<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; ">To long for the list, so here's the relevant part...<BR><DIV><BR><DIV>Begin forwarded message:</DIV><BR class="Apple-interchange-newline"><BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT face="Helvetica" size="3" color="#000000" style="font: 12.0px Helvetica; color: #000000"><B>From: </B></FONT><FONT face="Helvetica" size="3" style="font: 12.0px Helvetica">Alexander Griekspoor <<A href="mailto:mek@mekentosj.com">mek@mekentosj.com</A>></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT face="Helvetica" size="3" color="#000000" style="font: 12.0px Helvetica; color: #000000"><B>Date: </B></FONT><FONT face="Helvetica" size="3" style="font: 12.0px Helvetica">13 juli 2005 15:44:06 GMT+02:00</FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT face="Helvetica" size="3" color="#000000" style="font: 12.0px Helvetica; color: #000000"><B>To: </B></FONT><FONT face="Helvetica" size="3" style="font: 12.0px Helvetica">Koen van der Drift <<A href="mailto:kvddrift@earthlink.net">kvddrift@earthlink.net</A>></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT face="Helvetica" size="3" color="#000000" style="font: 12.0px Helvetica; color: #000000"><B>Cc: </B></FONT><FONT face="Helvetica" size="3" style="font: 12.0px Helvetica">Charles Parnot <<A href="mailto:charles.parnot@gmail.com">charles.parnot@gmail.com</A>>, BioCocoa-dev <<A href="mailto:biococoa-dev@bioinformatics.org">biococoa-dev@bioinformatics.org</A>></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT face="Helvetica" size="3" color="#000000" style="font: 12.0px Helvetica; color: #000000"><B>Subject: </B></FONT><FONT face="Helvetica" size="3" style="font: 12.0px Helvetica"><B>Re: [Biococoa-dev] Sequence Structure</B></FONT></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">Just a quick remark:<DIV><BR class="khtml-block-placeholder"></DIV><DIV>I thought that the idea was to have the NSData be the char array, so no separate const char*, that IS the NSData object already. </DIV><DIV>So to go over the list</DIV><BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">BCSequence</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "> const char *sequence; </DIV></BLOCKQUOTE><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "> -> is NSData so this one goes away, if you want access to the data, you would do: [sequenceData bytes]; which gives you the pointer</DIV><BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "> NSData *sequenceData;</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "> NSArray *symbolArray;</DIV></BLOCKQUOTE> -> this one only if we decide to cache it, otherwise, this would be a method only. So what was the consensus again on this?<BR><BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "> BCSymbolSet *symbolSet;</DIV></BLOCKQUOTE> <DIV>Cheers,</DIV><DIV>Alex<BR><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><DIV><DIV>On 13-jul-2005, at 15:19, 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; ">Hi,</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; ">After all the talking in the last week or so, I felt like coding again was playing last night with a possible new BCSequence-only structure. It will also include the char string and NSData ivars. For starters, I want to do just the immutable version, of course we can add stuff for the mutable sequence too later.<SPAN class="Apple-converted-space"> </SPAN>I need to read the chat log again to see if you guys came up with a good solution for that.</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; ">However, so far I have:</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; ">BCSequence</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>const char *sequence;</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>NSData *sequenceData;</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>NSArray *symbolArray;</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>BCSymbolSet *symbolSet;</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 can re-use most of the methods that are now in BCSequence and BCAbstractSequence, including the code that guesses the sequence type if there is no symbolset defined.<SPAN class="Apple-converted-space"> </SPAN>I am not sure if we also should add the BCSequenceType back in there. I think the symbolset is enough.</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; ">Let me know what you guys think of this, and if this is a good way forward.<SPAN class="Apple-converted-space"> </SPAN>In order not to screw up the project I won't commit anything until we all agree on this (or another) approach. I will make some code availabe for download, though.</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; min-height: 14px; "></DIV></BLOCKQUOTE></DIV></DIV></DIV></BLOCKQUOTE></DIV><DIV> </DIV><BR></BODY></HTML>