pgb_liv\php_ms\Reader\FastaReader
A FASTA parser that creates a new iterable object that will return a database entry on each iteration.
- Author: Andrew Collins
Synopsis
- // members
- private $filePath;
- private $fileHandle;
- private $filePeek;
- private Protein $current;
- private integer $key = 0;
- private FastaInterface $format;
- // methods
- public void __construct()
- public Protein current()
- public void key()
- public void next()
- public void rewind()
- public void valid()
- private string getLine()
- private string peekLine()
- private Protein parseEntry()
- private string parseSequence()
Hierarchy
Implements
Coverage
| Methods | 70% | 7 / 10 |
| Lines | 93.15% | 68 / 73 |
Violations
PHPMessDetector
| Line | Rule | Message |
|---|---|---|
| 185 | StaticAccess | Avoid using static access to class '\pgb_liv\php_ms\Reader\FastaEntry\FastaEntryFactory' in method 'parseEntry'. |
| 190 | StaticAccess | Avoid using static access to class '\pgb_liv\php_ms\Reader\FastaEntry\FastaEntryFactory' in method 'parseEntry'. |
Members
private
- $current
—
pgb_liv\php_ms\Core\Protein
The current protein that will be returned by the current() method - $fileHandle
- $filePath
- $filePeek
- $format
—
pgb_liv\php_ms\Reader\FastaEntry\FastaInterface
The FASTA format engine to use for parsing - $key
Methods
private
- getLine() — Gets the next line and increments the file iterator
- parseEntry() — Parses the current chunk into a Protein object
- parseSequence() — Parses the sequence block from the FASTA file and returns the sequence without any line ending or formatting
- peekLine() — Gets the next line, though does not move the file iterator
public
History
-
2019-04-02T13:48:22+01:00 (commit #f90fad3)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Code tidy
-
2019-04-01T14:53:41+01:00 (commit #cc91234)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Fixed IonSort using outdated methods Fixed digest performing NME on single AA sequences Changed handling of database data, allows for a single sequence to map to multiple formats. Should be better suited for PEFF
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2019-03-07T14:10:17+00:00 (commit #94a43a5)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Skips invalid peptides
-
2017-10-25T14:16:01+01:00 (commit #d497193)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Minor code tidy
-
2017-10-25T11:32:31+01:00 (commit #ccae3f8)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Fixed various documentation and import issues
-
2017-10-24T16:05:10+01:00 (commit #b2240f0)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Tweaked PHPMD rules
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2017-10-09T12:40:37+01:00 (commit #f01dd5f)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Fixed mzIdentML reader appending empty sequences to proteins Fixed FastaReader parsing stop codon
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2017-07-12T15:41:04+01:00 (commit #f0b8ea5)
Author: Andrew Collins (detritus@blueyonder.co.uk) / Commiter: Andrew Collins (detritus@blueyonder.co.uk)
Added unit tests Fixed FASTA parser incorrectly handling missing description
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2017-07-10T14:02:20+01:00 (commit #7f8830c)
Author: Andrew Collins (detritus@blueyonder.co.uk) / Commiter: Andrew Collins (detritus@blueyonder.co.uk)
Fixed PEFF writer using incorrect slash Refactored fasta reader/writers Added PEFF testing
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2017-05-31T14:38:50+01:00 (commit #68bb326)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Fixed MzML merge not updating precursor references Fixed FastaReader failing if protein did not have a description text after the identifier
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2017-05-09T17:19:06+01:00 (commit #cfe67d8)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Fixed Unimod fasta regex Added Fasta/PEFF writer support
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2017-05-08T17:36:37+01:00 (commit #7de6913)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Added PEFF support Added support for modifications on proteins
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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
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2017-03-15T13:16:16+00:00 (commit #4a04057)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
no message
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2017-03-15T13:05:46+00:00 (commit #4580de0)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Fixed failure if whitespace at top of file
-
2017-03-15T12:55:07+00:00 (commit #7242894)
Author: detritus (detritus@blueyonder.co.uk) / Commiter: detritus (detritus@blueyonder.co.uk)
Added additional coverage sites