[Biojava-l] SequencePoster <-> SequencePanel

[Kalle Näslund]

Maximilian Haeussler wrote:

> Hi everyone,
> still searching for something similar to SequencePanel that does not 
> throw exceptions in a JScrollPane...while doing this, I stumbled upon 
> SequencePoster. Hum...the javadoc for both looks very very similar, if 
> not identical... can someone give me a hint on the difference between 
> SequencePanel and SequencePoster?
> This question sounds rather stupid, but doing a diff on both didn't 
> really help, and I don't really know where to search. And in the 
> demos-dir, there are EmblViewer and BeadDemo but they look really 
> pretty similar...
>
> Thanks
> Max
>
>
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Its highly probable that i have nailed down the reason you are seeing 
lots of IndexOutOfBoundsException being thrown.
SequencePanel. The actual output will most likely look something like this.

java.lang.IndexOutOfBoundsException: max must exceed min: min=1, max=-18
        at 
org.biojava.bio.symbol.RangeLocation.<init>(RangeLocation.java:61)
        at 
org.biojava.bio.gui.sequence.GUITools.getVisibleRange(GUITools.java:36)
        at 
org.biojava.bio.gui.sequence.FeatureBlockSequenceRenderer.paint(FeatureBlockSequenceRenderer.java:216)
        at 
org.biojava.bio.gui.sequence.SequenceRendererWrapper.paint(SequenceRendererWrapper.java:160)

I have a fix for this problem ( developed with help from Matthew ). BUT, 
it seems like the fix might cause some rendering
issues. Atleast that was my initial thougt, untill a few hours ago, when 
i checked out a fresh sourceetree and tried out the
demo applications, and it seems the current sourcetree has the same 
rendering issus as my fixed version.

The rendering issues i am talking about is that some of the demos render 
LOTS of empty space behind the sequences. From
a quick look it looks like it first renders the sequence, and then an 
equaly large empty part, behind the sequence.

I see this behaviour with the following demo applications

seqviewer.BeadDemo
seqviewer.EmblViewer2

What these two things share, is that they both use SequencePanel.

What i would like, if that anyone can just take a quick look at the 
BeadDemo and EmblViewer2 demos, and just check that
they see the same rendering problem as i see, so i am 100% its not a bug 
i have introduced somehow.

If thats the case, i would feel comfortable in commiting the changes 
that will fix the Exception throwing. And i can then try
to find out why the SequencePanel renders lots of blank space.

regards Kalle