Changeset 1823:fb105c3cd60f in orange-bioinformatics


Ignore:
Timestamp:
06/11/13 13:17:45 (10 months ago)
Author:
Flashpoint <vid.flashpoint@…>
Branch:
default
Parents:
1822:8634a5cd44d4 (diff), 1804:4981b5cd8411 (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.
Message:

Merged biolab/orange-bioinformatics into default

Files:
2 edited

Legend:

Unmodified
Added
Removed
  • _bioinformatics/widgets/OWSetEnrichment.py

    r1804 r1823  
    6969    def __init__(self, parent=None, signalManager=None, name="Gene Set Enrichment Analysis", **kwargs): 
    7070        OWWidget.__init__(self, parent, signalManager, name, **kwargs) 
    71         self.inputs = [("Example Table", ExampleTable, self.setData, Default), ("Reference", ExampleTable, self.setReference)] 
    72         self.outputs = [("Selected Examples", ExampleTable)] 
     71        self.inputs = [("Data", ExampleTable, self.setData, Default), ("Reference", ExampleTable, self.setReference)] 
     72        self.outputs = [("Data subset", ExampleTable)] 
    7373 
    7474        self.speciesIndex = 0 
     
    204204            with orngServerFiles.DownloadProgress.setredirect(self.progressBarSet): 
    205205                all, local = obiGeneSets.list_all(), obiGeneSets.list_local() 
    206                 organisms = set(obiTaxonomy.essential_taxids() + [t[1] for t in all]) 
     206                organisms = set(obiTaxonomy.essential_taxids() + filter(None, [t[1] for t in all])) 
    207207            self.progressBarFinished() 
    208208 
     
    268268        for hierarchy, t_id, _ in self.genesets: 
    269269            collect(collection[t_id], hierarchy) 
     270 
     271        #add genesets without species identifiers 
     272        collection[taxid].update(collection[None]) 
    270273        return collection[taxid] 
    271274 
  • _bioinformatics/widgets/OWSetEnrichment.py

    r1810 r1823  
    404404            return 
    405405 
     406        self.updateGenematcher() 
     407 
    406408        self.progressBarInit() 
    407         self.updateGenematcher() 
    408409        self.currentAnnotatedCategories = categories = self.selectedCategories() 
    409410 
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