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Service

Table of Contents

Classes

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 field lists the entries the index correlates with, and the I field the index values themselves, one per amino acid : the original BioPHP parser left both aside, so the data of the entry was never available.

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 EntrezReferenceInterface 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 GenomeReferenceInterface 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\Parser\Entity 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.