Class NextProtDb
- java.lang.Object
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- org.snpeff.nextProt.NextProtDb
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public class NextProtDb extends java.lang.Object
Parse NetxProt XML file and build a databasehttp://www.nextprot.org/
How this works: - NextProtDb Main class to parse a directory with NextPort XML files. Each XML file is quite large (several GB compressed) so it cannot be fully loaded and parse in memory on a "standard laptop" Once all markers are created (by the marker factory) the database is serialized to a file
- NextProtMarkerFactory Factory that creates all NextProt Markers. This object is shared across all XML handlers
- NextProtHandler This is a handler used to extract the relevant data from an XML file. One handler is created for each XML file, all handlers share the NextProtMarkerFactory
- NextProtSequenceConservation The markers are analyzed for sequence conservation patterns. If the marker type has high conservation, this is set in the NextProtMarker to keep in mind when predicting effects. For instance, a marker that has 100% conservation would be highly affected by a non-synonymous variant.
- NextProtXmlNode This is the basic "XML" node for the information we need to extract to create the Markers
- NextProtXmlIsoform: Specified an isoform protein / transcript
- NextProtXmlAnnotation: An annotation is a controlled vocabulary term (CvTerm) associated with one or more Locations in an Isoform. Example: "For transcript TR_1234, amino acid 25 is a phosphorylation site" In this case we have: "TR_1234": The Isoform "amino acid 25": The Location in the Isoform "phosphorylation site": The controlled vocabulary term
- NextProtXmlEntry: A set of annotations
- Author:
- pablocingolani
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Constructor Summary
Constructors Constructor Description NextProtDb(java.lang.String xmlDirName, Config config)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description boolean
parse()
Parse all XML files in a directoryvoid
saveDatabase()
void
setDebug(boolean debug)
void
setVerbose(boolean verbose)
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Constructor Detail
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NextProtDb
public NextProtDb(java.lang.String xmlDirName, Config config)
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