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
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