A B C D E F G I L M N P R S T U V W
All Classes All Packages

A

addProtrefName(String) - Method in class de.julielab.jules.ae.genemapping.resources.ncbigene.EntrezgeneProt

B

BIOLOGICAL_PROCESS - Static variable in class de.julielab.jules.ae.genemapping.resources.GOExport

BioThesaurusIproClassMerger - Class in de.julielab.jules.ae.genemapping.resources

C

CELLULAR_COMPONENT - Static variable in class de.julielab.jules.ae.genemapping.resources.GOExport

characters(char[], int, int) - Method in class de.julielab.jules.ae.genemapping.resources.UniprotFreeTextHandler

This method holds the text between two tags for modification purposes.

ContextIndexGenerator - Class in de.julielab.jules.ae.genemapping.resources

ContextIndexGenerator(File, File, String) - Constructor for class de.julielab.jules.ae.genemapping.resources.ContextIndexGenerator

constructor which creates index in the specified directory on the disk

createIndex() - Method in class de.julielab.jules.ae.genemapping.resources.NameCentricSynonymIndexGenerator

Creates the synonym index.

createIndex() - Method in class de.julielab.jules.ae.genemapping.resources.SynonymIndexGenerator

create the index, i.e.

createIndex(String) - Method in class de.julielab.jules.ae.genemapping.resources.ContextIndexGenerator

create the index, i.e.

createIndex(String) - Method in class de.julielab.jules.ae.genemapping.resources.SynonymDisambiguationIndexGenerator

create the index, i.e.

createSpellingIndex(File, File) - Static method in class de.julielab.jules.ae.genemapping.resources.SpellCheckerIndexGenerator

D

de.julielab.jules.ae.genemapping.resources - package de.julielab.jules.ae.genemapping.resources

de.julielab.jules.ae.genemapping.resources.ncbigene - package de.julielab.jules.ae.genemapping.resources.ncbigene

de.julielab.jules.ae.genemapping.resources.util - package de.julielab.jules.ae.genemapping.resources.util

determineMissingTaxIds(File, File, File, File) - Static method in class de.julielab.jules.ae.genemapping.resources.ncbigene.GeneXMLUtils

DictionaryFamilyDomainFilter - Class in de.julielab.jules.ae.genemapping.resources

Removes gene synonyms from the given dictionary that look like gene families or gene domains or are otherwise unspecific.This is yet another dictionary cleaning algorithm besied DictionaryGeneralFilter and the DictCleaner.pl script in the update_resources_and_indices directory.

DictionaryFamilyDomainFilter() - Constructor for class de.julielab.jules.ae.genemapping.resources.DictionaryFamilyDomainFilter

DictionaryGeneralFilter - Class in de.julielab.jules.ae.genemapping.resources

Takes a gene dictionary and outputs a smaller dictionary containing only entries that do not match a set of negative patterns.

DictionaryGeneralFilter() - Constructor for class de.julielab.jules.ae.genemapping.resources.DictionaryGeneralFilter

E

EG2ENTREZGENE_PROT_FILENAME - Static variable in class de.julielab.jules.ae.genemapping.resources.ncbigene.GeneXMLUtils

EG2SUMMARY_FILENAME - Static variable in class de.julielab.jules.ae.genemapping.resources.ncbigene.GeneXMLUtils

endDocument() - Method in class de.julielab.jules.ae.genemapping.resources.UniprotFreeTextHandler

endElement(String, String, String) - Method in class de.julielab.jules.ae.genemapping.resources.UniprotFreeTextHandler

endElement moves data acquired by characters() into storage structure, updates tag hierarchy information (level -1) & resets all switches in case an entry ended

entrezgeneProt - Variable in class de.julielab.jules.ae.genemapping.resources.ncbigene.GeneXmlExtract

EntrezgeneProt - Class in de.julielab.jules.ae.genemapping.resources.ncbigene

Represents the Entrezgene_prot element of the gene XML format.

EntrezgeneProt() - Constructor for class de.julielab.jules.ae.genemapping.resources.ncbigene.EntrezgeneProt

EUTILS - Static variable in class de.julielab.jules.ae.genemapping.resources.GeneXMLDownloader

extractAndWriteGeneInfoToFile(OutputStream, OutputStream, OutputStream, InputStream) - Static method in class de.julielab.jules.ae.genemapping.resources.ncbigene.GeneXMLUtils

extractGeneInfoFromXml(InputStream) - Static method in class de.julielab.jules.ae.genemapping.resources.ncbigene.GeneXMLUtils

F

freetextFiles - Variable in class de.julielab.jules.ae.genemapping.resources.UniprotFreeTextHandler

G

geneId - Variable in class de.julielab.jules.ae.genemapping.resources.ncbigene.GeneXmlExtract

GeneMapperResourcesException - Exception in de.julielab.jules.ae.genemapping.resources.util

GeneMapperResourcesException() - Constructor for exception de.julielab.jules.ae.genemapping.resources.util.GeneMapperResourcesException

GeneMapperResourcesException(String) - Constructor for exception de.julielab.jules.ae.genemapping.resources.util.GeneMapperResourcesException

GeneMapperResourcesException(String, Throwable) - Constructor for exception de.julielab.jules.ae.genemapping.resources.util.GeneMapperResourcesException

GeneMapperResourcesException(String, Throwable, boolean, boolean) - Constructor for exception de.julielab.jules.ae.genemapping.resources.util.GeneMapperResourcesException

GeneMapperResourcesException(Throwable) - Constructor for exception de.julielab.jules.ae.genemapping.resources.util.GeneMapperResourcesException

geneTrackStatus - Variable in class de.julielab.jules.ae.genemapping.resources.ncbigene.GeneXmlExtract

The text content of the Gene-track_status element

geneTrackStatusValue - Variable in class de.julielab.jules.ae.genemapping.resources.ncbigene.GeneXmlExtract

The content of the 'value' attribute of the Gene-track_status element

GeneXMLDownloader - Class in de.julielab.jules.ae.genemapping.resources

Alternative to GeneXMLFromASN1Extractor.

GeneXMLDownloader() - Constructor for class de.julielab.jules.ae.genemapping.resources.GeneXMLDownloader

GeneXmlExtract - Class in de.julielab.jules.ae.genemapping.resources.ncbigene

GeneXmlExtract() - Constructor for class de.julielab.jules.ae.genemapping.resources.ncbigene.GeneXmlExtract

GeneXMLFromASN1Extractor - Class in de.julielab.jules.ae.genemapping.resources

Alternative to GeneXMLDownloader.

GeneXMLFromASN1Extractor() - Constructor for class de.julielab.jules.ae.genemapping.resources.GeneXMLFromASN1Extractor

GeneXMLUtils - Class in de.julielab.jules.ae.genemapping.resources.ncbigene

GeneXMLUtils() - Constructor for class de.julielab.jules.ae.genemapping.resources.ncbigene.GeneXMLUtils

getMapping() - Method in class de.julielab.jules.ae.genemapping.resources.IDReplacer

getMetaFiles(File) - Static method in class de.julielab.jules.ae.genemapping.resources.ncbigene.GeneXMLUtils

Returns the file objects for the meta information files retrieved from NCBI Gene XML data.

GOExport - Class in de.julielab.jules.ae.genemapping.resources

GOExport() - Constructor for class de.julielab.jules.ae.genemapping.resources.GOExport

I

IDReplacer - Class in de.julielab.jules.ae.genemapping.resources

This class takes as input a database or table-shaped file, a database source ID column index, an ID mapping file and an source ID mapping file column index.

IDReplacer(File, int, File, int) - Constructor for class de.julielab.jules.ae.genemapping.resources.IDReplacer

IDReplacer(File, int, File, int, File) - Constructor for class de.julielab.jules.ae.genemapping.resources.IDReplacer

isFiltered(CandidateFilter, String) - Static method in class de.julielab.jules.ae.genemapping.resources.DictionaryFamilyDomainFilter

Checks the synonym for length and token number and if it looks as though it wouldn't designate a concrete gene but rather a family or domain.

L

LinnaeusApplication - Class in de.julielab.jules.ae.genemapping.resources

LinnaeusApplication(String) - Constructor for class de.julielab.jules.ae.genemapping.resources.LinnaeusApplication

LinnaeusApplication.Index - Enum in de.julielab.jules.ae.genemapping.resources

M

main(String[]) - Static method in class de.julielab.jules.ae.genemapping.resources.BioThesaurusIproClassMerger

main(String[]) - Static method in class de.julielab.jules.ae.genemapping.resources.ContextIndexGenerator

To execute the ContextIndexGenerator start it with the following command-line arguments:
arg0: path to resources directory arg1: path to context indices directory

main(String[]) - Static method in class de.julielab.jules.ae.genemapping.resources.DictionaryFamilyDomainFilter

main(String[]) - Static method in class de.julielab.jules.ae.genemapping.resources.DictionaryGeneralFilter

main(String[]) - Static method in class de.julielab.jules.ae.genemapping.resources.GeneXMLDownloader

main(String[]) - Static method in class de.julielab.jules.ae.genemapping.resources.GeneXMLFromASN1Extractor

The path to the gene2xml program to use.

main(String[]) - Static method in class de.julielab.jules.ae.genemapping.resources.GOExport

main(String[]) - Static method in class de.julielab.jules.ae.genemapping.resources.IDReplacer

main(String[]) - Static method in class de.julielab.jules.ae.genemapping.resources.LinnaeusApplication

main(String[]) - Static method in class de.julielab.jules.ae.genemapping.resources.NameCentricSynonymIndexGenerator

To execute the ContextIndexGenerator start it with the following command-line arguments:
arg0: path to resources directory arg1: path to synonym indices directory

main(String[]) - Static method in class de.julielab.jules.ae.genemapping.resources.SpellCheckerIndexGenerator

main(String[]) - Static method in class de.julielab.jules.ae.genemapping.resources.SynonymDisambiguationIndexGenerator

To execute the ContextIndexGenerator start it with the following command-line arguments:
arg0: path to resources directory arg1: path to context indices directory

main(String[]) - Static method in class de.julielab.jules.ae.genemapping.resources.SynonymIndexGenerator

To execute the ContextIndexGenerator start it with the following command-line arguments:
arg0: path to resources directory arg1: path to synonym indices directory

main(String[]) - Static method in class de.julielab.jules.ae.genemapping.resources.UniprotDictCreator

main(String[]) - Static method in class de.julielab.jules.ae.genemapping.resources.UniprotFreeTextExtractor

MOLECULAR_FUNCTION - Static variable in class de.julielab.jules.ae.genemapping.resources.GOExport

N

NameCentricSynonymIndexGenerator - Class in de.julielab.jules.ae.genemapping.resources

Synonym or gene name centric indexer, new as of March 11, 2019.

NameCentricSynonymIndexGenerator(File, File) - Constructor for class de.julielab.jules.ae.genemapping.resources.NameCentricSynonymIndexGenerator

P

process(String) - Method in class de.julielab.jules.ae.genemapping.resources.GOExport

protrefDesc - Variable in class de.julielab.jules.ae.genemapping.resources.ncbigene.EntrezgeneProt

protrefName - Variable in class de.julielab.jules.ae.genemapping.resources.ncbigene.EntrezgeneProt

R

RANGE - de.julielab.jules.ae.genemapping.resources.LinnaeusApplication.Index

readEntries(File) - Method in class de.julielab.jules.ae.genemapping.resources.UniprotDictCreator

readMapping() - Method in class de.julielab.jules.ae.genemapping.resources.IDReplacer

refSeqStatus - Variable in class de.julielab.jules.ae.genemapping.resources.ncbigene.GeneXmlExtract

The status of the gene sequence analysis, see https://www.ncbi.nlm.nih.gov/books/NBK3841/#EntrezGene.Summary_2 and https://www.ncbi.nlm.nih.gov/books/NBK21091/table/ch18.T.refseq_status_codes/?report=objectonly.

replace() - Method in class de.julielab.jules.ae.genemapping.resources.IDReplacer

S

SPECIFIC - de.julielab.jules.ae.genemapping.resources.LinnaeusApplication.Index

SpellCheckerIndexGenerator - Class in de.julielab.jules.ae.genemapping.resources

SpellCheckerIndexGenerator() - Constructor for class de.julielab.jules.ae.genemapping.resources.SpellCheckerIndexGenerator

startDocument() - Method in class de.julielab.jules.ae.genemapping.resources.UniprotFreeTextHandler

startElement(String, String, String, Attributes) - Method in class de.julielab.jules.ae.genemapping.resources.UniprotFreeTextHandler

This method sets all necessary switches (tag attributes) and updates tag hierarchy information.

summary - Variable in class de.julielab.jules.ae.genemapping.resources.ncbigene.GeneXmlExtract

SynonymDisambiguationIndexGenerator - Class in de.julielab.jules.ae.genemapping.resources

SynonymDisambiguationIndexGenerator(File, File, String) - Constructor for class de.julielab.jules.ae.genemapping.resources.SynonymDisambiguationIndexGenerator

constructor which creates index in the specified directory on the disk

SynonymIndexGenerator - Class in de.julielab.jules.ae.genemapping.resources

SynonymIndexGenerator(File, File) - Constructor for class de.julielab.jules.ae.genemapping.resources.SynonymIndexGenerator

T

tagSpecies(String) - Method in class de.julielab.jules.ae.genemapping.resources.LinnaeusApplication

taxId - Variable in class de.julielab.jules.ae.genemapping.resources.ncbigene.GeneXmlExtract

TAXIDS_FILENAME - Static variable in class de.julielab.jules.ae.genemapping.resources.ncbigene.GeneXMLUtils

toString() - Method in class de.julielab.jules.ae.genemapping.resources.ncbigene.EntrezgeneProt

toString() - Method in class de.julielab.jules.ae.genemapping.resources.ncbigene.GeneXmlExtract

U

UncheckedGeneMapperResourcesException - Exception in de.julielab.jules.ae.genemapping.resources.util

UncheckedGeneMapperResourcesException() - Constructor for exception de.julielab.jules.ae.genemapping.resources.util.UncheckedGeneMapperResourcesException

UncheckedGeneMapperResourcesException(String) - Constructor for exception de.julielab.jules.ae.genemapping.resources.util.UncheckedGeneMapperResourcesException

UncheckedGeneMapperResourcesException(String, Throwable) - Constructor for exception de.julielab.jules.ae.genemapping.resources.util.UncheckedGeneMapperResourcesException

UncheckedGeneMapperResourcesException(String, Throwable, boolean, boolean) - Constructor for exception de.julielab.jules.ae.genemapping.resources.util.UncheckedGeneMapperResourcesException

UncheckedGeneMapperResourcesException(Throwable) - Constructor for exception de.julielab.jules.ae.genemapping.resources.util.UncheckedGeneMapperResourcesException

uniprot2EntrezMap - Variable in class de.julielab.jules.ae.genemapping.resources.UniprotFreeTextHandler

UniprotDictCreator - Class in de.julielab.jules.ae.genemapping.resources

UniprotDictCreator() - Constructor for class de.julielab.jules.ae.genemapping.resources.UniprotDictCreator

UniprotFreeTextExtractor - Class in de.julielab.jules.ae.genemapping.resources

UniprotFreeTextExtractor() - Constructor for class de.julielab.jules.ae.genemapping.resources.UniprotFreeTextExtractor

UniprotFreeTextHandler - Class in de.julielab.jules.ae.genemapping.resources

UniprotFreeTextHandler(String) - Constructor for class de.julielab.jules.ae.genemapping.resources.UniprotFreeTextHandler

V

valueOf(String) - Static method in enum de.julielab.jules.ae.genemapping.resources.LinnaeusApplication.Index

Returns the enum constant of this type with the specified name.

values() - Static method in enum de.julielab.jules.ae.genemapping.resources.LinnaeusApplication.Index

Returns an array containing the constants of this enum type, in the order they are declared.

W

writeEntries(File) - Method in class de.julielab.jules.ae.genemapping.resources.UniprotDictCreator

writeGeneInfoToFile(List<GeneXmlExtract>, OutputStream, OutputStream, OutputStream) - Static method in class de.julielab.jules.ae.genemapping.resources.ncbigene.GeneXMLUtils

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