Package org.biojava.bio.program.blast2html
package org.biojava.bio.program.blast2html
Code for generating HTML reports from blast output
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ClassDescriptionAbstract implementation of
AlignmentStyler
, contains utility methods for generating a set of HTML styles from a list of RGB colours.Class to do simple HTML colouring of sequence alignments.Takes a SAX event stream and a HTMLRenderer to produce a HTML Blast like program report.Interface for specifying whether a particular pair of residues/bases should be coloured.Takes a database ID and some configuration properties ( such as base URL ) and returns either a URL or a full anchor tag.A simple defaultURLGeneratorFactory
which returns a singleNcbiDatabaseURLGenerator
instance.Simple URL generator for EMBL at the EBI.Renders HTML version of blast-like output.Simple URL generator for Entrez at the NCBI.Simple implementation for specifying markup styles.Interface for a factory method to return a list of 0, 1 or moreDatabaseURLGenerator
instances.