<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; "><DIV><DIV>Am 03.07.2005 um 13:45 schrieb Koen van der Drift:</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 3, 2005, at 6:12 AM, Philipp Seibel 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"><BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">I like the parser idea, particularly if it is already written by you ;-)</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">I won't be of any help with C++, though!</DIV> <BR></BLOCKQUOTE><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">this is no problem, because there is no much need of c++ except from expression templates.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">The parser isn't allready written by me sorry ;-), but i'm working on 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; ">I'd like to know the different sequence formats i should implement, that i can finish the parsers for the sequence io first.</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; ">Check out BCSequenceReader and BCReader (deprecated, but still in the project for reference) for some formats, just note that these methods still need a lot of work, annotations and features are still not completely implemented. Note that there a re already various parsers out there that could be of help, eg lucegene, bioperl and more.</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; ">What I don't understand yet is why the sequence parser framework is at the bottom of your picture. This implies to me that it is the basis for all the other frameworks? Why not put BCFoundation with BCSymbol and BCSequence there, that seems much more logical to me.</DIV></BLOCKQUOTE><DIV><BR class="khtml-block-placeholder"></DIV><DIV>In terms of importance you are right, but i wanted to show that you can't use BCFoundation without BCParser, because the BCFoundation-IO depends on the parsers. The same with all other BCXXXFrameworks.</DIV><BR><BLOCKQUOTE type="cite"> <BR><BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Very good summary of the discussion. </DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">I think we should try to implement the string thing in different ways and test the performance, to see which one is the best.</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; ">Maybe you can already post some sample code here, so we can get an idea what you have in mind.</DIV></BLOCKQUOTE><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Just give me one more week. I started the project a couple of days before.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Here is a short description:</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>The base class is a BCParser, that can be instantiated with NSData or contentsOfURL etc. (just like NSXMLParser). The parser has a event driven architecture, which means that it calls delegate methods whenever it founds specific information in the parsed data (NSXMLParser ;-)). Errors are reported with the NSError class. Here is a first unfinished example of the BCGenBankParser delegate methods:</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" color="#760F50" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;">@interface</SPAN></FONT><FONT class="Apple-style-span" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;"> NSObject (BCGenBankParserDelegateMethods)</SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal Monaco; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;">- (</SPAN></FONT><FONT class="Apple-style-span" color="#760F50" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;">void</SPAN></FONT><FONT class="Apple-style-span" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;">)parserDidBeginSequence:(BCParser *)parser;</SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal Monaco; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" color="#236E25" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;">// General Information</SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;">- (</SPAN></FONT><FONT class="Apple-style-span" color="#760F50" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;">void</SPAN></FONT><FONT class="Apple-style-span" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;">)parser:(BCParser *)parser foundDefinition:(NSString *)definition;</SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;">- (</SPAN></FONT><FONT class="Apple-style-span" color="#760F50" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;">void</SPAN></FONT><FONT class="Apple-style-span" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;">)parser:(BCParser *)parser foundAccession:(NSString *)accession;</SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;">- (</SPAN></FONT><FONT class="Apple-style-span" color="#760F50" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;">void</SPAN></FONT><FONT class="Apple-style-span" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;">)parser:(BCParser *)parser foundKeywords:(NSArray *)keywords;</SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal Monaco; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" color="#236E25" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;">// References</SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;">- (</SPAN></FONT><FONT class="Apple-style-span" color="#760F50" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;">void</SPAN></FONT><FONT class="Apple-style-span" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;">)parser:(BCParser *)parser didBeginReferenceForRange:(NSRange)range;</SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;">- (</SPAN></FONT><FONT class="Apple-style-span" color="#760F50" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;">void</SPAN></FONT><FONT class="Apple-style-span" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;">)parser:(BCParser *)parser foundReferenceAuthors:(NSArray *)keywords;</SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;">- (</SPAN></FONT><FONT class="Apple-style-span" color="#760F50" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;">void</SPAN></FONT><FONT class="Apple-style-span" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;">)parser:(BCParser *)parser foundReferenceTitle:(NSString *)title;</SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;">- (</SPAN></FONT><FONT class="Apple-style-span" color="#760F50" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;">void</SPAN></FONT><FONT class="Apple-style-span" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;">)parser:(BCParser *)parser foundReferenceJournal:(NSString *)journal;</SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;">- (</SPAN></FONT><FONT class="Apple-style-span" color="#760F50" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;">void</SPAN></FONT><FONT class="Apple-style-span" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;">)parserDidEndReference:(BCParser *)parser;</SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal Monaco; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;">- (</SPAN></FONT><FONT class="Apple-style-span" color="#760F50" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;">void</SPAN></FONT><FONT class="Apple-style-span" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;">)parser:(BCParser *)parser foundSequence:(NSString *)sequence;</SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal Monaco; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;">- (</SPAN></FONT><FONT class="Apple-style-span" color="#760F50" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;">void</SPAN></FONT><FONT class="Apple-style-span" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;">)parserDidEndSequence:(BCParser *)parser;</SPAN></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 10px/normal Monaco; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT class="Apple-style-span" color="#760F50" face="Monaco" size="2"><SPAN class="Apple-style-span" style="font-size: 10px;">@end</SPAN></FONT></DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>thats it for the moment.</DIV><DIV>feel free to comment the concept.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>cheers,</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Phil</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR class="khtml-block-placeholder"></DIV><BR><BLOCKQUOTE type="cite"><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> <BR class="Apple-interchange-newline"></BLOCKQUOTE></DIV><BR></BODY></HTML>