def __init__(self, obid=None):
ob.__init__(self)
self.MAX_INLINE_SEQUENCE_LENGTH = 50000
self.MAX_INLINE_FEATURE_COUNT = 100
self.AboutMe['default'][0]['heading'] = 'BRDF Sequence Object'
self.AboutMe['default'][0]['text'] = """
This page displays a sequence object from the BRDF database. Contents include:
<ul>
<li> Basic sequence information - the sequence, length, molecule type
<li> Blast or other search annotation if available
<li> A graphical feature display if features have been loaded
<li> A trace viewer if there is a trace file linked to the sequence. The clipped off ends
are usually shaded gray in this view, the sequence corresponding to that shown in the basic
sequence information panel is unshaded. In some cases there may be no shading, if the
drawing code could not determine where the clipping started. Some ABI files seem to
adopt a convention of starting the clipped sequence at position zero, and it may be possible to
identify the start of clipping using this rule, even when we have not shaded the clipped
region.
</ul>
In the BRDF database schema, sequence objects are stored in a table called
biosequenceob. Various types of sequence can be stored in this table - for example,
nucleotide, protein, mRNA sequence, genomic sequence. Also, various types of
sequence model can be stored in addition to the common models of nucleic and amino acid symbol strings -
for example, other models of sequences include regular expressions and HMMs.
</p>
The type of a sequence object is stored in the sequencetype field of this table.
The current set of types that are supported in this database are recorded in an ontology called
AGSEQUENCE_ONTOLOGY (you can browse this ontology by selecting ONTOLOGIES from the drop down list
of search types on the main page, and entering AGSEQUENCE_ONTOLOGY as the search phrase).
<p/>
A Sequence Object in the BRDF database may have relationships with other types of object
in the database. For example, if the sequence is a primary sequence resulting from lab work, then
there is a relation between the biological sample used in the sequencing experiment and one or more
lab resources (vectors, primers); a sequence may be the product of a gene and thus related to
a BRDF geneticob record; if we have searched sequence databases (e.g. via BLAST) and
found similar sequences and stored these search results in the BRDF schema, then this involves a
relationship with a database search run and another (hit) biosequence. All of the possible relationships that a
sequence object may have with other objects in the database are depicted by icons in the information
map section of the page.
<p/>
The icon is composed of the sequenceob symbol connected to the symbols for the related objects
by horizontal lines. Where the database does not yet contain any related objects for a sequence,
the icon for that relationship is greyed out.
<p/>
We may store various types of facts about a given sequence object - for example, features of the
sequence; or miscellaneous facts specific to a given project. Each type of fact supported by the
BRDF is depicted by a line connecting the sequence symbol, to a square box labelled info, with the type of
fact appearing to the right of the icon. Where the database does not yet contain any facts
of a given type for a sequence object, the info icon is greyed out.
"""
if obid != None:
con = databaseModule.getConnection()
self.initFromDatabase(obid, con)
con.close()
def __init__(self):
ob.__init__(self)
def __init__(self):
ob.__init__(self)
self.AboutMe['default'][0]['heading'] = 'BRDF Batch Object'
self.AboutMe['default'][0]['text'] = """
def __init__(self):
ob.__init__(self)
self.listChunkLink = None
self.listAboutLink = ' '
self.fastaURL = None
self.genbankURL = None
def __init__(self):
ob.__init__(self)
self.AboutMe['default'][0]['heading'] = 'BRDF Lab Resource Object'
self.AboutMe['default'][0]['text'] = """