[Biojava-l] Displaying a simple alignment blastoutput-like[Scanned]

[Louise Ott]

Posting all the code won't help because everything is visible except the 
object of OtherAlignmentPanel.
I already tested the same code but with a SequencePanel and a 
SequencePanelWrapper added to my frame (with one sequence to display) and it 
worked fine.

So if there is a problem, I think this can be only in the code I already 
posted.

(And the code is really really big, is would be hard to read)

Sorry for my poor english, i'm french, I don't always use the good words to 
explain my problem :)

--------------------------------------------------
From: "Jolyon Holdstock" <jolyon.holdstock at ogt.co.uk>
Sent: Tuesday, February 09, 2010 4:40 PM
To: "Louise Ott" <anjolou at hotmail.com>; <biojava-l at lists.open-bio.org>
Subject: RE: [Biojava-l] Displaying a simple alignment 
blastoutput-like[Scanned]

> Does nothing become visible, if so how are you calling the panels/frame to 
> display?
>
> Can you post all your code?
>
> -----Original Message-----
> From: Louise Ott [mailto:anjolou at hotmail.com]
> Sent: 09 February 2010 15:18
> To: biojava-l at lists.open-bio.org
> Subject: [Biojava-l] Displaying a simple alignment 
> blastoutput-like[Scanned]
>
>
> Hi all !
> I read and followed all the advices i found on the net and in this mailing 
> list and i came to this :
>
> public class OtherAlignmentPanel extends TranslatedSequencePanel {
>    public otherAlignmentPanel(Alignment ali) { 
> this.setSequence((SymbolList) ali); 
> this.setBackground(Color.white);        this.setPreferredSize(new 
> Dimension(MainFrame.screenSize.width -40, MainFrame.screenSize.height - 
> 15));
>        MultiLineRenderer multi = new MultiLineRenderer(); 
> AlignmentRenderer render1 = new AlignmentRenderer(); 
> AlignmentRenderer render2 = new AlignmentRenderer(); 
> AlignmentRenderer render3 = new AlignmentRenderer(); 
> SymbolSequenceRenderer symbol = new SymbolSequenceRenderer();
>        render1.setLabel(ali.getLabels().get(0)); 
> render1.setRenderer(symbol);
>        multi.addRenderer(render1);
>        render2.setLabel(ali.getLabels().get(1)); 
> render2.setRenderer(symbol);
>        multi.addRenderer(render2);
>        render3.setLabel(ali.getLabels().get(2)); 
> render3.setRenderer(symbol);
>        multi.addRenderer(render3);
>        this.setRenderer(multi);    }
> }
>
> I created the panel in a frame like this :
>        Sequence seq1;        seq1 = 
> ProteinTools.createGappedProteinSequence(hspHits.getHsp().get(0).getHspQseq(), 
> "query");
>        Sequence seq2;        seq2 = 
> ProteinTools.createGappedProteinSequence(hspHits.getHsp().get(0).getHspHseq(), 
> "hit");
>        Sequence seq3;        seq3 = 
> ProteinTools.createGappedProteinSequence(hspHits.getHsp().get(0).getHspMidline(), 
> "midline");
>        Map<String, Sequence> list = new HashMap(); 
> list.put("query", seq1);        list.put("middle", seq2); 
> list.put("hit", seq3);
>        SimpleAlignment ali = new SimpleAlignment((Map) list); 
> OtherAlignmentPanel pane = new otherAlignmentPanel(ali); this.add(pane);
>
>
>
> My problems :- First, it just shows nothing ! I am totally lost, it has 
> been 3 days i am just trying to display this simple alignment but it 
> doesn't work !!- I really would like the lines to be wrapped like in the 
> blast output, so i tryied with the SequencePanelWrapper, but it doesn't 
> work either...
> Is there any simple solution ??What did i do wrong in my code ?
>
>
> Have a nice day and thanks !
> Louise
>
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