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.