pgb_liv\php_ms\Reader\MzIdentMlReader1r2
- Author: Andrew Collins
Synopsis
- // Inherited constants from MzIdentMlReader1r1
- const PROTOCOL_SPECTRUM = 'spectrum';
- const PROTOCOL_PROTEIN = 'protein';
- // Inherited members from MzIdentMlReader1r1
- protected $xmlReader;
- // Inherited methods from MzIdentMlReader1r1
- public void __construct()
- protected void getAdditionalSearchParams()
- public void getAnalysisCollection()
- public array getAnalysisData()
- public void getAnalysisProtocolCollection()
- public void getAnalysisSoftwareList()
- protected void getAnalysisSoftware()
- protected void getDbSequence()
- protected void parseDbSequenceParam()
- public void getDataCollection()
- protected array getEnzymes()
- public void getInputs()
- protected void getModification()
- protected void getModificationParams()
- protected void getParentTolerance()
- protected Peptide getPeptide()
- protected void getPeptideSequence()
- public void getProteinDetectionList()
- public void getProteinDetectionProtocol()
- protected void getSearchDatabase()
- protected void getSearchModification()
- protected void getSeq()
- public void getSequenceCollection()
- protected void getSpecifityRules()
- protected void getSpectraData()
- protected void getSpectrumIdentificationProtocol()
- public void setRankFilter()
- // Inherited methods from PsiXmlTrait
- public void getCvParamName()
- protected void getCvParam()
- protected void getUserParam()
- protected void getAttributeId()
Hierarchy
Coverage
| Methods | 0% | 0 / 0 |
| Lines | 0% | 0 / 0 |
Tasks
| Line | Task |
|---|---|
| 113 | This should link to getProteinDetectionList |
Constants
| Name | Value |
|---|---|
| PROTOCOL_SPECTRUM | 'spectrum' |
| PROTOCOL_PROTEIN | 'protein' |
Members
protected
- $xmlReader
Methods
Inherited from pgb_liv\php_ms\Reader\MzIdentMlReader1r1
protected
- getAdditionalSearchParams()
- getAnalysisSoftware()
- getDbSequence()
- getEnzymes() — The list of enzymes used in experiment
- getModification()
- getModificationParams()
- getParentTolerance()
- getPeptide()
- getPeptideSequence()
- getSearchDatabase()
- getSearchModification()
- getSeq()
- getSpecifityRules()
- getSpectraData()
- getSpectrumIdentificationProtocol()
- parseDbSequenceParam()
public
- getAnalysisCollection()
- getAnalysisData()
- getAnalysisProtocolCollection()
- getAnalysisSoftwareList()
- getDataCollection()
- getInputs()
- getProteinDetectionList() — The protein list resulting from a protein detection process.
- getProteinDetectionProtocol()
- getSequenceCollection()
- setRankFilter() — Sets the rank limit for retrieved identifications.
Inherited from pgb_liv\php_ms\Reader\HupoPsi\PsiXmlTrait
protected
- getAttributeId()
- getCvParam() — Creates an array object from a CvParam object
- getUserParam()
public
- getCvParamName() — {@inheritdoc}
History
-
2017-07-19T17:42:32+01:00 (commit #2f535f4)
Author: Andrew Collins (detritus@blueyonder.co.uk) / Commiter: Andrew Collins (detritus@blueyonder.co.uk)
Fixed error if no fragment tolerance information in protocol
-
2017-04-19T17:02:35+01:00 (commit #81c98fa)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Fixed Sonar issues
-
2017-04-18T17:01:19+01:00 (commit #6727a89)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Added additional MzIdentML parser support Partitioned code to allow branching between 1.1/1.2
-
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
-
2017-03-30T17:42:57+01:00 (commit #5842bc4)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Added all PSI-MS specified enzymes
-
2017-01-13T13:24:39+00:00 (commit #09d6bb9)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Fixed incorrect constant usage
-
2017-01-13T13:17:36+00:00 (commit #3c2d727)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Fixed warnings generated by XML missing doctype Added DigestRegularExpression as boiler plate code for all regular expression suitable enzyme
-
2017-01-11T15:23:51+00:00 (commit #2a88d63)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Added Trpysin digestion unit test
-
2017-01-11T13:56:23+00:00 (commit #91a55ef)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Improved filtering and digestion documentation
-
2017-01-11T13:40:21+00:00 (commit #9d6bc95)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Added peptide filtering by length
-
2017-01-10T17:57:46+00:00 (commit #acca036)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Fixed compile error due to multiple constructors
-
2017-01-10T17:51:30+00:00 (commit #b3dacff)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Added initial Protein code Added initial Peptide code Added initial digestion code Improved Fasta and MGF tests