<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; ">Wait! <DIV><BR class="khtml-block-placeholder"></DIV><DIV>Ok, let me begin with Charles question what I'm talking about. The answer is yes, the sequence can have a delegate and still be a model yes.</DIV><DIV>BUT, let me try to convince what I meant with my remark and how we can do it in a better way. </DIV><DIV>First, the model-view-controller (MVC) design pattern. BCSequence is our model class, it contains the data. The idea behind this pattern is that the model never has any idea about the view its data is presented in, and is thus also not responsible for updates, data changes etc. This is all controlled by the controller which insulated both from each other and keeps both in sync. So if for instance the users edits the sequence in the gui, this should be picked up by the controller which makes sure the edit is forwarded to the model object. Thus, it would not make sense to have the model for instance being a delegate of the view, hence bypassing the controller. Also, why should the controller be the delegate of the model? The ONLY one changing the model is the controller, so if it does it should know already right! </DIV><DIV>Now, I admit there are situations that this is not completely true. Imagine a alignment controller A which aligns several sequences and communicates this via an alignment view. Now the same sequences could potentially be altered by a different controller B which presents the user with a standard sequence editing window. Now of course we would like controller A to redo the alignment and update the view. According to the MVC pattern it would be controller B's task to initiate the update of A (via delegation or notification), so officially no problem and still no need for the model to contain notifications/delegations. Still, sometimes it would be handy to be able to monitor the changes made to a model object if multiple controllers potentially edit the same model object.</DIV><DIV>Now what, notifications, delegations. I don't like the idea of sending "public" notifications into the air, and remember if we create or edit sequences a lot (which you do with model objects), this could create a lot of overhead, and could clog the notification system). Now delegates is more direct, but then again, you could only have one delegate, a severe limit for situations as described above!! In addition, in both case to make it work the code (most notable the accessors) will have to be polluted with delegation invocations (plus a check whether there actually is a delegate, plus a check whether the delegate responds to that call) or notification dispatches. Aaaaaahhh!!!</DIV><DIV><SPAN class="Apple-style-span">Luckily there's something better, called Key-value-observing (KVO), allowing exactly what you guys are looking for, available in 10.3 or higher (now, did we all agree already that 10.3 is our lower limit). It's part of the famous "binding" system, and allows controllers to register themselves as observers for certain properties of the model object and get notifications when these changes so they can do their things. Sounds pretty good huh! How does it work? We just have to be key-value-coding (KVC) compliant, which we are already, hooray! NSObject provides automatic support! If we decide that at somepoints we need more control, there are additional methods that can be called to trigger observers like <FONT class="Apple-style-span" face="Monaco" size="3"><SPAN class="Apple-style-span" style="font-size: 11px;">did</SPAN></FONT><FONT class="Apple-style-span" face="Monaco" size="3"><SPAN class="Apple-style-span" style="font-size: 11px;">ChangeValueForKey. </SPAN><FONT class="Apple-style-span" face="Helvetica">I strongly suggest to not go for delegates, not for notifications, but for KVO, which means we don't have to do anything, nice huh! Here's more info on KVO:</FONT></FONT></SPAN></DIV><DIV><A href="http://developer.apple.com/documentation/Cocoa/Conceptual/KeyValueObserving/KeyValueObserving.html">http://developer.apple.com/documentation/Cocoa/Conceptual/KeyValueObserving/KeyValueObserving.html</A></DIV><DIV><BR class="khtml-block-placeholder"></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><BR class="khtml-block-placeholder"></DIV><DIV><BR><DIV><DIV>On 9-jul-2005, at 8:28, 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; ">On Jul 8, 2005, at 9:39 PM, Koen van der Drift 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; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">On Jul 9, 2005, at 12:19 AM, Charles Parnot wrote:</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> <BR><BLOCKQUOTE type="cite"><BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Hmm, although certainly nice to have a link between a view and ultimately the sequence, this is the task of a controller class, not the model... The model shouldn't know/care of the view. It might be nice, if we add controllers to the framework that do this though..</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Alex</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; ">I am not sure what you both mean. Just to add to the confusion: BCSequence can have a delegate and still be a model, 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; 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; ">Why not let BCSequence post notifications when something has changed? This way it is ot conected to a view, but and any object (including a controller or a view) can respond 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; 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; ">Yes, the standard in Cocoa seems to have both a delegate and accompanying notifications, which the delegate always get without subscribing.</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><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></DIV></BODY></HTML>