<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; ">I'm not sure, the question is how heavy the annotations will be, I think not too much. The question why I'm kind of reluctant is the idea for instance that NSAttributedString would be separated into an NSString and an NSStringAttributes object, somehow this doesn't make sense to make. It will also be more problematic to keep things in sync after editing, and would certainly require all kinds of notification and delegates "hacks" to make it work. In the end I don't think we even need light weight sequences so much. After all, we're passing around pointers to objects, so imagine a bcalignment, it will get the pointers to the sequences, it will use the ivar to the raw data to get access to the char arrays, and do it stuff. Whether or not the bcsequence object contains the annotations or not doesn't make a millisecond or kb or ram difference!! This is one of the nicest things of the char array setup in fact. I don't like the idea of a separate record for the annotations too much. The question in the end comes to whether we see the sequence as the center of our universe, also containing annotations, or whether we see the metadata as the most important part, with one of its attributes being the sequence data in the form of a bcsequence object. I don't get the overall picture. If you really want to do the separation, it would make even more sense to me to make BCSequence the metadata/annotations object and have a separate BCSequenceData object...<DIV>Alex</DIV><DIV><BR class="khtml-block-placeholder"><DIV><BR class="khtml-block-placeholder"><DIV><DIV><DIV>On 8-jul-2005, at 2:26, Koen van der Drift wrote:</DIV><BR class="Apple-interchange-newline"><BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">On Jul 6, 2005, at 6:30 PM, Charles Parnot wrote:</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV> <BR><BLOCKQUOTE type="cite"><BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">One of the things I also read about on the biopython mailinglist is that we could keep the BCSequenceXXX classes very light, and create a new class BCSequenceRecord, that is used to store all info from a datafile. In that case, the BCSequence is just one of the key/value pairs.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">cheers,</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">- Koen.</DIV> <BR></BLOCKQUOTE><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Sorry, Koen, but I have no idea what you are talking about here!</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV> <BR></BLOCKQUOTE><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">What I am suggesting is that we keep the BCSequence class just for managing the sequence, such as creating, inserting, etc, and thus keep it very lightweight. To store any annotations and features we create a new class BCSequenceRecord. This is what will be created in the IO classes, and it will have a BCSequence object in one of its key-value pairs. So we remove NSMutableDictionary *annotations from BCAbstractSequence and move it to BCSequenceRecord.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">The advantage is that when you are just dealing with sequences, you want it to be as small as possible, and don't have the additional luggage of all the annotations.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Does that make more sense?</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">- Koen.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; 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