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rodrigoSantamaria / Voronto

Mapper for gene expression to ontologies
http://vis.usal.es/voronto/
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java.lang.NullPointerException #1

Closed josegarciamanteiga closed 11 years ago

josegarciamanteiga commented 11 years ago

Hi, I'm a new user of Voronto, I have no experience with java but I managed to use custom ontologies by saving the obo files using a search in amigo.geneontology. I used several keywords and then selected all GO terms in the results and downloaded in obo format. It worked fine. Then I downloaded the Gaf from RGD for rat genes annotation. Fine. Now I have done another research but I have exported only one GO Term (mRNA cis splicing, via spliceosome (GO:0045292)) into obo format. The same dataset and Gaf file and it gives me the following error:

java.lang.NullPointerException at es.usal.voronto.model.voronoi.BernhardtTessellation.recursiveComputeVoronoi(BernhardtTessellation.java:240) at es.usal.voronto.model.voronoi.BernhardtTessellation.(BernhardtTessellation.java:110) at es.usal.voronto.view.VoronoiVisualization.(VoronoiVisualization.java:179) at es.usal.voronto.control.Voronto$Task.doInBackground(Voronto.java:244) at es.usal.voronto.control.Voronto$Task.doInBackground(Voronto.java:1) at javax.swing.SwingWorker$1.call(SwingWorker.java:296) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334) at java.util.concurrent.FutureTask.run(FutureTask.java:166) at javax.swing.SwingWorker.run(SwingWorker.java:335) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603) at java.lang.Thread.run(Thread.java:722)

Could you please tell me what has gone wrong? Why did it work before with another obo file, downloaded in the same way but with many more GO terms? Does it need a minimum GO terms to complete a set of Ontologies for it to work? Thanks in advance

rodrigoSantamaria commented 11 years ago

Hi, Voronto was originally designed for large ontologies, and therefore undertested on small ontology trees. What you reported is a bug that occurs when the tree has a root node with only one child. It has been solved, along with another side issue (the number of annotated genes was not correctly shown when hovering a term, in the case of custom ontologies). The new version has been uploaded to vis.usal.es/voronto and also the code submitted here.

Thanks for reporting the issue, Rodrigo

rodrigoSantamaria commented 11 years ago

The new version of Voronto allows to select the root GO term to use for the visualization, so it might easen your work somehow

rodrigoSantamaria commented 11 years ago

Hi, Today we uploaded a new version that, for GO ontologies, allow to specify the root term. It might be handy for your analysis

Cheers, Rodrigo