comparison smart_toolShed/commons/core/sql/ITableMapAdaptator.py @ 0:e0f8dcca02ed

Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

0:e0f8dcca02ed

# Copyright INRA (Institut National de la Recherche Agronomique)
# http://www.inra.fr
# http://urgi.versailles.inra.fr
#
# This software is governed by the CeCILL license under French law and
# abiding by the rules of distribution of free software.  You can  use, 
# modify and/ or redistribute the software under the terms of the CeCILL
# license as circulated by CEA, CNRS and INRIA at the following URL
# "http://www.cecill.info". 
#
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# modify and redistribute granted by the license, users are provided only
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## Interface for TableMapAdaptator 
#
class ITableMapAdaptator(object):
  
    ## Insert a map instance
    #
    # @param obj map or set
    # @param delayed boolean must the insert be delayed 
    #
    # @warning old name was insAMap
    #
    def insert(self, obj, delayed=False):
        pass

        
    ## Insert a list of Map or Set or Match instances
    #
    # @param l a list of object instances
    # @param delayed boolean
    #
    # @warning old name was insMapList
    #
    def insertList(self, l, delayed = False):
        pass
    
    ## Give a list of the distinct seqName/chr present in the table
    #
    # @return lDistinctContigNames string list
    #
    # @warning old name was getContig_name
    #
    def getSeqNameList(self):
        pass
    
    
    ## Give a list of Map instances having a given seq name
    #
    # @param seqName string seq name
    # @return lMap list of instances
    #
    # @warning old name was get_MapList_from_contig
    #
    def getMapListFromSeqName(self, seqName):
        pass
    
    
    ## Return a list of Set instances from a given sequence name
    #
    # @param seqName string sequence name
    # @return lSets list of Set instances
    #
    # @warning old name was getSetList_from_contig 
    #
    def getSetListFromSeqName( self, seqName ):
        pass

    
    ## Give a map instances list overlapping a given region
    #
    # @param seqName string seq name
    # @param start integer start coordinate
    # @param end integer end coordinate
    # @return lMap list of map instances
    #
    # @warning old name was getMapList_from_qcoord
    #
    def getMapListOverlappingCoord(self, seqName, start, end):
        pass
    
    
    ## Return a list of Set instances overlapping a given region
    #   
    # @param seqName string sequence name
    # @param start integer start coordinate
    # @param end integer end coordinate
    # @return lSet list of Set instances
    #
    # @warning old name was getSetList_from_qcoord
    #
    def getSetListOverlappingCoord( self, seqName, start, end ):
        pass