<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; "><DIV><BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">John, I am sure I speak for the others too that I would hate to see you leave, so again, we should try all our efforts to come to a good way out of this.</DIV></BLOCKQUOTE><DIV>Yes, absolutely!! It would be really a pity to see you leave John. You have made absolutely a major contribution to the project, and it would be a shame to see a person leave with your experience and skills. I hope you decide to take the gamble, perhaps wait a bit till we can either see whether or not we are heading in the right direction, and jump back in. Already having the opinions and critical eye of someone who is sceptical about our approach would be very helpful!</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Again, I have been always in favour of first of all only 1 approach, either typed or untyped bcsequences, and I have always been in favour of typed sequences. I still would like to see only one approach, but recently I feel more and more attracted to the untyped sequences approach for several reasons:</DIV><DIV>- a uniform and simple interface for new developers (and ourselves). Trying (and failing) to explain our approach even to myself on the WWDC told me we were doing something wrong</DIV><DIV>- we have a way of typing in my opinion, the symbolsets, I'm convinced (at least hope) that this should be able to give enough typing and error checking, also during runtime (by explicit testing ourselves).</DIV><DIV>- it largely reduces the number of subclasses to only 2 (mutable vs immutable), and solves a problem I haven't seen a decent alternative for, the 2d-inheritance problem.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Perhaps I was most convinced by the appearance of more and more omni-graffle schemes. I couldn't understand a single one instantly, way to complex, way to many arrows, code-duplication all over, methods spread all over, difficult initializers, tricks, etc. For me they made only one thing really clear, not the structure we should pick, but the structure we should not pick.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Again, it would be a real pity to leave, if you want to use some of the classes like they are now in your own projects I would say go ahead, we'll work the license out later. We can always release the current "snapshot" under a bsd license. But I hope your needs are not immediate and that you are willing to hang around and see how things develop. I hope it will change your mind later, and that the framework can be of great use. In the mean time your advice would be indispensable!</DIV><DIV>Cheers,</DIV><DIV>Alex</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>On 11-jul-2005, at 15:25, Koen van der Drift wrote:</DIV><BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">On Jul 11, 2005, at 8:44 AM, John Timmer wrote:</DIV> <BR><BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Well, it's starting very poorly for me.<SPAN class="Apple-converted-space"> </SPAN>If I'm the only one arguing the</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">alternative, then I the majority should rule.<SPAN class="Apple-converted-space"> </SPAN>Unfortunately, that makes the</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">resulting framework a poor choice for my work/coding style, so I don't</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">expect I will use it for much more than sequence format translations and</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">perhaps alignments.<SPAN class="Apple-converted-space"> </SPAN>Since I won't be using the main classes, I doubt I'll</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">contribute much to their coding in the future.</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; ">Well, that's not good news at 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; ">We should really try to find a solution for this situation. You have contributed quite some code and it would be a shame to see you leave because of this. I guess in your own project that uses BioCocoa you could always create your own subclasses of BCSequence to suit your needs, but that's a half baked solution, I admit.</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; ">My understanding is that the main reason you prefer the typed sequences, is that you can avoid sending the wrong type of sequence to the wrong operation, is that correct?<SPAN class="Apple-converted-space"> </SPAN>Because this is unavoidable for untyped sequences, we should do our best to find a solution for this. Alex's suggestion, using the symbolset, seems a good step forward. On the other hand, untyped sequences make implementing the immutable/mutable classes much easier.</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; ">John, I am sure I speak for the others too that I would hate to see you leave, so again, we should try all our efforts to come to a good way out of this.</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; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></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; min-height: 14.0px"><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>Microsoft is not the answer,</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>Microsoft is the question,</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>NO is the answer</FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px; font: 12.0px Helvetica; min-height: 14.0px"><BR></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="3" style="font: 12.0px Helvetica">*********************************************************</FONT></P> </DIV><BR></BODY></HTML>