<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; ">About the IO discussion. <DIV>If we want a separate IO framework(s), I would suggest to keep all IO in one framework, the examples you give are all sequence related, so would depend only on the core framework (BCFoundation) right. If say the HMM framework would need some kind of special structure, than we can always opt to either define the structure in the foundation, but put all other stuff in the HMM framework, or place the HMM specific IO in the HMM framework as it is probably consists of only a few methods anyway. </DIV><DIV>But my main question is whether we really want to separate the IO framework as being independent. BCFoundation is so much related with IO that I don't really see a need to separate them. Most important, I don't think the IO will be so much code that it will be a large framework, or that it will make the foundation so bloated. It's two files right now! So why don't we make BCFoundation contain the IO like it does now. And the HMM framework contains its IO etc. <DIV>IMHO a basic core that defines sequences and can IO them doesn't have to be separated in two, I see it as one core. Similar to the fact that NSString can also IO them without the need of an IO framework.</DIV><DIV>Cheers, </DIV><DIV>Alex</DIV><DIV><BR class="khtml-block-placeholder"><DIV><BR class="khtml-block-placeholder"><DIV><BR><DIV><DIV>On 4-jul-2005, at 1:20, 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 3, 2005, at 3:12 PM, Philipp Seibel 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"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Sorry, but i got lost :-). I just meant that we can't put all io of all Frameworks in one IOFramework, because this IOFramework will then depend on all Frameworks ( Foundation ,HMM, Phylogenetics, etc.) because it will use the structure classes of all of them. To solve this problem, we will need a seperate IOFramework for each of the Frameworks.</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; ">Aha, but now I understand :) I didn't realize that you were assuming different data structures for each data format.<SPAN class="Apple-converted-space"> </SPAN>Maybe we should put some effort in creating a general internal data format that will also allow easy<SPAN class="Apple-converted-space"> </SPAN>exchange between the various formats.</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><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; ">_______________________________________________</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Biococoa-dev mailing list</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><A href="mailto:Biococoa-dev@bioinformatics.org">Biococoa-dev@bioinformatics.org</A></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><A href="https://bioinformatics.org/mailman/listinfo/biococoa-dev">https://bioinformatics.org/mailman/listinfo/biococoa-dev</A></DIV><DIV style="margin-top: 0px; margin-right: 0px; 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