Changeset 1643:2cfa80dac3d3 in orange-bioinformatics


Ignore:
Timestamp:
04/20/12 03:16:59 (2 years ago)
Author:
mitar
Branch:
default
Children:
1644:e455af7d00bd, 1645:b542c4ab17b1
Message:

Fixing some imports. Marking widgets as prototypes.

Files:
23 edited

Legend:

Unmodified
Added
Removed
  • _bioinformatics/obiGO.py

    r1636 r1643  
    984984        os.rename(filename + ".part", filename) 
    985985 
    986 from . from obiTaxonomy import pickled_cache 
     986from .obiTaxonomy import pickled_cache 
    987987 
    988988@pickled_cache(None, [("GO", "taxonomy.pickle"), ("Taxonomy", "ncbi_taxonomy.tar.gz")]) 
  • _bioinformatics/obiGene.py

    r1636 r1643  
    33import os, time 
    44 
    5 from Orange.orng . import orngServerFiles 
     5from Orange.orng import orngServerFiles 
    66 
    77from . import obiTaxonomy 
  • _bioinformatics/obiGeneAtlas.py

    r1636 r1643  
    260260        return dd[name] 
    261261    else: 
    262         import .obiTaxonomy as tax 
     262        from . import obiTaxonomy as tax 
    263263        ids = tax.to_taxid(name, mapTo=TAXID_TO_ORG.keys()) 
    264264        if ids: 
  • _bioinformatics/obiGeneSets.py

    r1636 r1643  
    1313from Orange.orng import orngServerFiles 
    1414 
    15 from . import obiGeneSets, obiGO, obiKEGG, obiTaxonomy 
     15from . import obiGO, obiKEGG, obiTaxonomy 
    1616 
    1717sfdomain = "gene_sets" 
     
    9999 
    100100    def update(self, input): 
     101        from . import obiGeneSets 
    101102        if isinstance(input, obiGeneSets.GeneSets): 
    102103            super(GeneSets, self).update(input) 
     
    156157    def split_by_hierarchy(self): 
    157158        """ Splits gene sets by hierarchies. """ 
     159        from . import obiGeneSets 
    158160        hd = dict((h,obiGeneSets.GeneSets()) for h in  self.hierarchies()) 
    159161        for gs in self: 
     
    163165def goGeneSets(org): 
    164166    """Returns gene sets from GO.""" 
     167    from . import obiGeneSets 
    165168 
    166169    ontology = obiGO.Ontology() 
     
    182185    Returns gene sets from KEGG pathways. 
    183186    """ 
    184     from . import obiKEGG2 as obiKEGG 
     187    from . import obiKEGG2 as obiKEGG, obiGeneSets 
    185188     
    186189    kegg = obiKEGG.KEGGOrganism(org) 
     
    250253    For now the description is skipped. 
    251254    """ 
     255 
     256    from . import obiGeneSets 
     257 
    252258    def hline(s): 
    253259        tabs = [tab.strip() for tab in s.split("\t")] 
     
    467473    hierarchy is a tuple also. 
    468474    """ 
     475    from . import obiGeneSets 
    469476    result = obiGeneSets.GeneSets() 
    470477 
  • _bioinformatics/widgets/OWDisplayProfiles.py

    r1636 r1643  
    77""" 
    88 
    9 from Orange.OrangeWidgets.OWGUI 
     9from Orange.OrangeWidgets import OWGUI 
    1010from Orange.OrangeWidgets.OWGraph import * 
    1111from Orange.OrangeWidgets.OWToolbars import ZoomSelectToolbar 
  • _bioinformatics/widgets/OWKEGGPathwayBrowser.py

    r1636 r1643  
    1313 
    1414import orange 
    15 from Orange.orng import orngMisc 
     15from Orange.orng import orngMisc, orngServerFiles 
    1616from Orange.orng.orngDataCaching import data_hints 
    1717from Orange.OrangeWidgets import OWGUI 
    1818from Orange.OrangeWidgets.OWWidget import * 
    1919 
    20 from .. import obiKEGG, orngServerFiles 
     20from .. import obiKEGG 
    2121from .. import obiTaxonomy 
    2222from .. import obiKEGG2 as obiKEGG 
  • _bioinformatics/widgets/prototypes/OWANOVA.py

    r1636 r1643  
    77<priority>1070</priority> 
    88<contact>Peter Juvan (peter.juvan@fri.uni-lj.si)</contact> 
     9<prototype>1</prototype> 
    910""" 
    1011 
  • _bioinformatics/widgets/prototypes/OWApproxProfiles.py

    r1636 r1643  
    77<priority>310</priority> 
    88<contact>Peter Juvan (peter.juvan@fri.uni-lj.si)</contact> 
     9<prototype>1</prototype> 
    910""" 
    1011 
  • _bioinformatics/widgets/prototypes/OWDataDistance.py

    r1636 r1643  
    77<priority>1160</priority> 
    88<contact>Peter Juvan (peter.juvan@fri.uni-lj.si)</contact> 
     9<prototype>1</prototype> 
    910""" 
    1011 
  • _bioinformatics/widgets/prototypes/OWDataFiles.py

    r1636 r1643  
    55<priority>1050</priority> 
    66<contact>Peter Juvan (peter.juvan@fri.uni-lj.si)</contact> 
     7<prototype>1</prototype> 
    78""" 
    89 
  • _bioinformatics/widgets/prototypes/OWDataFilesSave.py

    r1636 r1643  
    55<priority>1055</priority> 
    66<contact>Peter Juvan (peter.juvan@fri.uni-lj.si)</contact> 
     7<prototype>1</prototype> 
    78""" 
    89 
  • _bioinformatics/widgets/prototypes/OWDataFilesSelector.py

    r1636 r1643  
    55<priority>1060</priority> 
    66<contact>Peter Juvan (peter.juvan@fri.uni-lj.si)</contact> 
     7<prototype>1</prototype> 
    78""" 
    89 
  • _bioinformatics/widgets/prototypes/OWDifferentiationScale.py

    r1636 r1643  
    1 """<name>Differentiation Scale</name> 
     1""" 
     2<name>Differentiation Scale</name> 
    23<description></description> 
     4<prototype>1</prototype> 
    35""" 
    46 
  • _bioinformatics/widgets/prototypes/OWDisplayMotifs.py

    r1636 r1643  
    44<contact>Tomaz Curk</contact> 
    55<icon>icons\GenomeMap.png</icon> 
     6<prototype>1</prototype> 
    67""" 
    78 
  • _bioinformatics/widgets/prototypes/OWEpistasisAnalysis.py

    r1636 r1643  
    44<icon>icons/EpistasisAnalysis.png</icon> 
    55<priority>1200</priority> 
     6<prototype>1</prototype> 
    67""" 
    78 
  • _bioinformatics/widgets/prototypes/OWExampleSelector.py

    r1636 r1643  
    55<priority>1070</priority> 
    66<contact>Peter Juvan (peter.juvan@fri.uni-lj.si)</contact> 
     7<prototype>1</prototype> 
    78""" 
    89 
  • _bioinformatics/widgets/prototypes/OWGeneAtlasTissueExpression.py

    r1636 r1643  
    22<name>Gene Atlas Tissue Expression</name> 
    33<description></description> 
     4<prototype>1</prototype> 
    45""" 
    56 
  • _bioinformatics/widgets/prototypes/OWHypTest.py

    r1636 r1643  
    77<priority>1071</priority> 
    88<contact>Peter Juvan (peter.juvan@fri.uni-lj.si)</contact> 
     9<prototype>1</prototype> 
    910""" 
    1011 
  • _bioinformatics/widgets/prototypes/OWImputeProfiles.py

    r1636 r1643  
    77<priority>1065</priority> 
    88<contact>Peter Juvan (peter.juvan@fri.uni-lj.si)</contact> 
     9<prototype>1</prototype> 
    910""" 
    1011 
  • _bioinformatics/widgets/prototypes/OWNormalization.py

    r1636 r1643  
    22<name>Normalization</name> 
    33<description>Gene Expression data normalization</description> 
     4<prototype>1</prototype> 
    45""" 
    56 
  • _bioinformatics/widgets/prototypes/OWNormalize.py

    r1636 r1643  
    1 ## Automatically adapted for numpy.oldnumeric Oct 04, 2007 by  
    2  
    31""" 
    42<name>Normalize Expression Array Data</name> 
     
    75<priority>1150</priority> 
    86<author>Peter Juvan (peter.juvan@fri.uni-lj.si)</author> 
     7<prototype>1</prototype> 
    98""" 
     9 
     10from __future__ import absolute_import 
    1011 
    1112""" 
    1213TODO: settingsList 
    1314""" 
    14  
    15 from __future__ import absolute_import 
    1615 
    1716import string, math 
  • _bioinformatics/widgets/prototypes/OWProcessChipData.py

    r1636 r1643  
    55<priority>1060</priority> 
    66<contact>Peter Juvan (peter.juvan@fri.uni-lj.si)</contact> 
     7<prototype>1</prototype> 
    78""" 
    89 
  • setup.py

    r1642 r1643  
    9191    ), 
    9292    'orange.widgets': ( 
    93         'bioinformatics = _bioinformatics.widgets', 
     93        'Bioinformatics = _bioinformatics.widgets', 
     94        # This should be unneeded, because module given should load (register) 
     95        # all wanted widgets and prototypes should just have a flag, but for now ... 
     96        'Prototypes = _bioinformatics.widgets.prototypes', 
    9497    ), 
    9598} 
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