Classes
\pgb_liv\php_ms\Constant
Name | Description | |
---|---|---|
ChemicalConstants | Static class containing chemical constant values in daltons. | EMPTY |
PhysicalConstants | Static class containing physical constant values in daltons. | EMPTY |
\pgb_liv\php_ms\Core
Name | Description | |
---|---|---|
AminoAcidComposition | Get molecular formula for common amino acids. | PASSED |
AminoAcidMono | Monoisotopic masses for common amino acids. | PASSED |
Chromosome | Class for chromosome identification object, provides storage for assigning a name, strand and version. | PASSED |
Gene | Class for gene object. | UNTESTED |
Identification | Class for spectra identification object, provides storage for assigning a modifiable sequence and scoring. | PASSED |
Modification | A modification object which may be applied to a peptide or protein | PASSED |
Organism | Class for organism object. | UNTESTED |
Peptide | A peptide object that encapsulates a modifiable sequence and provides additional properties | PASSED |
Protein | A protein object that encapsulates a modifiable sequence and provides additional properties | PASSED |
Tolerance | Class to encapsulate tolerance values with their unit type. | PASSED |
Transcript | Class for transcript object. | UNTESTED |
\pgb_liv\php_ms\Core\Database
Name | Description | |
---|---|---|
AbstractDatabase | Abstract class for database object. | UNTESTED |
DatabaseFactory | Factory method to identify correct class for a given prefix that may appear in a FASTA | UNTESTED |
DefaultDatabase | Class for default database. | UNTESTED |
EnsembleGDatabase | Class for Ensemble Gene (ENSG) database | UNTESTED |
EnsembleGenscanDatabase | Class for Ensemble GENSCAN (GENSCAN) database | UNTESTED |
EnsemblePDatabase | Class for Ensemble Protein (ENSP) database | UNTESTED |
EnsembleTDatabase | Class for Ensemble Transcript (ENST) database | UNTESTED |
NeXtProtDatabase | Class for NeXtProt (nxp) database | UNTESTED |
UniProtSpDatabase | Class for UniProtKB/Swiss-Prot (sp) database | UNTESTED |
UniProtTrDatabase | Class for UniProtKB/TrEMBL (tr) database | UNTESTED |
\pgb_liv\php_ms\Core\Entry
Name | Description | |
---|---|---|
ChromosomeProteinEntry | A protein entity object for adding references to a protein object. | PASSED |
DatabaseEntry | A database entry element, allows for assigning an object to a specific database reference | UNTESTED |
ProteinEntry | A protein entity object for adding references to a protein object. | PASSED |
\pgb_liv\php_ms\Core\Spectra
Name | Description | |
---|---|---|
FragmentIon | Fragment Ion Class. | EMPTY |
PrecursorIon | Precursor Ion class. | PASSED |
\pgb_liv\php_ms\Reader
Name | Description | |
---|---|---|
FastaReader | A FASTA parser that creates a new iterable object that will return a database entry on each iteration. | PASSED |
MgfReader | An MGF reader that creates a new iterable object that will return a raw entry on each iteration. | PASSED |
MzIdentMlReader1r1 | No description available | UNTESTED |
MzIdentMlReader1r2 | No description available | EMPTY |
MzIdentMlReaderFactory | No description available | UNTESTED |
PxdInfo | No description available | PASSED |
\pgb_liv\php_ms\Reader\FastaEntry
Name | Description | |
---|---|---|
DefaultFastaEntry | A fallback object to use if unable to safely parse fasta data | UNTESTED |
EnsembleFastaEntry | FASTA entry parser to map Ensemble header to protein elements | UNTESTED |
FastaEntryFactory | Factory method attempts to find the correct parser for known FASTA entry headers | UNTESTED |
PeffFastaEntry | FASTA entry parser to map generic PEFF headers to protein elements | UNTESTED |
UniProtFastaEntry | FASTA entry parser to map UniProt header to protein elements | PASSED |
\pgb_liv\php_ms\Reader\HupoPsi
Name | Description | |
---|---|---|
PsiVerb | Constant class for storing commonly used verbs across HUPO-PSI parsed files | EMPTY |
\pgb_liv\php_ms\Search
Name | Description | |
---|---|---|
MascotSearch | Client to perform Mascot search and results retrieval | PASSED |
MsgfPlusSearch | Client to perform MS-GF+ search and results retrieval | PASSED |
\pgb_liv\php_ms\Search\Parameters
Name | Description | |
---|---|---|
AbstractSearchParameters | Abstract class containing generic filtering methods | PASSED |
MascotSearchParameters | Encapsulation class for Mascot search parameters | PASSED |
MsgfPlusSearchParameters | Encapsulation class for MS-GF+ search parameters | PASSED |
\pgb_liv\php_ms\Statistic
Name | Description | |
---|---|---|
FalseDiscoveryRate | Class for calculating False Discovery Rate (FDR) from a object scores | UNTESTED |
\pgb_liv\php_ms\Utility\Digest
Name | Description | |
---|---|---|
AbstractDigest | Abstract class for digestion algorithms. | PASSED |
Digest2Iodobenzoate | No description available | PASSED |
DigestArgC | No description available | PASSED |
DigestAspN | No description available | PASSED |
DigestAspNAmbic | No description available | PASSED |
DigestChymotrypsin | No description available | PASSED |
DigestCnbr | No description available | PASSED |
DigestFactory | Factory class for digestion algorithms. | PASSED |
DigestFormicAcid | No description available | PASSED |
DigestGlutamylEndopeptidase | No description available | PASSED |
DigestLeukocyteElastase | No description available | PASSED |
DigestLysC | No description available | PASSED |
DigestLysCP | No description available | PASSED |
DigestPepsinA | No description available | PASSED |
DigestProlineEndopeptidase | No description available | PASSED |
DigestRegularExpression | A base digestion class that can be used to perform digestion with a valid regular expression. | PASSED |
DigestTrypChymo | No description available | PASSED |
DigestTrypsin | Trypsin digestion for generated trypsinated peptides. | PASSED |
DigestTrypsinP | No description available | PASSED |
DigestV8DE | No description available | PASSED |
DigestV8E | No description available | PASSED |
\pgb_liv\php_ms\Utility\Filter
Name | Description | |
---|---|---|
AbstractFilter | Abstract class containing generic filtering methods | PASSED |
FilterCharge | Creates an instance of a spectra filter than can be used with a list of spectra to remove those which do not it the criteria. | PASSED |
FilterLength | Creates an instance of a peptide filter than can be used with a list of peptides to remove those which do not it the criteria. | PASSED |
FilterMass | Creates an instance of a filter than can be used with a list to remove those which do not fit the criteria. | PASSED |
FilterRetentionTime | Creates an instance of a filter than can be used with a list to remove those which do not fit the criteria. | PASSED |
\pgb_liv\php_ms\Utility\Fragment
Name | Description | |
---|---|---|
AFragment | Generates the A ions from a peptide | PASSED |
AbstractFragment | Abstract class containing generic filtering methods | PASSED |
AbstractFragmentReverse | Abstract class containing generic filtering methods | PASSED |
BFragment | Generates the B ions from a peptide | PASSED |
CFragment | Generates the C ions from a peptide | PASSED |
FragmentFactory | Helper methods to get fragmentation types by instrument type | PASSED |
XFragment | Generates the X ions from a peptide | PASSED |
YFragment | Generates the Y ions from a peptide | PASSED |
ZFragment | Generates the Z ions from a peptide | PASSED |
\pgb_liv\php_ms\Utility\Sort
Name | Description | |
---|---|---|
AbstractSort | Abstract class containing generic sorting methods | UNTESTED |
IdentificationSort | Creates an instance of an identification sort class. | UNTESTED |
IonSort | Creates an instance of an ion sort class. | UNTESTED |
\pgb_liv\php_ms\Writer
Name | Description | |
---|---|---|
FastaWriter | A file writer class for creating FASTA files. | PASSED |
MgfWriter | A file writer class for creating Mascot Generic Format (MGF) files. | PASSED |
MzIdentMlWriter | Class for generating mzIdentML files from a protein/peptide object hierarchy | UNTESTED |
ProBedWriter | A file writer class for creating proBed files. | UNTESTED |
\pgb_liv\php_ms\experimental
Name | Description | |
---|---|---|
MzMlMerge | Performs the merging of two or more MzML files into a single MzML file. | EMPTY |