Hi Jonathan and the List,
Thanks a lot for this verbose explanation and especially for pointing
out where my GFF3 problem may be caused.
Please note, that the version I have been experiencing this problem
with is 1.11.0.
I have now checked out the code from sourceforge and added the
following lines to
src/java/apollo/dataadapter/gff3/GFF3Adapter.java
if (oboParser == null) {
try {
Collection<String> fnames = getOBOFilenames();
logger.info("Loading OBO files: " + fnames);
oboParser = new OBOParser(fnames, true);
}
catch (IOException e) {
throw new ApolloAdapterException("Error reading OBO file: " +
e.getMessage());
}
catch (OBOParseException e) {
throw new ApolloAdapterException("Error parsing OBO file: " +
e.getMessage());
}
}
starting from line 480.
This way the gff file gets successfully loaded. The feature (in my
case only one small polypeptide) is now
listed under Apollo's "Annotation" Menu (within the Main menu). When
clicking on it, it also gets
displayed in the "Evidence Panel" correctly and the main window is
zoomed into the correct
location . So - somehow some information
However, nothing is displayed (I checked the Display Panel button and
also set the maximum row for this
feature to 100. I tried several different chado-xml and gff
combination (different peptides, different chromosomes, etc. ).
The loading seem fine and the data is somehow "known" but does not get
displayed.
I have uploaded screenshots showing what I mean here:
http://www.biocompute.de/Apollo-ClickingOnFeatureJumpsToCorrectRegion.png
http://www.biocompute.de/Apollo-ImportedFeatureAppearsInAnnotations.png
http://www.biocompute.de/Apollo-NewEvidenceTierCanBeConfigured.png
http://www.biocompute.de/Apollo-NewEvidenceTierCanBeConfigured-2.png
http://www.biocompute.de/Apollo-NewEvidenceDoesNotShow.png
Maybe you have another suggestion for me? Or even a fix?
Thanks a lot!
Sandra
P.S.
By the way, when downloading Apollo sources from sourceforge and
trying to compile using javac/ant or javac/make
the compilation of
apollo/gui/detailviewers/sequencealigner/renderers/
AnnotationRenderer.java
fails with an error about a missing package "package
sun.text.CompactShortArray does not exist".
This class may have existed in Java 4, however, Java 5 and 6 do not
have it (Apollo requires Java 5). Please also see
http://java.sun.com/products/jdk/faq/faq-sun-packages.html
However, commenting out the import helps. So - maybe the
CompactShortArray$Iterator class is not used after all?
On 2009-Jun-20, at 5:48 AM, Jonathan Crabtree wrote:
Hi all,
I only just learned of the 1.11.0 release a couple of days ago, as I
seem to have allowed my apollo mailing list subscription to expire.
We're planning to run a workshop that uses Apollo in just over a
week, so I was checking out the status of the 1.11.0 release. (I'm
eager to use the latest release because I sorely missed the Types
panel in 1.10.0!)
Anyway, to the point. There seem to be at least a couple of rather
severe bugs in this release, for which I'm about to commit patches.
I just wanted to give everyone a heads-up, because these issues are
serious enough that you might want to reconsider upgrading to 1.11.0
until they're patched. (Although if I'm the only one who's noticed
them, perhaps they're not so serious!) Also, I noticed a recent e-
mail from Sandra Loevenich about a GFF3 import problem that sounds
as though it could be caused by bug #3 on my list (see below.)
So here's a quick rundown on the major issues:
1. Apollo crashes/hangs when displaying sequences that contain
"Ns". It doesn't necessarily happen immediately, but as soon as you
zoom far enough in on a region with Ns (e.g., by using the Ctrl-Z/
zoom to feature shortcut) the main display will freeze and stop
updating. I traced this to an apparently undocumented change in
DNAUtils.java, which in version 1.10.0 was capable of reverse
complementing sequences with Ns, but in 1.11.0 will throw an
IllegalArgumentException if given an 'N' (see DNAUtils.complement)
2. After fixing bug #1 there's still a problem with zooming in too
far in regions with Ns, this time an array out of bounds exception
in ScaleView.drawGaps. I'm less sure of this one because I don't
remember how coordinates are handled in Apollo, but comparing it to
Sequence.getResiduesImpl I think it's fairly clear that the loop in
drawGaps goes 1 base too far. I'm not sure how/when this change was
introduced, but reducing the upper bound of the loop by 1 gets the
gaps to render correctly in the example sequence I'm testing with.
3. (This may be the cause of Sandra's issue.) There's a logic error
in GFF3Adapter, whereby the oboParser only gets initialized when
getCurationSet() is called. This is fine if you load your original
data from GFF and then attempt to layer additional GFF annotations
(via addToCurationSet), but it's not so good if you load your
original data from a different source (chado, chadoxml, etc.) and
then try to layer GFF annotations on top. You'll get a
NullPointerException on the oboParser, from what I remember. The
fix is simply to move the oboParser initialization to a different
method.
4. The NavigationBar is broken for the chado/JDBC adapter; whatever
you tell it to do it just ends up reloading the same initial gene or
region. There's a fix for this going into ChadoAdapter.java.
5. The chado/JDBC option searchHitsHaveFeatLocs cannot be set to
false. It used to be supported, but appears to have been broken
when the underlying SQL was modified. Set it to false and the
adapter will generate invalid SQL. I started working on this but
don't have a completed fix yet (mostly because I realized that I
don't need it for our upcoming workshop.)
That's all I've found so far. #1 and #2 are obviously the most
serious, although the patches are extremely small. Let me know if
you have trouble replicating any of these, or see any problems with
the patches I'm about to commit.
Jonathan
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