Changeset 1874:b3e32cc5cf6f in orange-bioinformatics


Ignore:
Timestamp:
10/08/13 10:43:26 (7 months ago)
Author:
Ales Erjavec <ales.erjavec@…>
Branch:
default
Message:

Added new style widget meta descriptions.

Location:
orangecontrib/bio/widgets
Files:
23 edited

Legend:

Unmodified
Added
Removed
  • orangecontrib/bio/widgets/OWBioMart.py

    r1873 r1874  
    1515import itertools 
    1616 
     17import Orange 
     18 
    1719from Orange.OrangeWidgets import OWConcurrent 
    1820from Orange.OrangeWidgets.OWWidget import * 
     
    2123from ..obiBioMart import * 
    2224 
     25NAME = "BioMart" 
     26DESCRIPTION = "Query BioMart service" 
     27ICON = "icons/BioMart.svg" 
     28PRIORITY = 2010 
     29 
     30INPUTS = [("Input ids", Orange.data.Table, "setData")] 
     31OUTPUTS = [("Example Table", Orange.data.Table)] 
     32 
     33REPLACES = ["_bioinformatics.widgets.OWBioMart.OWBioMart"] 
     34 
     35 
    2336socket.setdefaulttimeout(60) 
    24                  
     37 
     38 
    2539def is_hidden(tree): 
    2640    return getattr(tree, "hidden", "false") != "false" or getattr(tree, "hideDisplay", "false") != "false" 
  • orangecontrib/bio/widgets/OWCustomSets.py

    r1873 r1874  
    1515 
    1616from Orange.bio.obiGeneSets import loadGMT, list_local, register, local_path, remove_local, modification_date, getGenesetsStats 
     17 
     18NAME = "Custom Gene Sets" 
     19DESCRIPTION = "Manage custom geneset files" 
     20ICON = "icons/customSets.svg" 
     21PRIORITY = 5000 
     22 
     23INPUTS = [] 
     24OUTPUTS = [] 
     25 
     26REPLACES = ["_bioinformatics.widgets.OWCustomSets.OWCustomSets"] 
     27 
    1728 
    1829class OWCustomSets(OWWidget): 
  • orangecontrib/bio/widgets/OWDicty.py

    r1873 r1874  
    1111import sys 
    1212 
     13import Orange 
    1314from Orange.orng import orngEnviron 
    1415from Orange.OrangeWidgets import OWGUI 
     
    1617 
    1718from .. import obiDicty 
     19 
     20NAME = "dictyExpress" 
     21DESCRIPTION = "Access to data in dictyExpress database." 
     22ICON = "icons/DictyExpress.svg" 
     23PRIORITY = 40 
     24 
     25 
     26INPUTS = [] 
     27OUTPUTS = [("Example table", Orange.data.Table)] 
     28 
     29REPLACES = ["_bioinformatics.widgets.OWDicty.OWDicty"] 
     30 
    1831 
    1932class MyTreeWidgetItem(QTreeWidgetItem): 
  • orangecontrib/bio/widgets/OWDisplayProfiles.py

    r1873 r1874  
    1313from Orange.OrangeWidgets.OWWidget import * 
    1414import statc 
     15 
     16NAME = "Data Profiles" 
     17DESCRIPTION = "Visualization of data profiles (e.g., time series)." 
     18ICON = "icons/ExpressionProfiles.svg" 
     19PRIORITY = 1030 
     20 
     21INPUTS = [("Examples", Orange.data.Table, "data", Multiple + Default)] 
     22OUTPUTS = [("Examples", Orange.data.Table)] 
     23 
     24REPLACES = ["_bioinformatics.widgets.OWDisplayProfiles.OWDisplayProfiles"] 
    1525 
    1626## format of data: 
  • orangecontrib/bio/widgets/OWFeatureSelection.py

    r1873 r1874  
    2626from ..obiExpression import * 
    2727from ..obiGEO import transpose 
     28 
     29 
     30NAME = "Differential expression" 
     31DESCRIPTION = "Gene differential expression scoring and selection." 
     32ICON = "icons/GeneSelection.svg" 
     33PRIORITY = 1010 
     34 
     35INPUTS = [("Examples", Orange.data.Table, "set_data")] 
     36OUTPUTS = [("Example table with selected genes", Orange.data.Table, Default), 
     37           ("Example table with remaining genes", Orange.data.Table), 
     38           ("Selected genes", Orange.data.Table)] 
     39 
     40REPLACES = ["_bioinformatics.widgets.OWFeatureSelection.OWFeatureSelection"] 
    2841 
    2942 
  • orangecontrib/bio/widgets/OWGEODatasets.py

    r1873 r1874  
    1818 
    1919from .. import obiGEO 
     20 
     21NAME = "GEO Data Sets" 
     22DESCRIPTION = "Access to Gene Expression Omnibus data sets." 
     23ICON = "icons/GEODataSets.svg" 
     24PRIORITY = 20 
     25 
     26INPUTS = [] 
     27OUTPUTS = [("Expression Data", Orange.data.Table)] 
     28 
     29REPLACES = ["_bioinformatics.widgets.OWGEODatasets.OWGEODatasets"] 
     30 
    2031 
    2132LOCAL_GDS_COLOR = Qt.darkGreen 
  • orangecontrib/bio/widgets/OWGOEnrichmentAnalysis.py

    r1873 r1874  
    2121 
    2222from .. import obiGene, obiGO, obiProb, obiTaxonomy 
     23 
     24NAME = "GO Browser" 
     25DESCRIPTION = "Enrichment analysis for Gene Ontology terms." 
     26ICON = "icons/GOBrowser.svg" 
     27PRIORITY = 2020 
     28 
     29INPUTS = [("Cluster Examples", Orange.data.Table, 
     30           "SetClusterDataset", Single + Default), 
     31          ("Reference Examples", Orange.data.Table, 
     32           "SetReferenceDataset")] 
     33 
     34OUTPUTS = [("Selected Examples", Orange.data.Table), 
     35           ("Unselected Examples", Orange.data.Table), 
     36           ("Example With Unknown Genes", Orange.data.Table), 
     37           ("Enrichment Report", Orange.data.Table)] 
     38 
     39REPLACES = ["_bioinformatics.widgets.OWGOEnrichmentAnalysis.OWGOEnrichmentAnalysis"] 
     40 
    2341 
    2442dataDir = orngServerFiles.localpath("GO") 
  • orangecontrib/bio/widgets/OWGeneAtlasTissueExpression.py

    r1873 r1874  
    1919 
    2020from .. import obiArrayExpress, obiGene, obiGeneAtlas 
     21 
     22NAME = "Gene Atlas Tissue Expression" 
     23DESCRIPTION = "" 
     24ICON = "icons/GeneExpressionAtlas.svg" 
     25PRIORITY = 5000 
     26 
     27INPUTS = [("Example Table", Orange.data.Table, "set_data")] 
     28OUTPUTS = [("Selected Genes", Orange.data.Table)] 
     29 
     30REPLACES = ["_bioinformatics.widgets.OWGeneAtlasTissueExpression.OWGeneAtlasTissueExpression"] 
     31 
    2132 
    2233TAXID_TO_ORG = obiGeneAtlas.TAXID_TO_ORG 
  • orangecontrib/bio/widgets/OWGeneInfo.py

    r1873 r1874  
    1919 
    2020from .. import obiGene, obiTaxonomy 
     21 
     22 
     23NAME = "Gene Info" 
     24DESCRIPTION = "Displays gene information from NCBI and other sources." 
     25ICON = "icons/GeneInfo.svg" 
     26PRIORITY = 2010 
     27 
     28INPUTS = [("Examples", Orange.data.Table, "setData")] 
     29OUTPUTS = [("Selected Examples", Orange.data.Table)] 
     30 
     31REPLACES = ["_bioinformatics.widgets.OWGeneInfo.OWGeneInfo"] 
     32 
    2133 
    2234class TreeModel(QAbstractItemModel): 
  • orangecontrib/bio/widgets/OWGeneMania.py

    r1873 r1874  
    1414 
    1515from .. import obiGeneMania 
     16 
     17NAME = "GeneMANIA" 
     18DESCRIPTION = "" 
     19ICON = "icons/GeneMANIA.svg" 
     20 
     21INPUTS = [("Input Genes", Orange.data.Table, "setData")] 
     22OUTPUTS = [("Network", Orange.network.Graph, Default), 
     23           ("Items", Orange.data.Table)] 
     24 
     25REPLACES = ["_bioinformatics.widgets.OWGeneMania.OWGeneMania"] 
     26 
    1627 
    1728class BarItemDelegate(QStyledItemDelegate): 
  • orangecontrib/bio/widgets/OWGenotypeDistances.py

    r1873 r1874  
    2020 
    2121from ..obiExperiments import separate_by, data_type, linearize, dist_pcorr, dist_eucl, dist_spearman 
     22 
     23NAME = "Genotype Distances" 
     24DESCRIPTION = "Compute distances between expression profiles of different experimental factors." 
     25ICON = "icons/GenotypeDistances.svg" 
     26PRIORITY = 1050 
     27 
     28INPUTS = [("Example Table", Orange.data.Table, "set_data")] 
     29OUTPUTS = [("Distances", Orange.core.SymMatrix), 
     30           ("Sorted Example Table", Orange.data.Table)] 
     31 
     32REPLACES = ["_bioinformatics.widgets.OWGenotypeDistances.OWGenotypeDistances"] 
     33 
    2234 
    2335def clone_attr(attr): 
  • orangecontrib/bio/widgets/OWGsea.py

    r1873 r1874  
    1919 
    2020from .. import obiGene, obiGeneSets, obiGsea, obiKEGG 
     21 
     22NAME = "GSEA" 
     23DESCRIPTION = "Gene set enrichment analysis." 
     24ICON = "icons/GSEA.svg" 
     25PRIORITY = 2025 
     26 
     27INPUTS = [("Examples", Orange.data.Table, "setData")] 
     28OUTPUTS = [("Examples with selected genes only", Orange.data.Table), 
     29           ("Results", Orange.data.Table), 
     30           ("Distance Matrix", Orange.core.SymMatrix)] 
     31 
     32REPLACES = ["_bioinformatics.widgets.OWGsea.OWGsea"] 
     33 
    2134 
    2235def nth(l, n): 
  • orangecontrib/bio/widgets/OWHeatMap.py

    r1873 r1874  
    2424 
    2525import functools 
     26 
     27NAME = "Heat Map" 
     28DESCRIPTION = "Heatmap visualization." 
     29ICON = "icons/Heatmap.svg" 
     30PRIORITY = 1040 
     31 
     32INPUTS = [("Examples", Orange.data.Table, "set_dataset")] 
     33OUTPUTS = [("Examples", Orange.data.Table, Single + Default)] 
     34 
     35REPLACES = ["_bioinformatics.widgets.OWHeatMap.OWHeatMap"] 
     36 
    2637 
    2738DEBUG = False 
  • orangecontrib/bio/widgets/OWKEGGPathwayBrowser.py

    r1873 r1874  
    3838from .. import obiKEGG 
    3939from .. import obiGeneSets 
     40 
     41 
     42NAME = "KEGG Pathways" 
     43DESCRIPTION = "Browse KEGG pathways that include an input set of genes." 
     44ICON = "icons/KEGGPathways.svg" 
     45PRIORITY = 2030 
     46 
     47INPUTS = [("Examples", Orange.data.Table, "SetData", Default), 
     48          ("Reference", Orange.data.Table, "SetRefData")] 
     49OUTPUTS = [("Selected Examples", Orange.data.Table, Default), 
     50           ("Unselected Examples", Orange.data.Table)] 
     51 
     52REPLACES = ["_bioinformatics.widgets.OWKEGGPathwayBrowser.OWKEGGPathwayBrowser"] 
     53 
    4054 
    4155USE_THREADING = True 
  • orangecontrib/bio/widgets/OWMAPlot.py

    r1873 r1874  
    1616 
    1717from .. import obiExpression 
     18 
     19NAME = "MA Plot" 
     20DESCRIPTION = "Normalize expression array data on a MA - plot" 
     21ICON = "icons/MAPlot.svg" 
     22PRIORITY = 5000 
     23 
     24INPUTS = [("Expression array", Orange.data.Table, "setData")] 
     25OUTPUTS = [("Normalized expression array", Orange.data.Table, Default), 
     26           ("Filtered expression array", Orange.data.Table)] 
     27 
     28REPLACES = ["_bioinformatics.widgets.OWMAPlot.OWMAPlot"] 
     29 
    1830 
    1931class ProgressBarDiscard(QObject): 
  • orangecontrib/bio/widgets/OWMeSHBrowser.py

    r1873 r1874  
    1616 
    1717from ..obiMeSH import * 
     18 
     19NAME = "MeSH Browser" 
     20DESCRIPTION = "Browse MeSH ontology." 
     21ICON = "icons/MeSHBrowser.svg" 
     22PRIORITY = 2040 
     23 
     24INPUTS = [("Reference data", Orange.data.Table, "getReferenceData"), 
     25          ("Cluster data", Orange.data.Table, "getClusterData")] 
     26 
     27OUTPUTS = [("Selected examples", Orange.data.Table)] 
     28 
     29REPLACES = ["_bioinformatics.widgets.OWMeSHBrowser.OWMeSHBrowser"] 
     30 
    1831 
    1932class MyQTableWidgetItem(QTableWidgetItem): 
  • orangecontrib/bio/widgets/OWMoleculeVisualizer.py

    r1873 r1874  
    2222 
    2323from .. import obiChem 
     24 
     25NAME = "Molecule Visualizer" 
     26DESCRIPTION = "Rendering of 2D structure of molecules based on their SMILES description." 
     27ICON = "icons/MoleculeVisualizer.svg" 
     28PRIORITY = 2050 
     29 
     30INPUTS = [("Molecules", Orange.data.Table, "setMoleculeTable", Default), 
     31          ("Molecule subset", Orange.data.Table, "setMoleculeSubset"), 
     32          ("Fragments", Orange.data.Table, "setFragmentTable")] 
     33OUTPUTS = [("Selected Molecules", Orange.data.Table)] 
     34 
     35REPLACES = ["_bioinformatics.widgets.OWMoleculeVisualizer.OWMoleculeVisualizer"] 
     36 
    2437 
    2538class dummy_module(object): 
  • orangecontrib/bio/widgets/OWPIPA.py

    r1873 r1874  
    1717 
    1818from .. import obiDicty 
     19 
     20(2, 'No such file or directory') 
     21NAME = "PIPA" 
     22DESCRIPTION = "Access data from PIPA RNA-Seq database." 
     23ICON = "icons/PIPA.svg" 
     24PRIORITY = 30 
     25 
     26INPUTS = [] 
     27OUTPUTS = [("Example table", Orange.data.Table)] 
     28 
     29REPLACES = ["_bioinformatics.widgets.OWPIPA.OWPIPA"] 
     30 
    1931 
    2032#def pyqtConfigure(object, **kwargs): 
  • orangecontrib/bio/widgets/OWPIPAx.py

    r1873 r1874  
    2121from .OWPIPA import (MyTreeWidgetItem, ListItemDelegate, 
    2222                    SelectionSetsWidget, SortedListWidget) 
     23 
     24NAME = "PIPAx" 
     25DESCRIPTION = "Access data from PIPA RNA-Seq database." 
     26ICON = "icons/PIPA.svg" 
     27PRIORITY = 35 
     28 
     29INPUTS = [] 
     30OUTPUTS = [("Example table", Orange.data.Table)] 
     31 
     32REPLACES = ["_bioinformatics.widgets.OWPIPAx.OWPIPAx"] 
    2333 
    2434try: 
  • orangecontrib/bio/widgets/OWQualityControl.py

    r1873 r1874  
    2424 
    2525from .OWGenotypeDistances import SetContextHandler 
     26 
     27NAME = "Quality Control" 
     28DESCRIPTION = "Experiment quality control" 
     29ICON = "icons/QualityControl.svg" 
     30PRIORITY = 5000 
     31 
     32INPUTS = [("Experiment Data", Orange.data.Table, "set_data")] 
     33OUTPUTS = [] 
     34 
     35REPLACES = ["_bioinformatics.widgets.OWQualityControl.OWQualityControl"] 
     36 
    2637 
    2738DEBUG = False 
  • orangecontrib/bio/widgets/OWSetEnrichment.py

    r1873 r1874  
    1616 
    1717from .. import obiGene, obiGeneSets, obiProb, obiTaxonomy 
     18 
     19NAME = "Gene Set Enrichment" 
     20DESCRIPTION = "" 
     21ICON = "icons/GeneSetEnrichment.svg" 
     22PRIORITY = 5000 
     23 
     24INPUTS = [("Data", Orange.data.Table, "setData", Default), 
     25          ("Reference", Orange.data.Table, "setReference")] 
     26OUTPUTS = [("Data subset", Orange.data.Table)] 
     27 
     28REPLACES = ["_bioinformatics.widgets.OWSetEnrichment.OWSetEnrichment"] 
     29 
    1830 
    1931def _toPyObject(variant): 
  • orangecontrib/bio/widgets/OWUpdateGenomicsDatabases.py

    r1873 r1874  
    88 
    99from Orange.OrangeWidgets.OWDatabasesUpdate import * 
     10 
     11NAME = "Databases" 
     12DESCRIPTION = "Update of systems biology data and knowledge bases." 
     13ICON = "icons/Databases.svg" 
     14PRIORITY = 10 
     15 
     16INPUTS = [] 
     17OUTPUTS = [] 
     18 
     19REPLACES = ["_bioinformatics.widgets.OWUpdateGenomicsDatabases.OWUpdateGenomicsDatabases"] 
     20 
    1021 
    1122class OWUpdateGenomicsDatabases(OWDatabasesUpdate):  
  • orangecontrib/bio/widgets/OWVulcanoPlot.py

    r1873 r1874  
    2727from .. import obiExpression 
    2828from ..obiGEO import transpose 
     29 
     30NAME = "Vulcano Plot" 
     31DESCRIPTION = "Plots fold change vs. p-value.)" 
     32ICON = "icons/VulcanoPlot.svg" 
     33PRIORITY = 1020 
     34 
     35INPUTS = [("Examples", Orange.data.Table, "setData")] 
     36OUTPUTS = [("Examples with selected attributes", Orange.data.Table)] 
     37 
     38REPLACES = ["_bioinformatics.widgets.OWVulcanoPlot.OWVulcanoPlot"] 
     39 
    2940 
    3041class GraphSelections(QObject): 
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