[Biojava-l] RestrictionEnzyme can't handle double sites

I think a solution requires the RestritionEnzyme class to be changed. Maybe changing getRecognitionSite() to return an array of Strings SymbolLists instead of a single String? -Jesse --- mark.schreiber at novartis.com mark.schreiber at novartis.com Wed Jun 22 21

RE: [Biojava-l] BLAST Parser for extracting all BLAST data?

Hi, everybody... I'm like GeorgesI want to extract data from BLAST files. I can have the alignements, no problem...But, now, I want the alignment between the 2 sequences (the lines with "+", "-" and some letters in George's example) because with this, we can see in a glance if the alig

RE: [Biojava-l] BLAST Parser for extracting all BLAST data?

Hi, With the example, I can extract all information I require except the length of query sequence. Is there any "hidden" method that can report the query length in parenthesis as (138 letters) in the sample output below? BTW, the addSubHitProperty() method doesn't report the Gaps data. Fortunatel

RE: [Biojava-l] BLAST Parser for extracting all BLAST data?

ArgghI didn't find what I wanted!! I used the program you gave me but with a light modification because it didn't recognize my XML file... The parser is, now, a BlastXMLParserFacade And it gave me everythings it found in the file. BUT not what I want!!GRRR...>:( >:( >:( There is a mar

AW: [Biojava-l] BLAST Parser for extracting all BLAST data?

if you don't find what you need through biojava, you can always write a small xml parser with for example jdom. 1 - download jdom.jar 2 - use the following code to find : 3 - replace the path of the xml file in the main method 4 - it prints out every found Element I hope it helps you Best, Chr

RE: AW: [Biojava-l] BLAST Parser for extracting all BLAST data?

Thank you for JDOM and the code... But, it generates a ton of exceptions and error because it doesn't find a DTD file (NCBI_BlastOutput.dtd) that I don't have... So, I don't know how to do... Sebastien --- "BIBIS, Garnier, Christophe" <[EMAIL PROTECTED]> a écrit : > > if you don't find what yo

RE: AW: AW: [Biojava-l] BLAST Parser for extracting all BLAST data?

I try the code you sent me. I just change the path of the XML file. But, in this file, there is this line : and I have exceptions and errors because of this line. If you want, I send the XML file so that you test it... But, I download the DTD and the MOD files necessary, I modified the DTD fil

[Biojava-l] Implementing a Feature

Hello, all. I am new to BioJava but finding it extremely useful. I'd like to add a few extra fields or methods to the SimpleFeature class and I'm wondering the best way to go about it? I have read through BioJava in Anger and also am wondering if there are any other documents out there t

RE: [Biojava-l] Implementing a Feature

The best thing to do is write your own class which extends SimpleFeature, or ignores SimpleFeature and just implements the Feature interface with all-new methods written from scratch, plus your new ones. If the extra methods are pretty generic, you could create a new interface which extends Fea

RE: AW: AW: [Biojava-l] BLAST Parser for extracting all BLAST data?

Easiest method (if you don't care about validating) is delete the DTD line in the XML. If you do need to validate, ensure you have your proxy settings stet correctly so the parser can access the DTD. Russell -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf

[Biojava-l] BLAST functionality

There have been a number of requests to the list (and directly to me) for increased functionality for the BLAST parsers (eg capturing more of the information in the report). Originally the design was lightweight and captured what most people wanted but as always there are always people who thin