def __init__(self): """ Initialize a CodingBlockGraph """ # Initialize from PacbpCollectionGraph PacbpCollectionGraph.__init__(self) # short name tag for printing self._short_name = "IWPCBG" # some GLOBAL variables that are required in class functions #self.ALTERNATIVE_ALIGNMENT_OVERLAP_RATIO = alternative_alignment_overlap_ratio # 08/04/09 smallest omsr size must be 3 (means 4 AAs overall aligned) # this is defined in settings.codingblockgraph #self.MINIMAL_OVERAL_SPANNING_RANGE_SIZE = minimal_overal_spanning_range_size # attribute needed to set the GeneTreeGraph into #self._GENETREE = None # attributes to cache OMSR and related data structures self._omsr = {} # Overall Minimal Spanning Range self._msr = {} # Minimal Spanning Range self._maxsr = {} # MAXimal Spanning Range
def __init__( self, alternative_alignment_overlap_ratio=ALTERNATIVE_ALIGNMENT_OVERLAP_RATIO ): """ Initialize a LowSimilarityRegionCodingBlockGraph """ # Initialize from PacbpCollectionGraph, NOT from CodingBlockGraph PacbpCollectionGraph.__init__(self) self._node_object = {} # in use for orf objects self.pacbps = {} # optional, not required # N.B. key of pacbps is different as # in CodingBlockGraph. # NOT: (pacb_identifier, node1, node2) # BUT: (node1, node2) # short name tag for printing self._short_name = "lsrCBG" # set special attributes needed self._splicedonorgraph = None self._spliceacceptorgraph = None self._stopcodongraph = None self._startcodongraph = None # dicts for data of VISTA like tracks self._paoc_per_organism = {} # attribute stays EMPTY!! self._pasc_per_organism = {} # attribute stays EMPTY!! # attribute needed to set the GeneTreeGraph into self._GENETREE = None # attribute for cexpanderanalyses data self._cexpander = None # attributes that are needed once added into a genestructure self.IS_FIRST = False self.IS_LAST = False self.IS_IGNORED = False self.IS_SPLITTED = True # this class is always IS_SPLITTED self.IS_5P_SPLITTED = True # this class is always IS_SPLITTED self.IS_3P_SPLITTED = True # this class is always IS_SPLITTED # set LowSimilarityRegion specific attributes self._omsr = {} self._forced_3p_ends = {} self._forced_5p_ends = {}
def __init__(self,alternative_alignment_overlap_ratio=ALTERNATIVE_ALIGNMENT_OVERLAP_RATIO): """ Initialize a LowSimilarityRegionCodingBlockGraph """ # Initialize from PacbpCollectionGraph, NOT from CodingBlockGraph PacbpCollectionGraph.__init__(self) self._node_object = {} # in use for orf objects self.pacbps = {} # optional, not required # N.B. key of pacbps is different as # in CodingBlockGraph. # NOT: (pacb_identifier, node1, node2) # BUT: (node1, node2) # short name tag for printing self._short_name = "lsrCBG" # set special attributes needed self._splicedonorgraph = None self._spliceacceptorgraph = None self._stopcodongraph = None self._startcodongraph = None # dicts for data of VISTA like tracks self._paoc_per_organism = {} # attribute stays EMPTY!! self._pasc_per_organism = {} # attribute stays EMPTY!! # attribute needed to set the GeneTreeGraph into self._GENETREE = None # attribute for cexpanderanalyses data self._cexpander = None # attributes that are needed once added into a genestructure self.IS_FIRST = False self.IS_LAST = False self.IS_IGNORED = False self.IS_SPLITTED = True # this class is always IS_SPLITTED self.IS_5P_SPLITTED = True # this class is always IS_SPLITTED self.IS_3P_SPLITTED = True # this class is always IS_SPLITTED # set LowSimilarityRegion specific attributes self._omsr = {} self._forced_3p_ends = {} self._forced_5p_ends = {}