<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; ">The discussion feature vs annotations is another one to tackle, I think an annotation is independent of position, a feature is. Author, creation date, species etc would be an annotation, phosphorylation, alpha-helix, etc would be a feature. But there are many things in the gray area. Again, I'm with charles, it doesn't make sense to separate annotations/features from sequences because we would end up with more lightweight sequences, we don't. In the end we have to keep both around, in one or two objects doesn't make a difference in ram (in fact, it's probably more because of overlap). In addition, it makes syncing much more difficult. If you are not interested in the annotations, don't touch them, we use pointers anyway so passing around of sequences with or without annotations doesn't make a difference. Finally, the particular problem you mention (large datafiles) has nothing to do with this problem, in your case simply ask the importer to not handle the metadata and only import the sequence (an option we definitely have to build in into the seqIO classes). Plus, BCSequence should have methods to ask a (sub)version of the sequence with or WITHOUT annotations. Charles gave an example already...<DIV>Alex<DIV><BR><DIV><DIV>On 9-jul-2005, at 14:02, 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 9, 2005, at 2:40 AM, Charles Parnot 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; ">But, still, your initial argument seems to be that BCSequence should remain a light object, hence no annotations. However, an additional ivar for the annotations will not make it heavier if it is set to nil.</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; ">What I want to avoid is that when a large datafile is read (eg pdb or swissprot) not all the metadata is stuffed in to the annotations, making the sequence object heavy.<SPAN class="Apple-converted-space"> </SPAN>However, sequence specific information such as C=C bonds, PTM, probably should be in the sequence object. Or would they then be called features?</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; 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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>Windows vs Mac</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 class="Apple-converted-tab"> </SPAN></SPAN>65 million years ago, there were more<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>dinosaurs than humans.</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 class="Apple-converted-tab"> </SPAN> </SPAN>Where are the dinosaurs now?</FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px; 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