<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">I'm initially working on a slightly more flexible version of the Vista alignment tool (or similarly the SinicView tool) while I wait for research results to compute. This is in part to learn Cocoa programming and in part because I find both tools to be very clumsy and lacking in their ability to easily add custom annotation tracks. Ultimately, I'd like an easy to extend platform for both evaluating alignments and visualizing them in various ways. Too many of these sorts of tools are extremely customized to one particular data source. <div><br></div><div><div>It isn't a major priority for me, but I figure that it's better to build functionality into a tool like this rather than create one shot command line tools as I've currently been doing. If I get somewhere useful with this, I'll be sure to send back changes and relevant classes.</div><div><br></div><div>Regards,</div><div><br></div><div>Alex</div><div><br></div><div><div><div><div><div><div><div><div><div><div><div>On 2008-09-22, at 5:07 PM, Scott Christley wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Hello Alex,<br><br>Yes, the project is still alive; however, many of the original developers have moved on to other things (though they might still be lurking on the list), so there is not much active development. I've been putting in code related to my research, e.g. suffix arrays, plus I have a bunch of local modifications dealing with managing gene expression data. I've recently tried getting the documentation in order.<br><br>I haven't used BCSequenceAlignment but from looking at the code, it doesn't look like much is there. Duplicating existing work on sequence alignment is probably not the best use of resources, better to add wrapper and handlers to BioCocoa for other tools.<br><br>By alignment visualization, do you mean something like JalView which gives a graphical output of CLUSTAL?<br><br>I'm happy to take any of your changes and merge them back into the source.<br><br>cheers<br>Scott<br><br>On Sep 22, 2008, at 1:47 PM, Alexander K. Hudek wrote:<br><br><blockquote type="cite">-----BEGIN PGP SIGNED MESSAGE-----<br></blockquote><blockquote type="cite">Hash: SHA1<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">I'm playing around with BioCocoa for an alignment visualization<br></blockquote><blockquote type="cite">application. It appears the project is no longer under active<br></blockquote><blockquote type="cite">development? Is there still interesting in continuing development? I'm<br></blockquote><blockquote type="cite">very new to Objective-C and Cocoa, but I'm not opposed to helping out.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">I've already had to modify the sequence reader class to allow it to<br></blockquote><blockquote type="cite">read sequences with gap characters, although I'm not sure if this was<br></blockquote><blockquote type="cite">the intended use of SequenceReader. Also, it looks like<br></blockquote><blockquote type="cite">BCSequenceAlignment is very far from being finished. Is this correct?<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Regards,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Alex<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Alexander K. Hudek<br></blockquote><blockquote type="cite">School of Computer Science, University of Waterloo<br></blockquote><blockquote type="cite">200 University Avenue West, Waterloo, ON, N2L 3G1, Canada<br></blockquote><blockquote type="cite">Phone: +1 519 888 4567 x37886 Fax: +1 519 885 1208<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">-----BEGIN PGP SIGNATURE-----<br></blockquote><blockquote type="cite">Version: GnuPG v1.4.8 (Darwin)<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">iEYEARECAAYFAkjYBGcACgkQAI69dtlP4E1AGQCfbibQzS7ND+crvBvS3Fd0XvQf<br></blockquote><blockquote type="cite">QHIAn2CmkZqifAaUIX3wZ0RO0wg3maRr<br></blockquote><blockquote type="cite">=utoz<br></blockquote><blockquote type="cite">-----END PGP SIGNATURE-----<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">_______________________________________________<br></blockquote><blockquote type="cite">Biococoa-dev mailing list<br></blockquote><blockquote type="cite"><a href="mailto:Biococoa-dev@bioinformatics.org">Biococoa-dev@bioinformatics.org</a><br></blockquote><blockquote type="cite"><a href="http://www.bioinformatics.org/mailman/listinfo/biococoa-dev">http://www.bioinformatics.org/mailman/listinfo/biococoa-dev</a><br></blockquote></div></blockquote></div><br><div> <span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Alexander K. Hudek</div><div>School of Computer Science, University of Waterloo</div><div><div>200 University Avenue West, Waterloo, ON, N2L 3G1, Canada</div><div>Phone: +1 519 888 4567 x37886 Fax: +1 519 885 1208</div> </div></div></span></div><br></div></div></div></div></div></div></div></div></div></div></body></html>