Blast Output Into Jsp/Html

Question

[Yann]

I would like to display a blast result in a jsp or html by parsing the xml result of blast without using BioJava? how can I do that?

[Pierre Lindenbaum]

parsing XML and echoing it ? there is no need for BioJava here.

[Pierre Lindenbaum]

What's the provenance of your blast result ? is it a DOM document in memory ? or is it a flat file stored on your computer ? Do you just want to print the XML in some HTML or do you want to redirect the user to the blast-XML file ?

[Niallhaslam]

Any particular reason not to use BioJava?

[Fred Fleche]

Do you real need to use the XML format? You could simply echo the default text format.

Answer 1

[Istvan Albert]

You can easily format an XML document into any other format via an XSLT stylesheet. You can even do it as a static page transformed directly in the browser with XSLT.

Find one of the many tutorials

Answer 2

[Pierre Lindenbaum]

• Parse your XML document to a DOM object in memory. http://www.java2s.com/Code/Java/XML/LoadinganXMLDocumentusingDOM.htm
• from the controller (the httpServlet) put this dom into the httpRequest.setAttribute("mydom",dom);
• write a XSLT stylesheet transforming the blast XML to the output of your choice. e;g; see my XSLT stylesheet http://code.google.com/p/lindenb/source/browse/trunk/src/xsl/xml2html.xsl .
• load this (stylesheet from the the httpServlet) and put it into the httpRequest.setAttribute("mystlesheet",xsl);
• redirect the request to your jsp
• on the JSP side, transform the XML document using the standard x:transform tag ( http://java.sun.com/developer/technicalArticles/javaserverpages/faster/ )

Answer 3

[Michael Schubert]

Have you looked at the built-in BLAST HTML output?

> blastn -help | grep -A1 html
 -html
   Produce HTML output?

> blastn -version
blastn: 2.2.24+
Package: blast 2.2.24, build Aug 12 2010 17:47:58

This applies not only to blastn but the other programs as well. There is also wwwblast for the older version of the NCBI tools.