by Cambridge Antibody Technology

Introduction

This tutorial covers the use of the Blast-like parsing framework to generate HTML representations of the Blast-like XML.

Here are some examples of the type of output you can generate.

• Blastp
• Blastn

Prerequisites are:

• an upto date copy of biojava
• the programs in the demos directory

Running the demos

To generate for yourself the above example HTML files, change directory to the demos directory of biojava. The following commands will generate the HTML to standard out:

java eventbasedparsing.Blast2HTML nucleic files/ncbiblast/blastn.out
java eventbasedparsing.Blast2HTML protein files/ncbiblast/blastp.out

You can choose an output file (instead of redirecting standard out) by adding a third argument to the command:

java eventbasedparsing.Blast2HTML protein files/ncbiblast/blastp.out blastp.html

Customising the Output

The HTMLRenderer constructor takes several parameters which allow customisation of the HTML.

• Style sheet: You can change the definition of the styles in the style sheet.
• Alignment width: The alignment width simply specifies the number of bases/residues per alignment block.
• URLGeneratorFactory: Returns a List of DatabaseURLGenerators. These are used to convert database ID’s to URL’s and links. You can create your own. See NcbiDatabaseURLGenerator for an example.
• AlignmentMarker: Delegates most of it’s operations to the ColourCommand and AlignmentStyler.
  • ColourCommand: Controls whether a pair of characters in the alignment are styled or not.
  • AlignmentStyler: Decides what style to apply to any given pair of characters.

E.g. To markup mismatches in red you would have a ColourCommand that decides only mismatches are coloured, and then an AlignmentStyler that colours any characters passed to it as red.

There are a couple of implementations of AlignmentStyler: SimpleAlignmentStyler and BlastMatrixAlignmentStyler - see the Javadocs for details.

Of course you can also use custom handlers to only pass on a subset of the output.