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" <[email protected]>
Sent: Tuesday, February 09, 2010 4:40 PM
To: "Louise Ott" <[email protected]>; <[email protected]>
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:[email protected]]
Sent: 09 February 2010 15:18
To: [email protected]
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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