[Biojava-l] Using Blast2HTML

[Richard Holland]

Are you sure the BioJava classes/jar files are on your classpath whilst
compiling? The constructor it mentions definitely exists so this is the
only thing I can think of that might be wrong.

cheers,
Richard

PS. Also make sure you're using the latest (1.4) release, or the latest
code from CVS.

On Mon, 2006-06-26 at 17:18 +0200, David Bourgais wrote:
> Hello
> 
> I would like to implement the Blast2HTML class.
> But this method failed suring compilation :
> 
> public HTMLRenderer configureBlastN( PrintWriter poOut ) {
> 		
> 		SimpleAlignmentStyler oStyler = new SimpleAlignmentStyler
> ( SimpleAlignmentStyler.SHOW_ALL );
> 		String oRed = "FFA2A2";
> 		oStyler.addStyle( "-", oRed );
> 		oStyler.addStyle( "N", oRed );
> 		oStyler.addStyle( "A", oRed );
> 		oStyler.addStyle( "T", oRed );
> 		oStyler.addStyle( "C", oRed );
> 		oStyler.addStyle( "G", oRed );
> 		
> 		AlignmentMarker oAlignmentMarker = new AlignmentMarker
> 		( new ColourCommand() {
> 			public  boolean  isColoured
> 			(  String poFirst, String poSecond ) {
> 				
> 				if ( poFirst.equals( poSecond ) ) {
> 					return false;
> 				} else {
> 					return true;
> 				}
> 			}
> 		} // end ColourCommand
> 		, oStyler
> 		);
> 		
> 		Properties oProps = new Properties();
> 		oProps.put( "db", "nucl" );
> 		
> 		DefaultURLGeneratorFactory durlgf = new DefaultURLGeneratorFactory();
> 		
> 		HTMLRenderer oRenderer = new HTMLRenderer(poOut,
> 				this.oStyleDefinition,
> 				50,
> 				durlgf,
> 				oAlignmentMarker,
> 				oProps);
> 		
> 		return oRenderer;
> 	}
> 
> My compiler told me :
> The constructor HTMLRenderer(PrintWriter, String, int,
> DefaultURLGeneratorFactory, AlignmentMarker, Properties) is undefined
> 
> How can I solve this problem.
> 
> Thank you very much for answer.
> 
> Regards.
> 
> David Bourgais
> 
> 
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-- 
Richard Holland (BioMart Team)
EMBL-EBI
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
UNITED KINGDOM
Tel: +44-(0)1223-494416