Package org.biojava.bio.program.blast2html

Code for generating HTML reports from blast output

Interface Summary

Interface	Description
ColourCommand	Interface for specifying whether a particular pair of residues/bases should be coloured.
DatabaseURLGenerator	Takes a database ID and some configuration properties ( such as base URL ) and returns either a URL or a full anchor tag.
URLGeneratorFactory	Interface for a factory method to return a list of 0, 1 or more DatabaseURLGenerator instances.

Class Summary

Class	Description
AbstractAlignmentStyler	Abstract implementation of AlignmentStyler, contains utility methods for generating a set of HTML styles from a list of RGB colours.
AlignmentMarker	Class to do simple HTML colouring of sequence alignments.
Blast2HTMLHandler	Takes a SAX event stream and a HTMLRenderer to produce a HTML Blast like program report.
DefaultURLGeneratorFactory	A simple default URLGeneratorFactory which returns a single NcbiDatabaseURLGenerator instance.
EbiDatabaseURLGenerator	Simple URL generator for EMBL at the EBI.
HTMLRenderer	Renders HTML version of blast-like output.
NcbiDatabaseURLGenerator	Simple URL generator for Entrez at the NCBI.
SimpleAlignmentStyler	Simple implementation for specifying markup styles.