Class HTMLRenderer

java.lang.Object
org.biojava.bio.program.blast2html.HTMLRenderer

public class HTMLRenderer extends Object
Renders HTML version of blast-like output.

Makes an assumption that the gap character is '-', should parameterize. Primary author - Colin Hardman (CAT) Other authors - Tim Dilks (CAT) Simon Brocklehurst (CAT) Stuart Johnston (CAT) Lawerence Bower (CAT) Derek Crockford (CAT) Neil Benn (CAT) Copyright 2001 Cambridge Antibody Technology Group plc. This code released to the biojava project, May 2001 under the LGPL license.

Version:
1.0
Author:
Cambridge Antibody Technology Group plc, Greg Cox
  • Constructor Details

    • HTMLRenderer

      public HTMLRenderer(PrintWriter poPrintWriter, String poStyleDef, int piAlignmentWidth, URLGeneratorFactory poFactory, AlignmentMarker poAlignmentMarker, Properties poOptions)
      Creates an HTMLRenderer, that outputs the HTML to the specified PrintWriter.

      The style definition is expected to defines the following styles

      • footer
      • alignment
      • dbRetrieve
      • titleLevel1
      • titleLevel1Sub
      • titleLevel2
      • titleLevel3
      • titleLevel3Sub
      • titleLevel4
      • summaryBodyLineOdd
      • summaryBodyLineEven invalid input: '<'/UL The Javascript function setStatus overrides status text for some links. The URLGeneratorFactory provides a list of objects that can convert a database ID into a URL for fetching the entry. Obviously this requires the ID to be parsed correctly. These URL's are used in two places, in the summary and detail sections. The first URLGenerator is used for the summary, and all for the detail.
      Parameters:
      poPrintWriter - - the output stream to write the HTML to.
      poStyleDef - - definition of styles, if null uses hard coded.
      piAlignmentWidth - width in characters of the alignment regions of output
      poFactory - URLGeneratorFactory provides an array of DatabaseURLGenerators, null for no links
      poAlignmentMarker - - for configurable markup of alignments, for no markup use null.
      poOptions - properties of
  • Method Details

    • setPrintWriter

      public void setPrintWriter(PrintWriter poPrintWriter)
      Set the PrintWriter to output the HTML to.
      Parameters:
      poPrintWriter - a PrintWriter
    • wasEmpty

      public boolean wasEmpty()
      Returns true if no HitSummary and no Hit elements were encountered
      Returns:
      boolean - true if no summary of Hit elements where encountered.
    • getHeaderDefinitions

      Returns the appropriate style and javascript definitions for this renderer.
      Returns:
      a String value