Hey Jonathan and Sandra, Sorry for the delayed response, I was away last week for a meeting.
Catching up on all the traffic discussed so far. We've had some work done by another developer and these issues have crept up in the latest release. A lot of the changes were done for the new sequence aligner editor. My fault for not looking more closely at the changes to make sure that nothing broke. I'll need to make sure that the partial fix doesn't break the new editor as well. I'll look at the different issues in more detail and get back to you guys. Cheers, Ed On Sat, 20 Jun 2009, Jonathan Crabtree wrote:
Hi Sandra, See below for interspersed comments: On Sat, Jun 20, 2009 at 10:13 AM, Sandra Lövenich <[email protected]> wrote: 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. We observed the problem in both 1.10.0 and 1.11.0, but I didn't check to see when it was introduced (and whether it ever worked correctly.) 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. Hm, that's strange. I thought I committed this fix last night. Did you check out the cvs HEAD or version 1.11.0? If the former then maybe my patch didn't make it in there somehow. 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. Thanks for the detailed debugging information. I took a quick look at your sample input files and determined that you can fix the problem by doing either of the following things: 1. Leave the GFF unchanged but modify the Shape used to draw the polypeptides. If you go to Preferences, select the "Types" tab and then "polypeptide" from the "Tier" pull-down menu and then change the Shape to any of the following your feature should show up (after you click on "Preview" or "Save", of course): DoubleHeadedArrow,Triangle,Zigzag,ThinRectangle. At this point your feature will appear _in the annotation area_. 2. Change the SO type in the GFF file from "polypeptide" to "match". Your feature will then appear _in the results area_. #2 seems like the most appropriate course of action given that your GFF3 feature has a "Target" attribute, which is typically only the case for search hits/matches. Let me know if you have trouble getting either of these approaches to work. I should mention that I think you may encounter other quirks with the GFF3 support. One thing I noticed, at least in 1.10.0 is that Apollo seems to rely on a sequence-region pragma to figure out where the annotations should go, rather than looking at the sequence id of the GFF features. The effect of this is that if you overlay a GFF file with annotations from several different chromosomes they will all go into the current display, unless the appropriate sequence-region pragmas are included. Another word of caution is that I don't know what, if anything, Apollo will do with polypeptide entries in the ##FASTA section of the GFF file, so if you want that sequence to be somehow associated with the loaded feature you should verify that Apollo is doing what you expect. 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? I noticed the same thing and I'm not sure what the deal is with that. I'm compiling on Ubuntu with a non-Sun JVM and don't have that class either. Any ideas, Ed? Jonathan
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