pgb_liv\php_ms\Search\Parameters\MsgfPlusSearchParameters
Encapsulation class for MS-GF+ search parameters
- Author: Andrew Collins
Synopsis
- // members
- private $outputFile;
- private $isotopeErrorRange;
- private $numOfThreads;
- private $fragmentationMethodId;
- private $ms2DetectorId;
- private $protocolId;
- private $tolerableTrypticTermini;
- private $modificationFile;
- private $minPeptideLength;
- private $maxPeptideLength;
- private $minPrecursorCharge;
- private $maxPrecursorCharge;
- private $numMatchesPerSpec;
- private $additionalFeatures;
- private $showQValue;
- private $chargeCarrierMass;
- // methods
- public void setOutputFile()
- public string getOutputFile()
- public void setIsotopeErrorRange()
- public void getIsotopeErrorRange()
- public void setNumOfThreads()
- public void getNumOfThreads()
- public void setFragmentationMethodId()
- public void getFragmentationMethodId()
- public void setMs2DetectorId()
- public void getMs2DetectorId()
- public void setEnzyme()
- public void setProtocolId()
- public void getProtocolId()
- public void setTolerableTrypticTermini()
- public void getTolerableTrypticTermini()
- public void setModificationFile()
- public string getModificationFile()
- public void setMinPeptideLength()
- public void getMinPeptideLength()
- public void setMaxPeptideLength()
- public void getMaxPeptideLength()
- public void setMinPrecursorCharge()
- public void getMinPrecursorCharge()
- public void setMaxPrecursorCharge()
- public void getMaxPrecursorCharge()
- public void setNumMatchesPerSpectrum()
- public void getNumMatchesPerSpectrum()
- public void setAdditionalFeatures()
- public void getAdditionalFeatures()
- public void setShowQValue()
- public void getShowQValue()
- public void setChargeCarrierMass()
- public void getChargeCarrierMass()
- public static string createModificationFile()
- // Inherited methods from AbstractSearchParameters
- public void setDatabases()
- public string getDatabases()
- public void setEnzyme()
- public void getEnzyme()
- public void setMissedCleavageCount()
- public void getMissedCleavageCount()
- public void getPrecursorTolerance()
- public void setPrecursorTolerance()
- public void setFragmentTolerance()
- public Tolerance getFragmentTolerance()
- public void setSpectraPath()
- public void getSpectraPath()
- public void setDecoyEnabled()
- public void isDecoyEnabled()
- public void addModification()
- public array getModifications()
- public void clearModifications()
- public void addFixedModification()
- public void getFixedModifications()
- public void addVariableModification()
- public void getVariableModifications()
Hierarchy
Extends
Implements
Coverage
| Methods | 97.06% | 33 / 34 |
| Lines | 71.43% | 80 / 112 |
Violations
Checkstyle
| Line | Column | Severity | Message |
|---|---|---|---|
| 107 | 8 | warning | Line exceeds 120 characters; contains 124 characters |
| 130 | 8 | warning | Line exceeds 120 characters; contains 160 characters |
| 133 | 8 | warning | Line exceeds 120 characters; contains 158 characters |
| 134 | 8 | warning | Line exceeds 120 characters; contains 149 characters |
| 136 | 8 | warning | Line exceeds 120 characters; contains 156 characters |
| 187 | 8 | warning | Line exceeds 120 characters; contains 159 characters |
Tasks
| Line | Task |
|---|---|
| 457 |
Members
private
- $additionalFeatures
- $chargeCarrierMass
- $fragmentationMethodId
- $isotopeErrorRange
- $maxPeptideLength
- $maxPrecursorCharge
- $minPeptideLength
- $minPrecursorCharge
- $modificationFile
- $ms2DetectorId
- $numMatchesPerSpec
- $numOfThreads
- $outputFile
- $protocolId
- $showQValue
- $tolerableTrypticTermini
Methods
public
- createModificationFile() — Creates a modification file from an array of modifications
- getAdditionalFeatures()
- getChargeCarrierMass()
- getFragmentationMethodId()
- getIsotopeErrorRange()
- getMaxPeptideLength()
- getMaxPrecursorCharge()
- getMinPeptideLength()
- getMinPrecursorCharge()
- getModificationFile() — Returns the modification file specified by setModificationFile.
- getMs2DetectorId()
- getNumMatchesPerSpectrum()
- getNumOfThreads()
- getOutputFile() — Gets the current output file path
- getProtocolId()
- getShowQValue()
- getTolerableTrypticTermini()
- setAdditionalFeatures() — If 0, only basic scores are reported.
- setChargeCarrierMass() — Mass of charge carrier, Default: mass of proton (1.00727649)
- setEnzyme() — Enzyme identifier.
- setFragmentationMethodId() — (0: as written in the spectrum or CID if no info (Default), 1: CID, 2: ETD, 3: HCD, 4: Merge spectra from the same precursor)
- setIsotopeErrorRange() — Takes into account of the error introduced by choosing non-monoisotopic peak for fragmentation.
- setMaxPeptideLength() — Maximum length of the peptide to be considered.
- setMaxPrecursorCharge() — Maximum precursor charge to consider.
- setMinPeptideLength() — Minimum length of the peptide to be considered.
- setMinPrecursorCharge() — Minimum precursor charge to consider.
- setModificationFile() — Modification file name.
- setMs2DetectorId() — (0: Low-res LCQ/LTQ (Default for CID and ETD), 1: High-res LTQ (Default for HCD), 2: TOF, 3: Q-Exactive)
- setNumMatchesPerSpectrum() — Expected false discovery rates (EFDRs) will be reported only when this value is 1.
- setNumOfThreads() — (Number of concurrent threads to be executed, Default: Number of available cores)
- setOutputFile() — Filename where the output (mzIdentML 1.1 format) will be written.
- setProtocolId() — Protocol identifier.
- setShowQValue() — If false, QValue and PepQValue are not reported.
- setTolerableTrypticTermini() — This parameter is used to apply the enzyme cleavage specificity rule when searching the database.
Inherited from pgb_liv\php_ms\Search\Parameters\AbstractSearchParameters
public
- addFixedModification()
- addModification()
- addVariableModification()
- clearModifications()
- getDatabases() — The sequence database(s) to be searched.
- getEnzyme()
- getFixedModifications()
- getFragmentTolerance() — Gets the Fragment Tolerance object
- getMissedCleavageCount()
- getModifications()
- getPrecursorTolerance()
- getSpectraPath()
- getVariableModifications()
- isDecoyEnabled()
- setDatabases()
- setDecoyEnabled()
- setEnzyme()
- setFragmentTolerance()
- setMissedCleavageCount()
- setPrecursorTolerance()
- setSpectraPath() — Sets the spectra file location
History
-
2019-04-02T13:48:22+01:00 (commit #f90fad3)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Code tidy
-
2019-04-02T11:54:45+01:00 (commit #c7d351b)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Code tidy
-
2018-09-25T18:01:54+01:00 (commit #beec9f4)
Author: Andrew Collins (detritus@blueyonder.co.uk) / Commiter: Andrew Collins (detritus@blueyonder.co.uk)
Fixed handling of ANY residues in mzidentml and MS-GF+ param generator
-
2017-10-25T09:20:00+01:00 (commit #57f57a0)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Minor code tidy
-
2017-07-24T08:33:56+01:00 (commit #f930cd2)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Fixed sonar issues
-
2017-07-12T14:53:50+01:00 (commit #b6bd42a)
Author: Andrew Collins (detritus@blueyonder.co.uk) / Commiter: Andrew Collins (detritus@blueyonder.co.uk)
Added search tests
-
2017-07-12T14:22:04+01:00 (commit #b6b32a2)
Author: Andrew Collins (detritus@blueyonder.co.uk) / Commiter: Andrew Collins (detritus@blueyonder.co.uk)
Added search params test coverage
-
2017-04-21T17:55:07+01:00 (commit #b85fd81)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Fixed MS-GF+ mod file creation using wrong method
-
2017-04-13T15:55:22+01:00 (commit #02f8b48)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Addded adapter code to translate between MzIdentML and MSGF params
-
2017-04-12T18:00:04+01:00 (commit #7965bf5)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Added first pass of MzIdentML reader
-
2017-04-11T17:03:38+01:00 (commit #d65dbda)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Added RT filter Added MGF Writer
-
2017-04-07T14:13:36+01:00 (commit #ccab280)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Added MSGF+ modification file generator
-
2017-04-04T18:36:34+01:00 (commit #9969a66)
Author: Andrew Collins (detritus@blueyonder.co.uk) / Commiter: Andrew Collins (detritus@blueyonder.co.uk)
Added additional validation to MsgfPlus Params
-
2017-03-31T18:19:53+01:00 (commit #3085645)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Tweaked Trypsin regexp to not split on line terminator Added Peptide support to mass filter Added additional methods to DigestInterface Added initial MS-GF+ code