pgb_liv\php_ms\Reader\MzIdentMlReader1r1

  • Author: Andrew Collins

Synopsis

class MzIdentMlReader1r1 implements MzIdentMlReader1Interface {
  • // constants
  • const PROTOCOL_SPECTRUM = 'spectrum';
  • const PROTOCOL_PROTEIN = 'protein';
}

Hierarchy

Uses

Implements

Coverage

Methods 0% 0 / 91
Lines 0% 0 / 739

Violations

PHPMessDetector

Line Rule Message
92 - 95 UnusedPrivateMethod Avoid unused private methods such as 'getAffiliation'.
97 - 100 UnusedPrivateMethod Avoid unused private methods such as 'getAmigiousResidue'.
117 - 120 UnusedPrivateMethod Avoid unused private methods such as 'getAnalysisParams'.
139 - 142 UnusedPrivateMethod Avoid unused private methods such as 'getAnalysisSampleCollection'.
179 - 182 UnusedPrivateMethod Avoid unused private methods such as 'getAuditCollection'.
184 - 187 UnusedPrivateMethod Avoid unused private methods such as 'getBibliographicReference'.
189 - 192 UnusedPrivateMethod Avoid unused private methods such as 'getContactRole'.
194 - 197 UnusedPrivateMethod Avoid unused private methods such as 'getCustomisations'.
285 - 288 UnusedPrivateMethod Avoid unused private methods such as 'getDatabaseFilters'.
290 - 293 UnusedPrivateMethod Avoid unused private methods such as 'getDatabaseName'.
295 - 298 UnusedPrivateMethod Avoid unused private methods such as 'getDatabaseTranslation'.
308 - 346 CyclomaticComplexity The method getEnzyme() has a Cyclomatic Complexity of 10. The configured cyclomatic complexity threshold is 10.
381 - 384 UnusedPrivateMethod Avoid unused private methods such as 'getExclude'.
386 - 389 UnusedPrivateMethod Avoid unused private methods such as 'getExternalFormatDocumentation'.
410 - 413 UnusedPrivateMethod Avoid unused private methods such as 'getFilter'.
415 - 418 UnusedPrivateMethod Avoid unused private methods such as 'getFilterType'.
420 - 423 UnusedPrivateMethod Avoid unused private methods such as 'getFragmentArray'.
430 - 433 UnusedPrivateMethod Avoid unused private methods such as 'getFragmentation'.
435 - 438 UnusedPrivateMethod Avoid unused private methods such as 'getFragmentationTable'.
440 - 443 UnusedPrivateMethod Avoid unused private methods such as 'getInclude'.
445 - 448 UnusedPrivateMethod Avoid unused private methods such as 'getInputSpectra'.
450 - 453 UnusedPrivateMethod Avoid unused private methods such as 'getInputSpectrumIdentifications'.
473 - 476 UnusedPrivateMethod Avoid unused private methods such as 'getIonType'.
478 - 481 UnusedPrivateMethod Avoid unused private methods such as 'getMassTable'.
483 - 486 UnusedPrivateMethod Avoid unused private methods such as 'getMeasure'.
519 - 523 ElseExpression The method getModification uses an else expression. Else is never necessary and you can simplify the code to work without else.
539 - 542 UnusedPrivateMethod Avoid unused private methods such as 'getOrganization'.
544 - 547 UnusedPrivateMethod Avoid unused private methods such as 'getParent'.
625 LongVariable Avoid excessively long variable names like $spectrumIdentificationItemRef. Keep variable name length under 20.
637 - 640 UnusedPrivateMethod Avoid unused private methods such as 'getPerson'.
651 LongVariable Avoid excessively long variable names like $proteinDetectionHypothesis. Keep variable name length under 20.
659 - 662 UnusedPrivateMethod Avoid unused private methods such as 'getProteinDetection'.
716 LongVariable Avoid excessively long variable names like $proteinAmbiguityGroup. Keep variable name length under 20.
750 - 753 UnusedPrivateMethod Avoid unused private methods such as 'getProvider'.
755 - 758 UnusedPrivateMethod Avoid unused private methods such as 'getResidue'.
760 - 763 UnusedPrivateMethod Avoid unused private methods such as 'getRole'.
765 - 768 UnusedPrivateMethod Avoid unused private methods such as 'getSample'.
770 - 830 CyclomaticComplexity The method getSearchDatabase() has a Cyclomatic Complexity of 12. The configured cyclomatic complexity threshold is 10.
770 - 830 NPathComplexity The method getSearchDatabase() has an NPath complexity of 480. The configured NPath complexity threshold is 200.
832 - 835 UnusedPrivateMethod Avoid unused private methods such as 'getSearchDatabaseRef'.
875 - 877 ElseExpression The method getSearchModification uses an else expression. Else is never necessary and you can simplify the code to work without else.
882 - 885 UnusedPrivateMethod Avoid unused private methods such as 'getSearchType'.
933 - 936 UnusedPrivateMethod Avoid unused private methods such as 'getSiteRegexp'.
938 - 948 UnusedPrivateMethod Avoid unused private methods such as 'getSoftwareName'.
950 - 953 UnusedPrivateMethod Avoid unused private methods such as 'getSourceFile'.
1008 - 1011 UnusedPrivateMethod Avoid unused private methods such as 'getSpectrumIdentification'.
1029 - 1031 ElseExpression The method getSpectrumIdentificationItem uses an else expression. Else is never necessary and you can simplify the code to work without else.
1220 - 1223 UnusedPrivateMethod Avoid unused private methods such as 'getSubSample'.
1225 - 1228 UnusedPrivateMethod Avoid unused private methods such as 'getSubstitutionModification'.
1264 - 1267 UnusedPrivateMethod Avoid unused private methods such as 'getTranslationTable'.
1269 - 1272 UnusedPrivateMethod Avoid unused private methods such as 'getCv'.
1274 - 1277 UnusedPrivateMethod Avoid unused private methods such as 'getCvList'.

Checkstyle

Line Column Severity Message
129 1 error Multi-line function call not indented correctly; expected 12 spaces but found 16
129 21 error Closing parenthesis of a multi-line function call must be on a line by itself
226 24 error Opening parenthesis of a multi-line function call must be the last content on the line
227 1 error Multi-line function call not indented correctly; expected 12 spaces but found 16
227 42 error Closing parenthesis of a multi-line function call must be on a line by itself
716 137 warning Line exceeds 120 characters; contains 137 characters
899 83 error Opening parenthesis of a multi-line function call must be the last content on the line
900 1 error Multi-line function call not indented correctly; expected 16 spaces but found 20
900 38 error Only one argument is allowed per line in a multi-line function call
900 53 error Closing parenthesis of a multi-line function call must be on a line by itself
1030 141 warning Line exceeds 120 characters; contains 141 characters
1132 132 warning Line exceeds 120 characters; contains 132 characters
1251 121 warning Line exceeds 120 characters; contains 121 characters

Tasks

Line Task
113 This should link to getProteinDetectionList
624 Nothing we can currently do with this data - yet

Constants

Name Value
PROTOCOL_SPECTRUM 'spectrum'
PROTOCOL_PROTEIN 'protein'

Members

private

  • $evidence
  • $filter — array
    Filters to apply
  • $inputs
  • $peptides — array
    Map of Peptide ID => Peptide object from Peptide list
  • $proteins — array
    Map of Protin ID => Protein object from DbSequence list

protected

  • $xmlReader

Methods

private

protected

public

Inherited from pgb_liv\php_ms\Reader\HupoPsi\PsiXmlTrait

protected

public

History