<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; "><DIV>Hi Koen,<DIV><BR class="khtml-block-placeholder"></DIV><DIV>Good work on the sequence reader! </DIV><DIV><DIV><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; ">I have a couple of more questions before I can continue</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; ">1. What's the difference between Nexus and Nexusfileandblocks ?</DIV></BLOCKQUOTE><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; ">2. How is the nona format defined, I couldn't find anything about this?</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; ">3. The MSF file now uses the string "Pileup" as a selector. However, when searching for the format definition, I found that this format uses a '!!NA' or '!!AA' instead. But I may have found the wrong info, so if anyone knows which is correct, please let me know.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV></BLOCKQUOTE><DIV>On 1-3 Peter should know most questions I guess, he wrote the original stuff ;-).<BR></DIV><DIV><BR class="khtml-block-placeholder"></DIV><BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">4. I am thinking about adding a plist file to the framework that contains all the file extensions of possible sequence files. This can then be used in openPanel (see the code that Alex supplied). The nice thing about this is, is that we can synchronize the entries with the methods in BCSequenceReader. Any reason I should not do this?</DIV></BLOCKQUOTE><DIV><BR class="khtml-block-placeholder"></DIV>Sounds great, that allows us also to update BioCocoa with new read methods and existing programs can just change the framework and new support is added to their program.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>I'm also fixing some stuff for EnzymeX in the reader classes, the moment it's done I'll post you (koen) the changes and you can sync them with your work:</DIV><DIV>- I've added support for reading sequence files that weren't saved as plain-text but as rtf, basically adding a check and converting the file to plain text before continuing with the normal format determination</DIV><DIV>- I've changed the raw reading method such that it becomes more greedy. Peter's variant reads in all lines as separate entries in the matrix dictionary (which is probably what you want in aligned phylogenetic sequence files, but not in EnzymeX where people usually read in a single sequence file. So I remove all return characters first. I had one person complaining that EnzX only read the first line when he tried to open his nicely in 80 char columns formatted text file.</DIV><DIV>Now the question is what the difference</DIV><DIV>- I am fixing the binary file format reading (Strider/GCK) to make them universal compatible, currently they fail on an Intel based macs due to endian-issues</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Finally, to come back to the question on the formats, perhaps we can learn from a classic sequence reader package called ReadSeq by d.g.gilbert.</DIV><DIV>It reads the following formats, which are outlined in the Formats textfile inside the src folder:</DIV><DIV> 1. IG/Stanford 10. Olsen (in-only)</DIV><DIV> 2. GenBank/GB 11. Phylip3.2</DIV><DIV> 3. NBRF 12. Phylip</DIV><DIV> 4. EMBL 13. Plain/Raw</DIV><DIV> 5. GCG 14. PIR/CODATA</DIV><DIV> 6. DNAStrider 15. MSF</DIV><DIV> 7. Fitch 16. ASN.1</DIV><DIV> 8. Pearson/Fasta 17. PAUP</DIV><DIV> 9. Zuker (in-only) 18. Pretty (out-only)</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Some of them we support, but some not, so we can even add a few formats, plus the source code nicely shows how to discriminate them.</DIV><DIV>The latest version switched from c to java and added even a few more formats, so there's plenty to add ;-) The source also contains many sample files for testing purposes.</DIV><DIV>I'm not sure where it can be found nowadays, so I put it temporarily on our server for you guys to download:</DIV><DIV><A href="http://www.mekentosj.com/temporary/readseq.zip">http://www.mekentosj.com/temporary/readseq.zip</A></DIV><DIV>Have a look at it and tell me what you think.</DIV><DIV>Cheers,</DIV><DIV>Alex</DIV><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; ">For those who feel like helping out, the way to implement the code is:</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; ">- remove white lines (optional)</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">- get each line</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">- extract annotations into a BCAnnotationsArray</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">- extract the sequence(s) into an NSString</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">- once done with all the sequences, create a BCSequence from each sequenceString</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">- add the annotations to each BCSequence</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">- add the new BCSequence(s) to the BCSequenceArray</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">- return the BCSequenceArray</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; ">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; ">_______________________________________________</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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