionSet, tabuList); } for (Iterator<IReaction> reaction = reactionSet.reactions().iterator(); reaction.hasNext();) { createIDsForReaction(reaction.next(), tabuList); } }