pgb_liv\php_ms\Reader\FastaEntry\EnsembleFastaEntry

FASTA entry parser to map Ensemble header to protein elements

Synopsis

class EnsembleFastaEntry implements FastaInterface {
  • // constants
  • const CHROMOSOME = 'chromosome';
  • const GENE = 'gene';
  • const GENE_BIOTYPE = 'gene_biotype';
  • const GENE_SYMBOL = 'gene_symbol';
  • const TRANSCRIPT = 'transcript';
  • const TRANSCRIPT_BIOTYPE = 'transcript_biotype';
  • const DESCRIPTION = 'description';
}

Hierarchy

Implements

Coverage

Methods 0% 0 / 2
Lines 0% 0 / 73

Violations

PHPMessDetector

Line Rule Message
70 - 149 CyclomaticComplexity The method getProtein() has a Cyclomatic Complexity of 16. The configured cyclomatic complexity threshold is 10.
70 - 149 NPathComplexity The method getProtein() has an NPath complexity of 324. The configured NPath complexity threshold is 200.
78 StaticAccess Avoid using static access to class '\pgb_liv\php_ms\Core\Database\DatabaseFactory' in method 'getProtein'.
116 StaticAccess Avoid using static access to class '\pgb_liv\php_ms\Core\Gene' in method 'getProtein'.
117 - 119 ElseExpression The method getProtein uses an else expression. Else is never necessary and you can simplify the code to work without else.
121 StaticAccess Avoid using static access to class '\pgb_liv\php_ms\Core\Database\EnsembleGDatabase' in method 'getProtein'.
134 StaticAccess Avoid using static access to class '\pgb_liv\php_ms\Core\Database\EnsembleTDatabase' in method 'getProtein'.

Constants

Name Value
CHROMOSOME 'chromosome'
GENE 'gene'
GENE_BIOTYPE 'gene_biotype'
GENE_SYMBOL 'gene_symbol'
TRANSCRIPT 'transcript'
TRANSCRIPT_BIOTYPE 'transcript_biotype'
DESCRIPTION 'description'

Methods

public

History