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 |