<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; ">See, that's what I mean, the diagram doesn't make sense to me already! What's the difference between bcsequence and bcsequencenucleotide. The implementation is even harder to get. Let's not throw everything away, but I would like to see how practically the one-for-all bcsequence would work. In addition, I have the feeling (but might be terribly wrong) that annotations are way simpler to implement if there's only one kind of sequence object. <DIV>If I understand it right, a BCSequence object than becomes "typed" on the basis of the BCSequenceSet it has been assigned right? Koen or Charles, could you do a proposal on what the BC world would look like if we choose this model of the general BCSequence object. Could you perhaps speculate/describe:</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>1 how you create such objects</DIV><DIV>2 what role sequence sets play in this</DIV><DIV>3 how one would be able to get its "type"</DIV><DIV>4 how you would do a simple reverse and what would be returned (for DNA and Protein) </DIV><DIV>5 how you would do a translation from DNA to Protein</DIV><DIV>6 how annotations would fit it?</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Pfeww, all our problems solved ;-) Just kidding, but if we can agree that these problems can be tackled nicely with a single BCSequence object in a way logical to ourselves and new users, IMHO I think we have our design... </DIV><DIV>Cheers,</DIV><DIV>Alex</DIV><DIV> <BR><DIV><DIV>On 4-jul-2005, at 7:27, Charles Parnot wrote:</DIV><BR class="Apple-interchange-newline"><BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">I mostly agree with all the discussions and ideas.</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; ">Of course, there is one point I want to make clear again: the BCSequence thing! And I will jump right to it!!!</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; ">I made a diagram to illustrate my points:</DIV> <BR><SPAN><DIV><Picture 1.png></DIV></SPAN><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, I renamed BCSequenceAbstract into BCSequenceRoot, because I just thought of that name and it sounds better...</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; ">First, there is no such thing as a class cluster in the current implementation. As Phil points out, all the subclasses are exposed. The BCSequence indeed uses a trick similar to class cluster, it is a placeholder class. The implementation is thus the confusing part. It is not very elaborate, though, and once you get past the point where the alloc-ed object can still change class at init, you have it all ;-)</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; ">Second, the basic idea of having BCSequence along the other objects is to provide two different types of classes: typed and not typed. Historically, the group was divided about 50/50 between the two options. I was on the side of having a one-for-all class that can be blindly sent any message and do something. I know Koen is also in favor of a unique sequence object that include all the possible types. In the end, we decided to keep both typed sequences and the one-for-all BCSequence. With a diagram like above, it is fairly easy to show the use of the different objects, no?</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; ">Finally, I just want to add that BCSequence does not require additional code and will probably not even need rewriting when we change the internals of the sequence classes, and should not require much in the future. In fact, I volunteer to maintain that code if we keep it! Not writing any code is something I can easily promise ;-)</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 all!</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; ">charles</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; ">Xgrid-at-Stanford</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Help science move fast forward:</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><A href="http://cmgm.stanford.edu/~cparnot/xgrid-stanford">http://cmgm.stanford.edu/~cparnot/xgrid-stanford</A></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; ">Charles Parnot</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><A href="mailto:charles.parnot@gmail.com">charles.parnot@gmail.com</A></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; min-height: 14px; "><BR></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> <BR class="Apple-interchange-newline"></BLOCKQUOTE></DIV><BR><DIV> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="3" style="font: 12.0px Helvetica">*********************************************************<SPAN class="Apple-converted-space"> </SPAN></FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="3" style="font: 12.0px Helvetica"><SPAN class="Apple-converted-space"> </SPAN>** Alexander Griekspoor **</FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="3" style="font: 12.0px Helvetica">*********************************************************<SPAN class="Apple-converted-space"> </SPAN></FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="3" style="font: 12.0px Helvetica"><SPAN class="Apple-converted-space"> </SPAN>The Netherlands Cancer Institute</FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="3" style="font: 12.0px Helvetica"><SPAN class="Apple-converted-space"> </SPAN>Department of Tumorbiology (H4)</FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="3" style="font: 12.0px Helvetica"><SPAN class="Apple-converted-space"> </SPAN>Plesmanlaan 121, 1066 CX, Amsterdam</FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="3" style="font: 12.0px Helvetica"><SPAN class="Apple-converted-space"> </SPAN>Tel:<SPAN class="Apple-converted-space"> </SPAN>+ 31 20 - 512 2023</FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="3" style="font: 12.0px Helvetica"><SPAN class="Apple-converted-space"> </SPAN>Fax:<SPAN class="Apple-converted-space"> </SPAN>+ 31 20 - 512 2029</FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="3" style="font: 12.0px Helvetica"><SPAN class="Apple-converted-space"> </SPAN>AIM: <A href="mailto:mekentosj@mac.com">mekentosj@mac.com</A></FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="3" style="font: 12.0px Helvetica"><SPAN class="Apple-converted-space"> </SPAN>E-mail: <A href="mailto:a.griekspoor@nki.nl">a.griekspoor@nki.nl</A></FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="3" style="font: 12.0px Helvetica"><SPAN class="Apple-converted-space"> </SPAN>Web: <A href="http://www.mekentosj.com">http://www.mekentosj.com</A></FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px; 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