pgb_liv\php_ms\Search\Parameters\MascotSearchParameters
Encapsulation class for Mascot search parameters
- Author: Andrew Collins
Synopsis
- // constants
- const UNIT_PPM = 'ppm';
- const MASS_MONO = 'Monoisotopic';
- const MASS_AVG = 'Average';
- // members
- private string $formVersion = '1.01';
- private string $intermediate = '';
- private string $searchType = 'MIS';
- private string $peak = 'AUTO';
- private string $repType = 'peptide';
- private integer $errTolRepeat = 0;
- private string $isShowAllModsEnabled = '';
- private $userName;
- private $userMail;
- private $title;
- private string $quantitation = 'None';
- private string $taxonomy = 'All Entries';
- private integer $peptideIsotopeError = 0;
- private string $charge = '2+';
- private string $mass = 'Monoisotopic';
- private string $fileFormat = 'Mascot generic';
- private $precursor;
- private string $instrument = 'Default';
- private string $report = 'Auto';
- // methods
- public void __construct()
- public void setIntermediate()
- public void getIntermediate()
- public void setFormVersion()
- public void getFormVersion()
- public void setSearchType()
- public void getSearchType()
- public void setRepType()
- public void getRepType()
- public void setErrorTolerantRepeat()
- public void getErrorTolerantRepeat()
- public void setPeak()
- public void getPeak()
- public void setShowAllModsEnabled()
- public void isShowAllModsEnabled()
- public void setUserName()
- public void getUserName()
- public void setUserMail()
- public void getUserMail()
- public void setTitle()
- public string getTitle()
- public void setQuantitation()
- public void getQuantitation()
- public void setTaxonomy()
- public void getTaxonomy()
- public void setPeptideIsotopeError()
- public void getPeptideIsotopeError()
- public void setCharge()
- public void getCharge()
- public void setFileFormat()
- public void getFileFormat()
- public void setPrecursor()
- public void getPrecursor()
- public void setInstrument()
- public void getInstrument()
- public void setReport()
- public void getReport()
- public void setMassType()
- public void getMassType()
- public void setMissedCleavageCount()
- // 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 | 100% | 40 / 40 |
| Lines | 100% | 112 / 112 |
Violations
PHPMessDetector
| Line | Rule | Message |
|---|---|---|
| 249 - 266 | CyclomaticComplexity | The method setFileFormat() has a Cyclomatic Complexity of 10. The configured cyclomatic complexity threshold is 10. |
| 295 - 317 | CyclomaticComplexity | The method setInstrument() has a Cyclomatic Complexity of 15. The configured cyclomatic complexity threshold is 10. |
Tasks
| Line | Task |
|---|---|
| 205 | Validate quantitation |
| 216 | Validate taxonomy |
| 326 | Validiate Report top limit |
Constants
| Name | Value |
|---|---|
| UNIT_PPM | 'ppm' |
| MASS_MONO | 'Monoisotopic' |
| MASS_AVG | 'Average' |
Members
private
- $charge
- $errTolRepeat
- $fileFormat
- $formVersion
- $instrument
- $intermediate
- $isShowAllModsEnabled
- $mass
- $peak
- $peptideIsotopeError
- $precursor
- $quantitation
- $repType
- $report
- $searchType
- $taxonomy
- $title
- $userMail
- $userName
Methods
public
- __construct()
- getCharge()
- getErrorTolerantRepeat()
- getFileFormat()
- getFormVersion()
- getInstrument()
- getIntermediate()
- getMassType()
- getPeak()
- getPeptideIsotopeError()
- getPrecursor()
- getQuantitation()
- getRepType()
- getReport()
- getSearchType()
- getTaxonomy()
- getTitle() — A text string which will be printed at the top of results report pages.
- getUserMail()
- getUserName()
- isShowAllModsEnabled()
- setCharge()
- setErrorTolerantRepeat()
- setFileFormat()
- setFormVersion()
- setInstrument()
- setIntermediate()
- setMassType()
- setMissedCleavageCount()
- setPeak()
- setPeptideIsotopeError()
- setPrecursor() — Certain data file formats, SCIEX API III, PerSeptive (.PKS), and Bruker (.XML), do not include m/z information for the precursor peptide.
- setQuantitation()
- setRepType()
- setReport()
- setSearchType()
- setShowAllModsEnabled()
- setTaxonomy()
- setTitle() — A text string which will be printed at the top of results report pages.
- setUserMail()
- setUserName()
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
-
2019-04-02T11:54:45+01:00 (commit #c7d351b)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Code tidy
-
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
-
2017-04-19T16:43:03+01:00 (commit #ba22061)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Fixed unit tests
-
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
-
2017-04-04T17:41:32+01:00 (commit #831a98c)
Author: Andrew Collins (detritus@blueyonder.co.uk) / Commiter: Andrew Collins (detritus@blueyonder.co.uk)
Required Search tolerances to use Tolerance class Added additional validation
-
2017-04-04T15:47:43+01:00 (commit #f1a1e63)
Author: Andrew Collins (detritus@blueyonder.co.uk) / Commiter: Andrew Collins (detritus@blueyonder.co.uk)
Add complete implementation of MS-GF+ search
-
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
-
2017-03-28T15:36:12+01:00 (commit #7197298)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Added tolerance class
-
2017-03-22T16:19:42+00:00 (commit #3ffb660)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Added additional tests and validation
-
2017-03-20T17:04:57+00:00 (commit #2deee3e)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Added default email for Mascot search tests Fixed checkstyle issues
-
2017-03-20T16:42:01+00:00 (commit #0c3635a)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Added Mascot job submission code and tests
-
2017-03-20T14:31:03+00:00 (commit #396e75f)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Added additional mascot parameter tests
-
2017-03-20T14:09:57+00:00 (commit #3d51f9b)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Added addition Params tests
-
2017-03-20T13:24:07+00:00 (commit #cbdb5ed)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Fixed title being incorrect returned
-
2017-03-20T13:15:51+00:00 (commit #ff7a3ed)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Added partial mascot search params class