Commits

Aleš Erjavec committed b3e32cc

Added new style widget meta descriptions.

Comments (0)

Files changed (23)

orangecontrib/bio/widgets/OWBioMart.py

 from collections import defaultdict
 import itertools
 
+import Orange
+
 from Orange.OrangeWidgets import OWConcurrent
 from Orange.OrangeWidgets.OWWidget import *
 
 from .. import obiBioMart
 from ..obiBioMart import *
 
+NAME = "BioMart"
+DESCRIPTION = "Query BioMart service"
+ICON = "icons/BioMart.svg"
+PRIORITY = 2010
+
+INPUTS = [("Input ids", Orange.data.Table, "setData")]
+OUTPUTS = [("Example Table", Orange.data.Table)]
+
+REPLACES = ["_bioinformatics.widgets.OWBioMart.OWBioMart"]
+
+
 socket.setdefaulttimeout(60)
-                
+
+
 def is_hidden(tree):
     return getattr(tree, "hidden", "false") != "false" or getattr(tree, "hideDisplay", "false") != "false"
 

orangecontrib/bio/widgets/OWCustomSets.py

 
 from Orange.bio.obiGeneSets import loadGMT, list_local, register, local_path, remove_local, modification_date, getGenesetsStats
 
+NAME = "Custom Gene Sets"
+DESCRIPTION = "Manage custom geneset files"
+ICON = "icons/customSets.svg"
+PRIORITY = 5000
+
+INPUTS = []
+OUTPUTS = []
+
+REPLACES = ["_bioinformatics.widgets.OWCustomSets.OWCustomSets"]
+
+
 class OWCustomSets(OWWidget):
 
     def __init__(self, parent=None, signalManager=None,

orangecontrib/bio/widgets/OWDicty.py

 from collections import defaultdict
 import sys
 
+import Orange
 from Orange.orng import orngEnviron
 from Orange.OrangeWidgets import OWGUI
 from Orange.OrangeWidgets.OWWidget import *
 
 from .. import obiDicty
 
+NAME = "dictyExpress"
+DESCRIPTION = "Access to data in dictyExpress database."
+ICON = "icons/DictyExpress.svg"
+PRIORITY = 40
+
+
+INPUTS = []
+OUTPUTS = [("Example table", Orange.data.Table)]
+
+REPLACES = ["_bioinformatics.widgets.OWDicty.OWDicty"]
+
+
 class MyTreeWidgetItem(QTreeWidgetItem):
     def __contains__(self, text):
         return any(text.upper() in str(self.text(i)).upper() for i in range(self.columnCount()))    

orangecontrib/bio/widgets/OWDisplayProfiles.py

 from Orange.OrangeWidgets.OWWidget import *
 import statc
 
+NAME = "Data Profiles"
+DESCRIPTION = "Visualization of data profiles (e.g., time series)."
+ICON = "icons/ExpressionProfiles.svg"
+PRIORITY = 1030
+
+INPUTS = [("Examples", Orange.data.Table, "data", Multiple + Default)]
+OUTPUTS = [("Examples", Orange.data.Table)]
+
+REPLACES = ["_bioinformatics.widgets.OWDisplayProfiles.OWDisplayProfiles"]
+
 ## format of data:
 ##     largestAdjacentValue
 ##     yq3

orangecontrib/bio/widgets/OWFeatureSelection.py

 from ..obiGEO import transpose
 
 
+NAME = "Differential expression"
+DESCRIPTION = "Gene differential expression scoring and selection."
+ICON = "icons/GeneSelection.svg"
+PRIORITY = 1010
+
+INPUTS = [("Examples", Orange.data.Table, "set_data")]
+OUTPUTS = [("Example table with selected genes", Orange.data.Table, Default),
+           ("Example table with remaining genes", Orange.data.Table),
+           ("Selected genes", Orange.data.Table)]
+
+REPLACES = ["_bioinformatics.widgets.OWFeatureSelection.OWFeatureSelection"]
+
+
 class ExpressionSignificance_TTest_PValue(ExpressionSignificance_TTest):
     def __call__(self, *args, **kwargs):
         return [(key, pval) for key, (t, pval) in \

orangecontrib/bio/widgets/OWGEODatasets.py

 
 from .. import obiGEO
 
+NAME = "GEO Data Sets"
+DESCRIPTION = "Access to Gene Expression Omnibus data sets."
+ICON = "icons/GEODataSets.svg"
+PRIORITY = 20
+
+INPUTS = []
+OUTPUTS = [("Expression Data", Orange.data.Table)]
+
+REPLACES = ["_bioinformatics.widgets.OWGEODatasets.OWGEODatasets"]
+
+
 LOCAL_GDS_COLOR = Qt.darkGreen
 
 TextFilterRole = OWGUI.OrangeUserRole.next()

orangecontrib/bio/widgets/OWGOEnrichmentAnalysis.py

 
 from .. import obiGene, obiGO, obiProb, obiTaxonomy
 
+NAME = "GO Browser"
+DESCRIPTION = "Enrichment analysis for Gene Ontology terms."
+ICON = "icons/GOBrowser.svg"
+PRIORITY = 2020
+
+INPUTS = [("Cluster Examples", Orange.data.Table,
+           "SetClusterDataset", Single + Default),
+          ("Reference Examples", Orange.data.Table,
+           "SetReferenceDataset")]
+
+OUTPUTS = [("Selected Examples", Orange.data.Table),
+           ("Unselected Examples", Orange.data.Table),
+           ("Example With Unknown Genes", Orange.data.Table),
+           ("Enrichment Report", Orange.data.Table)]
+
+REPLACES = ["_bioinformatics.widgets.OWGOEnrichmentAnalysis.OWGOEnrichmentAnalysis"]
+
+
 dataDir = orngServerFiles.localpath("GO")
 
 def listAvailable():

orangecontrib/bio/widgets/OWGeneAtlasTissueExpression.py

 
 from .. import obiArrayExpress, obiGene, obiGeneAtlas
 
+NAME = "Gene Atlas Tissue Expression"
+DESCRIPTION = ""
+ICON = "icons/GeneExpressionAtlas.svg"
+PRIORITY = 5000
+
+INPUTS = [("Example Table", Orange.data.Table, "set_data")]
+OUTPUTS = [("Selected Genes", Orange.data.Table)]
+
+REPLACES = ["_bioinformatics.widgets.OWGeneAtlasTissueExpression.OWGeneAtlasTissueExpression"]
+
+
 TAXID_TO_ORG = obiGeneAtlas.TAXID_TO_ORG
 
 class OWGeneAtlasTissueExpression(OWWidget):

orangecontrib/bio/widgets/OWGeneInfo.py

 
 from .. import obiGene, obiTaxonomy
 
+
+NAME = "Gene Info"
+DESCRIPTION = "Displays gene information from NCBI and other sources."
+ICON = "icons/GeneInfo.svg"
+PRIORITY = 2010
+
+INPUTS = [("Examples", Orange.data.Table, "setData")]
+OUTPUTS = [("Selected Examples", Orange.data.Table)]
+
+REPLACES = ["_bioinformatics.widgets.OWGeneInfo.OWGeneInfo"]
+
+
 class TreeModel(QAbstractItemModel):
     def __init__(self, data, header, parent):
         QAbstractItemModel.__init__(self, parent)

orangecontrib/bio/widgets/OWGeneMania.py

 
 from .. import obiGeneMania
 
+NAME = "GeneMANIA"
+DESCRIPTION = ""
+ICON = "icons/GeneMANIA.svg"
+
+INPUTS = [("Input Genes", Orange.data.Table, "setData")]
+OUTPUTS = [("Network", Orange.network.Graph, Default),
+           ("Items", Orange.data.Table)]
+
+REPLACES = ["_bioinformatics.widgets.OWGeneMania.OWGeneMania"]
+
+
 class BarItemDelegate(QStyledItemDelegate):
     BarRole = OWGUI.OrangeUserRole.next() 
     BarForegroundRole = OWGUI.OrangeUserRole.next()

orangecontrib/bio/widgets/OWGenotypeDistances.py

 
 from ..obiExperiments import separate_by, data_type, linearize, dist_pcorr, dist_eucl, dist_spearman
 
+NAME = "Genotype Distances"
+DESCRIPTION = "Compute distances between expression profiles of different experimental factors."
+ICON = "icons/GenotypeDistances.svg"
+PRIORITY = 1050
+
+INPUTS = [("Example Table", Orange.data.Table, "set_data")]
+OUTPUTS = [("Distances", Orange.core.SymMatrix),
+           ("Sorted Example Table", Orange.data.Table)]
+
+REPLACES = ["_bioinformatics.widgets.OWGenotypeDistances.OWGenotypeDistances"]
+
+
 def clone_attr(attr):
     newattr = attr.clone()
     def get_value_from(ex, w=None):

orangecontrib/bio/widgets/OWGsea.py

 
 from .. import obiGene, obiGeneSets, obiGsea, obiKEGG
 
+NAME = "GSEA"
+DESCRIPTION = "Gene set enrichment analysis."
+ICON = "icons/GSEA.svg"
+PRIORITY = 2025
+
+INPUTS = [("Examples", Orange.data.Table, "setData")]
+OUTPUTS = [("Examples with selected genes only", Orange.data.Table),
+           ("Results", Orange.data.Table),
+           ("Distance Matrix", Orange.core.SymMatrix)]
+
+REPLACES = ["_bioinformatics.widgets.OWGsea.OWGsea"]
+
+
 def nth(l, n):
     return [ a[n] for a in l ]
 

orangecontrib/bio/widgets/OWHeatMap.py

 
 import functools
 
+NAME = "Heat Map"
+DESCRIPTION = "Heatmap visualization."
+ICON = "icons/Heatmap.svg"
+PRIORITY = 1040
+
+INPUTS = [("Examples", Orange.data.Table, "set_dataset")]
+OUTPUTS = [("Examples", Orange.data.Table, Single + Default)]
+
+REPLACES = ["_bioinformatics.widgets.OWHeatMap.OWHeatMap"]
+
+
 DEBUG = False
 
 #BUG: OWHeatMap does not support heatmaps which need a image which is larger than maxint X maxint pixels!

orangecontrib/bio/widgets/OWKEGGPathwayBrowser.py

 from .. import obiKEGG
 from .. import obiGeneSets
 
+
+NAME = "KEGG Pathways"
+DESCRIPTION = "Browse KEGG pathways that include an input set of genes."
+ICON = "icons/KEGGPathways.svg"
+PRIORITY = 2030
+
+INPUTS = [("Examples", Orange.data.Table, "SetData", Default),
+          ("Reference", Orange.data.Table, "SetRefData")]
+OUTPUTS = [("Selected Examples", Orange.data.Table, Default),
+           ("Unselected Examples", Orange.data.Table)]
+
+REPLACES = ["_bioinformatics.widgets.OWKEGGPathwayBrowser.OWKEGGPathwayBrowser"]
+
+
 USE_THREADING = True
 
 if USE_THREADING:

orangecontrib/bio/widgets/OWMAPlot.py

 
 from .. import obiExpression
 
+NAME = "MA Plot"
+DESCRIPTION = "Normalize expression array data on a MA - plot"
+ICON = "icons/MAPlot.svg"
+PRIORITY = 5000
+
+INPUTS = [("Expression array", Orange.data.Table, "setData")]
+OUTPUTS = [("Normalized expression array", Orange.data.Table, Default),
+           ("Filtered expression array", Orange.data.Table)]
+
+REPLACES = ["_bioinformatics.widgets.OWMAPlot.OWMAPlot"]
+
+
 class ProgressBarDiscard(QObject):
     def __init__(self, parent, redirect):
         QObject.__init__(self, parent)

orangecontrib/bio/widgets/OWMeSHBrowser.py

 
 from ..obiMeSH import *
 
+NAME = "MeSH Browser"
+DESCRIPTION = "Browse MeSH ontology."
+ICON = "icons/MeSHBrowser.svg"
+PRIORITY = 2040
+
+INPUTS = [("Reference data", Orange.data.Table, "getReferenceData"),
+		  ("Cluster data", Orange.data.Table, "getClusterData")]
+
+OUTPUTS = [("Selected examples", Orange.data.Table)]
+
+REPLACES = ["_bioinformatics.widgets.OWMeSHBrowser.OWMeSHBrowser"]
+
+
 class MyQTableWidgetItem(QTableWidgetItem):
 	""" Our implementation of QTable item allowing numerical sorting.  """
 	def __init__(self,table,text):

orangecontrib/bio/widgets/OWMoleculeVisualizer.py

 
 from .. import obiChem
 
+NAME = "Molecule Visualizer"
+DESCRIPTION = "Rendering of 2D structure of molecules based on their SMILES description."
+ICON = "icons/MoleculeVisualizer.svg"
+PRIORITY = 2050
+
+INPUTS = [("Molecules", Orange.data.Table, "setMoleculeTable", Default),
+		  ("Molecule subset", Orange.data.Table, "setMoleculeSubset"),
+		  ("Fragments", Orange.data.Table, "setFragmentTable")]
+OUTPUTS = [("Selected Molecules", Orange.data.Table)]
+
+REPLACES = ["_bioinformatics.widgets.OWMoleculeVisualizer.OWMoleculeVisualizer"]
+
+
 class dummy_module(object):
 	def __init__(self, name):
 		self.name = name

orangecontrib/bio/widgets/OWPIPA.py

 
 from .. import obiDicty
 
+(2, 'No such file or directory')
+NAME = "PIPA"
+DESCRIPTION = "Access data from PIPA RNA-Seq database."
+ICON = "icons/PIPA.svg"
+PRIORITY = 30
+
+INPUTS = []
+OUTPUTS = [("Example table", Orange.data.Table)]
+
+REPLACES = ["_bioinformatics.widgets.OWPIPA.OWPIPA"]
+
+
 #def pyqtConfigure(object, **kwargs):
 #    if hasattr(object, "pyqtConfigure"):
 #        object.pyqtConfigure(**kwargs)

orangecontrib/bio/widgets/OWPIPAx.py

 from .OWPIPA import (MyTreeWidgetItem, ListItemDelegate,
                     SelectionSetsWidget, SortedListWidget)
 
+NAME = "PIPAx"
+DESCRIPTION = "Access data from PIPA RNA-Seq database."
+ICON = "icons/PIPA.svg"
+PRIORITY = 35
+
+INPUTS = []
+OUTPUTS = [("Example table", Orange.data.Table)]
+
+REPLACES = ["_bioinformatics.widgets.OWPIPAx.OWPIPAx"]
+
 try:
     from ast import literal_eval
 except ImportError:

orangecontrib/bio/widgets/OWQualityControl.py

 
 from .OWGenotypeDistances import SetContextHandler
 
+NAME = "Quality Control"
+DESCRIPTION = "Experiment quality control"
+ICON = "icons/QualityControl.svg"
+PRIORITY = 5000
+
+INPUTS = [("Experiment Data", Orange.data.Table, "set_data")]
+OUTPUTS = []
+
+REPLACES = ["_bioinformatics.widgets.OWQualityControl.OWQualityControl"]
+
+
 DEBUG = False
 
 @contextmanager

orangecontrib/bio/widgets/OWSetEnrichment.py

 
 from .. import obiGene, obiGeneSets, obiProb, obiTaxonomy
 
+NAME = "Gene Set Enrichment"
+DESCRIPTION = ""
+ICON = "icons/GeneSetEnrichment.svg"
+PRIORITY = 5000
+
+INPUTS = [("Data", Orange.data.Table, "setData", Default),
+          ("Reference", Orange.data.Table, "setReference")]
+OUTPUTS = [("Data subset", Orange.data.Table)]
+
+REPLACES = ["_bioinformatics.widgets.OWSetEnrichment.OWSetEnrichment"]
+
+
 def _toPyObject(variant):
     val = variant.toPyObject()
     if isinstance(val, type(NotImplemented)): # PyQt 4.4 converts python int, floats ... to C types

orangecontrib/bio/widgets/OWUpdateGenomicsDatabases.py

 
 from Orange.OrangeWidgets.OWDatabasesUpdate import *
 
+NAME = "Databases"
+DESCRIPTION = "Update of systems biology data and knowledge bases."
+ICON = "icons/Databases.svg"
+PRIORITY = 10
+
+INPUTS = []
+OUTPUTS = []
+
+REPLACES = ["_bioinformatics.widgets.OWUpdateGenomicsDatabases.OWUpdateGenomicsDatabases"]
+
+
 class OWUpdateGenomicsDatabases(OWDatabasesUpdate): 
     def __init__(self, parent=None, signalManager=None, name="Databases", **kwds):
         OWDatabasesUpdate.__init__(self, parent, signalManager, name, domains = \

orangecontrib/bio/widgets/OWVulcanoPlot.py

 from .. import obiExpression
 from ..obiGEO import transpose
 
+NAME = "Vulcano Plot"
+DESCRIPTION = "Plots fold change vs. p-value.)"
+ICON = "icons/VulcanoPlot.svg"
+PRIORITY = 1020
+
+INPUTS = [("Examples", Orange.data.Table, "setData")]
+OUTPUTS = [("Examples with selected attributes", Orange.data.Table)]
+
+REPLACES = ["_bioinformatics.widgets.OWVulcanoPlot.OWVulcanoPlot"]
+
+
 class GraphSelections(QObject):
     """ Selection manager using a union of rectangle areas 
     """
Tip: Filter by directory path e.g. /media app.js to search for public/media/app.js.
Tip: Use camelCasing e.g. ProjME to search for ProjectModifiedEvent.java.
Tip: Filter by extension type e.g. /repo .js to search for all .js files in the /repo directory.
Tip: Separate your search with spaces e.g. /ssh pom.xml to search for src/ssh/pom.xml.
Tip: Use ↑ and ↓ arrow keys to navigate and return to view the file.
Tip: You can also navigate files with Ctrl+j (next) and Ctrl+k (previous) and view the file with Ctrl+o.
Tip: You can also navigate files with Alt+j (next) and Alt+k (previous) and view the file with Alt+o.