Package org.biojava.bio.program.blast2html

Code for generating HTML reports from blast output

See:
          Description

Interface Summary
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
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.
 

Package org.biojava.bio.program.blast2html Description

Code for generating HTML reports from blast output