Changeset 1827:d9c6f60c5632 in orange-bioinformatics


Ignore:
Timestamp:
06/27/13 10:41:15 (10 months ago)
Author:
Flashpoint <vid.flashpoint@…>
Branch:
default
Message:

Removed the select/unselect all gene sets check box from OWSetEnrichment.py widget

Location:
_bioinformatics
Files:
2 edited

Legend:

Unmodified
Added
Removed
  • _bioinformatics/obiGeneAtlasSets.py

    r1826 r1827  
    44from Orange.bio.obiGeneAtlas import run_simple_query 
    55from Orange.bio.obiGeneSets import GeneSets, GeneSet 
     6import time 
    67 
    78def display_string(string): 
     
    1011regulation = "updown" 
    1112organism   = "Homo sapiens" 
    12 condition  = "cell_line" 
     13condition  = "organism_part" 
    1314org_code   = "9606" 
    1415max_pvalue = 1e-5 
     
    2728 
    2829for start in range(no_of_pages+1): 
     30    start = time.time() 
    2931    query = run_simple_query(regulation=regulation, organism=organism, condition=condition, start=start*no_of_genes, rows=no_of_genes) 
    3032    for result in query["results"]: 
    3133        i += 1 
    32         #print result["gene"]["name"] + "\t" + str(i) # For printing out gene names and the current number of genes during debugging 
     34        print result["gene"]["name"] + "\t" + str(i) # For printing out gene names and the current number of genes during debugging 
    3335        for exp in result["expressions"]:  
    3436            diff_exp = [e for e in exp["experiments"] if e["pvalue"] <= max_pvalue] # Use only genes that are significantly diff. expressed 
     
    3840                except: 
    3941                    sets[exp["efoTerm"], exp["efoId"]].append(result["gene"]["name"]) 
     42    print time.time() - start 
    4043         
    4144gene_sets = [] 
     
    5053final_set = GeneSets(gene_sets) 
    5154 
    52 #print final_set 
    53 #exit() 
     55print final_set 
     56exit() 
    5457 
    5558from Orange.bio.obiGeneSets import register 
  • _bioinformatics/widgets/OWSetEnrichment.py

    r1825 r1827  
    9898        self.speciesComboBox = OWGUI.comboBox(self.controlArea, self, 
    9999                      "speciesIndex", "Species", 
    100                       callback=lambda :self.data and self.updateAnnotations(), 
     100                      callback=lambda: self.data and self.updateAnnotations(), 
    101101                      debuggingEnabled=0) 
    102102 
     
    185185        self.connect(self.groupsWidget, SIGNAL("itemClicked(QTreeWidgetItem *, int)"), self.subsetSelectionChanged) 
    186186 
    187         self.omnibox = 1                                                                  ## A FUNCTION CALL TO HANDLE SELECTING/DESELECTING gene sets 
    188         OWGUI.checkBox(self.controlArea, self, "omnibox", "Select/Unselect all gene sets")#, callback= lambda :self.allSetsChanged()) 
    189  
    190187        OWGUI.button(self.controlArea, self, "Commit", callback=self.commit) 
    191188 
     
    275272        collection[taxid].update(collection[None]) 
    276273        return collection[taxid] 
    277  
    278  
    279  
    280  
    281 ## AN ATTEMPT TO ENABLE/DISABLE all gene sets at once 
    282 #    def allSetsChanged(self): 
    283 #        print self.omnibox 
    284 #        print self.getHierarchyCheckState() 
    285 #        print self.categoriesCheckState 
    286 #        print self.selectedCategories() 
    287          
    288  
    289274 
    290275    def setHierarchy(self, hierarchy): 
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