| ParseAaindexManager | Class ParseAaindexManager An AAINDEX1 entry describes a numerical property of the twenty amino acids, not a sequence, so this class exposes plain scalars rather than the Sequence/Feature entities of ParseDbAbstractManager. Its data fields are single letter tags whose continuation lines start with a space, the GenBank way. The C (correlated entries) and I (index values) fields are not decomposed : they are fixed numeric tables the original BioPHP parser never touched either. |
| ParseBlocksManager | Class ParseBlocksManager A BLOCKS entry describes an ungapped conserved region of a protein family, not a sequence, so this class exposes plain scalars rather than the Sequence/Feature entities of ParseDbAbstractManager. |
| ParseEmblManager | Class ParseEmblManager EMBL flat files use the same "one field per record type, feature table shared with GenBank" shape as GenBank's LOCUS/DEFINITION/ACCESSION/.../FEATURES/ORIGIN, only the line tags differ (2-char codes like ID/AC/DE/OS/OC/RN/FT/SQ instead of full keywords). |
| ParseEntrezManager | Class ParseEntrezManager An Entrez genome record describes a whole genome the way GenBank describes an entry : same LOCUS columns, same 12-character label column. It carries neither a FEATURES table nor an ORIGIN sequence though, so it holds annotation only and this class exposes plain scalars and EntrezReference objects rather than the Sequence/Feature entities of ParseDbAbstractManager. |
| ParseEpdManager | Class ParseEpdManager An EPD entry describes a promoter. It borrows the two character tag layout of EMBL, but its fields carry different things, so this class exposes plain scalars rather than the Sequence/Feature entities of ParseDbAbstractManager. The three dated events the format defines are all read here, where the original BioPHP parser had commented two of them out. |
| ParseExpasyEnzymeManager | Class ParseExpasyEnzymeManager ExPASy ENZYME entries describe an enzyme by its EC number, not a sequence - like ParsePdbManager and ParsePrositeManager, this class does not reuse the Sequence/Feature entities of ParseDbAbstractManager. Not to be confused with RestrictionEnzymeManager, which covers restriction endonucleases (a completely different Legacy/ExPASy database). |
| ParseGenbankManager | Class ParseGenbankManager |
| ParseGenomeManager | Class ParseGenomeManager A genome record sums up how far an organism has been sequenced. It holds statistics and a list of references rather than a sequence, so this class exposes plain scalars and GenomeReference objects rather than the Sequence/Feature entities of ParseDbAbstractManager. Its continuation lines are indented with a tab. |
| ParseHgbaseManager | Class ParseHgbaseManager An HGBase entry describes a human mutation and the population it was observed in, not a sequence, so this class exposes plain scalars rather than the Sequence/Feature entities of ParseDbAbstractManager. Its lines are a label, a tab, then the data. |
| ParseKeggAbstractManager | Class ParseKeggAbstractManager KEGG describes metabolism through several files - compound, enzyme, reaction, ortholog, genome - written in one same grammar : a label in the first twelve columns, its data from the thirteenth, a line leaving the label column blank continuing the field above it, and "///" closing the record. That grammar and the ENTRY and NAME fields every record carries live here; each subclass adds the fields of its own file. |
| ParseKeggCompoundManager | Class ParseKeggCompoundManager A compound record describes one metabolite : its formula, the reactions it takes part in, the enzymes acting on it and the pathways it belongs to. |
| ParseKeggEnzymeManager | Class ParseKeggEnzymeManager An enzyme record gathers what KEGG knows of one EC number : the reaction it catalyses, what it consumes and produces, the genes coding for it and the diseases a defect in it causes. |
| ParseKeggGenomeManager | Class ParseKeggGenomeManager A genome record names one sequenced organism KEGG holds pathways for, and ties it to the NCBI taxonomy. Not to be confused with ParseGenomeManager, which reads the sequencing statistics of the Legacy "DOGS" records. |
| ParseKeggOrthologManager | Class ParseKeggOrthologManager An ortholog record groups the genes of different organisms that descend from one common ancestral gene and do the same job, which is what lets a pathway be carried from one species to another. |
| ParseKeggReactionManager | Class ParseKeggReactionManager A reaction record states one biochemical conversion : its equation, written with the compound identifiers on either side of an arrow, and the enzymes that catalyse it. |
| ParseNcbiLitManager | Class ParseNcbiLitManager The NCBI journal list describes periodicals, not sequences, so this class exposes plain scalars rather than the Sequence/Feature entities of ParseDbAbstractManager. It is the only format the library reads whose fields are "Label: value" pairs and whose entries are closed by a row of dashes rather than a double slash. |
| ParsePdbManager | Class ParsePdbManager PDB structure files describe 3D atomic coordinates, not GenBank/EMBL-style annotated sequences, so this parser does not reuse the Sequence/Feature entities of ParseDbAbstractManager - it exposes its own plain Domain\Model objects instead. |
| ParsePdbstrManager | Class ParsePdbstrManager A PDBSTR entry describes one member of a structural family in a single MEMBER line, so this class exposes plain scalars rather than the Sequence/Feature entities of ParseDbAbstractManager. Not to be confused with ParsePdbManager, which reads the atomic coordinate files themselves. |
| ParsePirManager | Class ParsePirManager A PIR entry qualifies most of its fields with "#key value" pairs, a pattern this class reads once and reuses everywhere. It exposes plain scalars rather than the Sequence/Feature entities of ParseDbAbstractManager. |
| ParsePmdManager | Class ParsePmdManager A PMD entry describes a mutation reported in the literature, not a sequence, so this class exposes plain scalars rather than the Sequence/Feature entities of ParseDbAbstractManager. |
| ParsePrfManager | Class ParsePrfManager A PRF entry describes a published protein. Its layout is a twelve character label column, a blank label meaning the line continues the one above, and indented sub-keys qualifying the field they follow. This class exposes plain scalars rather than the Sequence/Feature entities of ParseDbAbstractManager. The SOURCE, KEYWORD, CROSSREF and SEQUENCE fields, which the original BioPHP parser declared without ever filling, are read here. |
| ParsePrintsManager | Class ParsePrintsManager A PRINTS entry describes a protein fingerprint, not a sequence, so this class exposes plain scalars rather than the Sequence/Feature entities of ParseDbAbstractManager. Its data fields are lower case three-character tags ending with a semicolon (gc;, gn;, ga;, gd;), unlike every other format the library reads. |
| ParseProdomManager | Class ParseProdomManager A ProDom entry describes a family of protein domains, not a sequence, so this class exposes plain scalars rather than the Sequence/Feature entities of ParseDbAbstractManager. Only the fields the original BioPHP parser read are decomposed : the alignment block (AL/CO) and the cross-references (DR) are left aside, as they were there. |
| ParsePrositeManager | Class ParsePrositeManager A PROSITE entry describes a motif (pattern, or matrix/profile), not an annotated sequence, so - like ParsePdbManager - this class does not reuse the Sequence/Feature entities of ParseDbAbstractManager. It uses the same 2-char-tag/3-space layout as EMBL and Swiss-Prot, so multi-line fields are read with the same lookahead approach as ParseEmblManager. The MA (matrix) field, which Legacy/motif.inc.php itself only half-implemented (buggy 3-level nesting), is kept as a raw string here rather than ported as-is. |
| ParseSwissprotManager | Class ParseSwissprotManager |
| ParseTransfacAbstractManager | Class ParseTransfacAbstractManager TRANSFAC ships one flat file per kind of record - matrix.dat, gene.dat, class.dat, cell.dat, factor.dat, site.dat - which all share the same grammar : a two-letter label in the first columns, its data from the fifth, "XX" lines spacing the fields apart and "//" closing the record. That grammar, the AC/ID/DT fields every record carries and the way a field spanning several lines is joined, live here; each subclass adds the fields of its own record. |
| ParseTransfacCellManager | Class ParseTransfacCellManager A cell record describes the cell type or cell line a transcription factor was obtained from, which is what ties a binding observation to the tissue it was seen in. |
| ParseTransfacClassManager | Class ParseTransfacClassManager A class record describes a structural family of transcription factors - zinc fingers, leucine zippers, helix-turn-helix - and lists the factors belonging to it. |
| ParseTransfacFactorManager | Class ParseTransfacFactorManager A factor record describes one transcription factor : its name and synonyms, the organism it comes from, the structural class it belongs to and its homologs in other species. |
| ParseTransfacGeneManager | Class ParseTransfacGeneManager A gene record names a gene whose regulation TRANSFAC describes, and points at the regulatory sites and composite elements found around it. |
| ParseTransfacMatrixManager | Class ParseTransfacMatrixManager A matrix record holds the nucleotide weight matrix describing what a transcription factor binds : one row per position of the binding site, counting how often each of A, C, G and T was observed there. |
| ParseTransfacSiteManager | Class ParseTransfacSiteManager A site record describes one regulatory element : the stretch of DNA a factor was found to bind, where it sits relative to the transcription start site of its gene, and which factor binds it. |
| ParseUnigeneManager | Class ParseUnigeneManager A UniGene entry groups the sequences believed to come from one gene. It carries no sequence of its own, so this class exposes plain scalars rather than the Sequence/Feature entities of ParseDbAbstractManager. The PROTSIM lines are kept raw, as ParsePrositeManager does for its matrix field: their layout varies and the original BioPHP parser never decomposed them. |