Package libSBtab :: Module Table :: Class Table

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Class Table

Base class for all BioTables

Provides functionality that all table types share

Instance Methods

__init__(self, table_pile=None)

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getDocument(self)

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addColumnsMapping(self, columns_mapping)

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addReference(self, reference_name, table=None, required=True)

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addToBeKnown(self, *sequence)

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changeToBeKnown(self, *sequence)

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addRequiredColumns(self, *columns)

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changeRequiredColumns(self, *columns)

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activateColumns(self)

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removeColumn(self, column_name)
removes a (all) columns with column_name

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changeColumns(self, sequence)

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changeAndActivateColumns(self, first_line)

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fromTSVFile(self, filename, append=False)

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fromTSVString(self, string, append=False)

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fromCSVReader(self, fobj, append=False)
Pseudo Constructor.

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toTSV(self, filename=None, csv_dialect=None)
Generates tab-seperated-values file from self.rows

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valid(self)
Validates the Table

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empty(self)

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clear(self)

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toSBML(self, outfile=None)
Generates SBML File from this table

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extractNicknames(self, force_extraction=False, clear=False)

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mergeTable(self, other_table)

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None

updateRow(self, index_or_row, dictionary)
Updates a row with a dictionary

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appendRow(self, row, auto_set_line_num=True)

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newRow(self)

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Row

addNewRow(self, dictionary=None)
adds a new Row to the table's rows and optionally updates by dict

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removeRow(self, index_or_row)

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sortRows(self, *sort_columns)

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getLine(self, line)

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getRow(self, index_or_row)

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findBy(self, attribute, value, part=None)

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getRows(self, dictionary=None, **kwds)

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className(self)

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index(self, row)

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getOption(self, option_name)

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__iter__(self)
Iterator over all rows.

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__len__(self)

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__nonzero__(self)

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__getattr__(self, name)

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Method Details

removeColumn(self, column_name)

removes a (all) columns with column_name

Parameters:

column_name (str) - name of the column to be removed

Returns:

None

fromCSVReader(self, fobj, append=False)

Pseudo Constructor. Parsing from File

toTSV(self, filename=None, csv_dialect=None)

Generates tab-seperated-values file from self.rows

filename will be created or overwritten if existing permissions must be present

valid(self)

Validates the Table

Validates the Table by validating each row. Empty table is invalid

updateRow(self, index_or_row, dictionary)

Updates a row with a dictionary

Parameters:

index_or_row ((int, Row)) - index(0, 1, ...) or Row Instance that should be updated
dictionary (dict) - Dict by which row is updated {attributeName : value, ...}

Returns: None

None

addNewRow(self, dictionary=None)

adds a new Row to the table's rows and optionally updates by dict

Parameters:

dictionary (dict) - optional dictionary, which is used to initialize new row

Returns: Row

the new (and updated) row

iter(self)

Iterator over all rows.

For Syntactic sugar like:
for row in table:
    ...