pgb_liv\php_ms\Writer\MzIdentMlWriter

PHPMessDetector

Line	Rule	Message
191	ShortVariable	Avoid variables with short names like $id. Configured minimum length is 3.
302	ShortVariable	Avoid variables with short names like $cv. Configured minimum length is 3.
427	ShortVariable	Avoid variables with short names like $id. Configured minimum length is 3.
449	ShortVariable	Avoid variables with short names like $id. Configured minimum length is 3.
469 - 471	ElseExpression	The method writeSearchDatabase uses an else expression. Else is never necessary and you can simplify the code to work without else.
496	ShortVariable	Avoid variables with short names like $id. Configured minimum length is 3.
532	ShortVariable	Avoid variables with short names like $id. Configured minimum length is 3.
550	ShortVariable	Avoid variables with short names like $id. Configured minimum length is 3.
559	ShortVariable	Avoid variables with short names like $id. Configured minimum length is 3.
662	ShortVariable	Avoid variables with short names like $id. Configured minimum length is 3.
830 - 897	CyclomaticComplexity	The method writeSequenceCollection() has a Cyclomatic Complexity of 13. The configured cyclomatic complexity threshold is 10.
922	ShortVariable	Avoid variables with short names like $id. Configured minimum length is 3.
990	ShortVariable	Avoid variables with short names like $id. Configured minimum length is 3.

Checkstyle

Line	Column	Severity	Message
106	16	error	Opening parenthesis of a multi-line function call must be the last content on the line
106	88	error	Only one argument is allowed per line in a multi-line function call
107	1	error	Multi-line function call not indented correctly; expected 8 spaces but found 12
107	87	error	Only one argument is allowed per line in a multi-line function call
107	102	error	Closing parenthesis of a multi-line function call must be on a line by itself
108	16	error	Opening parenthesis of a multi-line function call must be the last content on the line
108	39	error	Only one argument is allowed per line in a multi-line function call
109	1	error	Multi-line function call not indented correctly; expected 8 spaces but found 12
109	108	error	Only one argument is allowed per line in a multi-line function call
109	120	error	Closing parenthesis of a multi-line function call must be on a line by itself
109	121	warning	Line exceeds 120 characters; contains 121 characters
282	24	error	Opening parenthesis of a multi-line function call must be the last content on the line
283	1	error	Multi-line function call not indented correctly; expected 8 spaces but found 12
283	102	error	Closing parenthesis of a multi-line function call must be on a line by itself
371	16	error	Opening parenthesis of a multi-line function call must be the last content on the line
371	43	error	Only one argument is allowed per line in a multi-line function call
371	60	error	Only one argument is allowed per line in a multi-line function call
371	92	error	Only one argument is allowed per line in a multi-line function call
371	106	error	Only one argument is allowed per line in a multi-line function call
372	1	error	Multi-line function call not indented correctly; expected 8 spaces but found 12
372	21	error	Closing parenthesis of a multi-line function call must be on a line by itself
387	24	error	Opening parenthesis of a multi-line function call must be the last content on the line
389	1	error	Multi-line function call not indented correctly; expected 8 spaces but found 16
389	69	error	Closing parenthesis of a multi-line function call must be on a line by itself
539	24	error	Opening parenthesis of a multi-line function call must be the last content on the line
540	1	error	Multi-line function call not indented correctly; expected 8 spaces but found 12
540	64	error	Closing parenthesis of a multi-line function call must be on a line by itself
541	121	warning	Line exceeds 120 characters; contains 121 characters
755	128	warning	Line exceeds 120 characters; contains 128 characters
776	131	warning	Line exceeds 120 characters; contains 131 characters

private

• flush()
• getId()
• getOboName()
• writeAnalysisCollection()
• writeAnalysisData()
• writeAnalysisProtocolCollection()
• writeAnalysisSoftware()
• writeAnalysisSoftwareList()
• writeAttributeNotNull() — Writes the attribute for as long as the value is not null
• writeCv()
• writeCvList()
• writeCvParam()
• writeDataCollection()
• writeDatabaseName()
• writeDbSequence()
• writeEnzyme()
• writeEnzymeName()
• writeEnzymes()
• writeFileFormat()
• writeFragmentTolerance()
• writeInputSpectra()
• writeInputs()
• writeModification()
• writeModificationParams()
• writeMzIdentMl()
• writeParentTolerance()
• writePeptide()
• writePeptideEvidence()
• writePeptideEvidenceRef()
• writePeptideSequence()
• writeSearchDatabase()
• writeSearchDatabaseRef()
• writeSearchModification()
• writeSearchType()
• writeSeq()
• writeSequenceCollection()
• writeSoftwareName()
• writeSpecificityRules()
• writeSpectraData()
• writeSpectrumIdFormat()
• writeSpectrumIdentification()
• writeSpectrumIdentificationItem()
• writeSpectrumIdentificationList()
• writeSpectrumIdentificationProtocol()
• writeSpectrumIdentificationResult()
• writeThreshold()
• writeTolerance()
• writeUserParam()

public

• __construct()
• addCv() — CV terms must be added prior to open being called
• addDecoyData()
• addEnzyme()
• addFragmentTolerance()
• addIdentifiedPrecursors()
• addModification()
• addParentTolerance()
• addScore() — Use the specified cvParam to map peptide scores
• addSearchData()
• addSoftware() — Software ID's must be added prior to open being called
• addSpectraData()
• close()
• open()