pgb_liv\php_ms\experimental\MzMlMerge

Performs the merging of two or more MzML files into a single MzML file.

Note this class is built for speed and does not correctly validate all fields.

Synopsis

class MzMlMerge {
  • // constants
  • const CV_MINUTE = 'UO:0000031';
}

Violations

PHPMessDetector

Line Rule Message
128 - 188 CyclomaticComplexity The method analyseFile() has a Cyclomatic Complexity of 13. The configured cyclomatic complexity threshold is 10.
128 - 188 NPathComplexity The method analyseFile() has an NPath complexity of 541. The configured NPath complexity threshold is 200.
262 - 337 CyclomaticComplexity The method writeSpectrum() has a Cyclomatic Complexity of 12. The configured cyclomatic complexity threshold is 10.
262 - 337 NPathComplexity The method writeSpectrum() has an NPath complexity of 401. The configured NPath complexity threshold is 200.

Checkstyle

Line Column Severity Message
170 17 error Opening parenthesis of a multi-line function call must be the last content on the line
170 115 error Only one argument is allowed per line in a multi-line function call
171 1 error Multi-line function call not indented correctly; expected 12 spaces but found 16
171 25 error Closing parenthesis of a multi-line function call must be on a line by itself
208 24 error Opening parenthesis of a multi-line function call must be the last content on the line
208 53 error Only one argument is allowed per line in a multi-line function call
209 1 error Multi-line function call not indented correctly; expected 16 spaces but found 20
209 59 error Closing parenthesis of a multi-line function call must be on a line by itself
316 17 error Opening parenthesis of a multi-line function call must be the last content on the line
316 115 error Only one argument is allowed per line in a multi-line function call
317 1 error Multi-line function call not indented correctly; expected 12 spaces but found 16
317 25 error Closing parenthesis of a multi-line function call must be on a line by itself

Tasks

Line Task
88 Validate input and output
195 verify analysis phase run

Constants

Name Value
CV_MINUTE 'UO:0000031'

Members

private

  • $dataFiles
  • $fractionOffsets
  • $idOffset
  • $indexOffset
  • $outputFiles
  • $paddingBetweenScans — integer
    The number of seconds that should be used as padding between scans.
  • $spectrumCount
  • $spectrumIdRef
  • $timeOffset

Methods

private

public

History