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

A

AbstractRegionExportService - Class in org.intermine.bio.webservice

Base class for Biological region export services.

AbstractRegionExportService(InterMineAPI) - Constructor for class org.intermine.bio.webservice.AbstractRegionExportService

Constructor.

add(Integer) - Method in class org.intermine.bio.web.model.ProteinAtlasExpressions.ExpressionList.StainingLevel

add(Map<String, String>) - Method in class org.intermine.bio.web.model.GeneExpressionAtlasDiseasesExpressions.ExpressionList

Put/add to the list

add(Map<String, String>) - Method in class org.intermine.bio.web.model.GeneExpressionAtlasTissuesExpressions.ExpressionList

Put/add to the list

add(Map<String, String>) - Method in class org.intermine.bio.web.model.ProteinAtlasExpressions.ExpressionList

Put/add to the map of expressions

addCollectionCount(String, String, Object, String) - Method in class org.intermine.bio.web.displayer.MetabolicGeneSummaryDisplayer.GeneSummary

Add collection count to the summary.

addCollectionDistinctCount(String, String, Object, String) - Method in class org.intermine.bio.web.displayer.MetabolicGeneSummaryDisplayer.GeneSummary

Add collection distinct count to the summary.

addCustom(String, String, Object, String, String) - Method in class org.intermine.bio.web.displayer.MetabolicGeneSummaryDisplayer.GeneSummary

Add a custom object to the displayer.

addImageLink(String, String, String, String) - Method in class org.intermine.bio.web.displayer.MetabolicGeneSummaryDisplayer.GeneSummary

Add a link to an image for the summary.

addLinkedFeature(String, DefaultModelledFeature) - Method in class org.intermine.webservice.server.complexes.ExportService.FeatureHolder

apply(Map<String, BigDecimal>, PopulationInfo, Map<String, PopulationInfo>, Double) - Method in class org.intermine.bio.web.widget.GeneLengthCorrectionCoefficient

asSearchConstraint() - Method in class org.intermine.bio.webservice.GenomicRegionSearchListInput.GenomicRegionSearchInfo

AttributeLinksController - Class in org.intermine.bio.web

Set up maps for attributeLinks.jsp

AttributeLinksController() - Constructor for class org.intermine.bio.web.AttributeLinksController

B

BEDExporter - Class in org.intermine.bio.web.export

Exports LocatedSequenceFeature objects in UCSC BED format.

BEDExporter(PrintWriter, List<Integer>, String, String, boolean, String) - Constructor for class org.intermine.bio.web.export.BEDExporter

Constructor.

BEDExportForm - Class in org.intermine.bio.web.struts

Form for sequence export in BED format

BEDExportForm() - Constructor for class org.intermine.bio.web.struts.BEDExportForm

BEDHttpExporter - Class in org.intermine.bio.web.export

An implementation of TableHttpExporter that exports LocatedSequenceFeature objects in BED format.

BEDHttpExporter() - Constructor for class org.intermine.bio.web.export.BEDHttpExporter

BEDQueryService - Class in org.intermine.bio.webservice

A service for exporting query results in UCSC BED format.

BEDQueryService(InterMineAPI) - Constructor for class org.intermine.bio.webservice.BEDQueryService

Constructor.

BEDQueryServlet - Class in org.intermine.bio.webservice

A servlet to hand off to the UCSC BED query service.

BEDQueryServlet() - Constructor for class org.intermine.bio.webservice.BEDQueryServlet

BIG_BATCH_SIZE - Static variable in class org.intermine.bio.web.export.BEDHttpExporter

The batch size to use when we need to iterate through the whole result set.

BIG_BATCH_SIZE - Static variable in class org.intermine.bio.web.export.GFF3HttpExporter

The batch size to use when we need to iterate through the whole result set.

binderToFeatures - Variable in class org.intermine.webservice.server.complexes.ExportService.FeatureHolder

BioExportServlet - Class in org.intermine.bio.webservice

A servlet to hand off to the GFF3-query-service.

BioExportServlet() - Constructor for class org.intermine.bio.webservice.BioExportServlet

BioLinkRedirectManager - Class in org.intermine.bio.web

Contructs an alternate object details link pointing to an external URL for use in results table.

BioLinkRedirectManager(Properties) - Constructor for class org.intermine.bio.web.BioLinkRedirectManager

BioQueryService - Class in org.intermine.bio.webservice

A service for exporting query results as gff3.

BioQueryService(InterMineAPI) - Constructor for class org.intermine.bio.webservice.BioQueryService

Constructor.

BioSequence - Class in org.intermine.bio.web.biojava

An implementation of the BioJava Sequence interface that uses InterMine objects underneath.

BioSequence(AbstractSequence, BioEntity) - Constructor for class org.intermine.bio.web.biojava.BioSequence

Create a new BioSequence from a BioEntity

BioSequenceFactory - Class in org.intermine.bio.web.biojava

A factory for creating BioSequence objects.

BioSequenceFactory.SequenceType - Enum in org.intermine.bio.web.biojava

Type of sequences.

BioWidgetUtil - Class in org.intermine.bio.web.widget

Utility methods for the flymine package.

BioWidgetUtil() - Constructor for class org.intermine.bio.web.widget.BioWidgetUtil

Constructor (required for widgets)

ByCellCountComparator() - Constructor for class org.intermine.bio.web.model.ProteinAtlasExpressions.ByCellCountComparator

ByLevelComparator() - Constructor for class org.intermine.bio.web.model.ProteinAtlasExpressions.ByLevelComparator

ByOverallLevelComparator() - Constructor for class org.intermine.bio.web.model.ProteinAtlasExpressions.ByOverallLevelComparator

ByPValueComparator() - Constructor for class org.intermine.bio.web.model.GeneExpressionAtlasDiseasesExpressions.ByPValueComparator

ByPValueComparator() - Constructor for class org.intermine.bio.web.model.GeneExpressionAtlasTissuesExpressions.ByPValueComparator

ByTStatisticComparator() - Constructor for class org.intermine.bio.web.model.GeneExpressionAtlasDiseasesExpressions.ByTStatisticComparator

ByTStatisticComparator() - Constructor for class org.intermine.bio.web.model.GeneExpressionAtlasTissuesExpressions.ByTStatisticComparator

C

canExport(List<Class<?>>) - Method in class org.intermine.bio.web.export.BEDExporter

canExport(List<Class<?>>) - Method in class org.intermine.bio.web.export.GFF3Exporter

canExport(List<Class<?>>) - Method in class org.intermine.bio.web.export.SequenceExporter

canExport(PagedTable) - Method in class org.intermine.bio.web.export.BEDHttpExporter

canExport(PagedTable) - Method in class org.intermine.bio.web.export.GFF3HttpExporter

canExport(PagedTable) - Method in class org.intermine.bio.web.export.SequenceHttpExporter

canExportStatic(List<Class<?>>) - Static method in class org.intermine.bio.web.export.BEDExporter

canExportStatic(List<Class<?>>) - Static method in class org.intermine.bio.web.export.GFF3Exporter

canExportStatic(List<Class<?>>) - Static method in class org.intermine.bio.web.export.SequenceExporter

CaseInsensitiveComparator() - Constructor for class org.intermine.bio.web.model.GeneExpressionAtlasDiseasesExpressions.CaseInsensitiveComparator

CaseInsensitiveComparator() - Constructor for class org.intermine.bio.web.model.GeneExpressionAtlasTissuesExpressions.CaseInsensitiveComparator

categorizeFeatureTypes(Set<String>, GenomicRegion) - Method in class org.intermine.bio.web.logic.GenomicRegionSearchService

Get all feature types from a list of sequence features

checkPathQuery(PathQuery) - Method in class org.intermine.bio.webservice.AbstractRegionExportService

No-op stub.

checkPathQuery(PathQuery) - Method in class org.intermine.bio.webservice.BEDQueryService

checkPathQuery(PathQuery) - Method in class org.intermine.bio.webservice.BioQueryService

No-op stub.

checkPathQuery(PathQuery) - Method in class org.intermine.bio.webservice.FastaQueryService

checkPathQuery(PathQuery) - Method in class org.intermine.bio.webservice.GenomicRegionBedService

checkPathQuery(PathQuery) - Method in class org.intermine.bio.webservice.GenomicRegionFastaService

checkPathQuery(PathQuery) - Method in class org.intermine.bio.webservice.GenomicRegionGFF3Service

checkPathQuery(PathQuery) - Method in class org.intermine.bio.webservice.GFFQueryService

ChromosomeInfo - Class in org.intermine.bio.web.model

This Java bean stores the information for span validation use.

ChromosomeInfo() - Constructor for class org.intermine.bio.web.model.ChromosomeInfo

compare(String, String) - Method in class org.intermine.bio.web.model.GeneExpressionAtlasDiseasesExpressions.ByPValueComparator

compare(String, String) - Method in class org.intermine.bio.web.model.GeneExpressionAtlasDiseasesExpressions.ByTStatisticComparator

compare(String, String) - Method in class org.intermine.bio.web.model.GeneExpressionAtlasDiseasesExpressions.CaseInsensitiveComparator

compare(String, String) - Method in class org.intermine.bio.web.model.GeneExpressionAtlasTissuesExpressions.ByPValueComparator

compare(String, String) - Method in class org.intermine.bio.web.model.GeneExpressionAtlasTissuesExpressions.ByTStatisticComparator

compare(String, String) - Method in class org.intermine.bio.web.model.GeneExpressionAtlasTissuesExpressions.CaseInsensitiveComparator

compare(String, String) - Method in class org.intermine.bio.web.model.ProteinAtlasExpressions.ByCellCountComparator

compare(String, String) - Method in class org.intermine.bio.web.model.ProteinAtlasExpressions.ByLevelComparator

compare(String, String) - Method in class org.intermine.bio.web.model.ProteinAtlasExpressions.ByOverallLevelComparator

compareTo(GenomicRegion) - Method in class org.intermine.bio.web.model.GenomicRegion

ComplexDisplayer - Class in org.intermine.bio.web.displayer

Displayer for gene/protein interactions using complex viewer

ComplexDisplayer(ReportDisplayerConfig, InterMineAPI) - Constructor for class org.intermine.bio.web.displayer.ComplexDisplayer

Construct with config and the InterMineAPI.

convertResultMapToHTML(Map<GenomicRegion, List<List<String>>>, Map<GenomicRegion, Map<String, Integer>>, List<GenomicRegion>, int, int, HttpSession) - Method in class org.intermine.bio.web.logic.GenomicRegionSearchService

Convert result map to HTML string.

createGenomicRegionsFromString(Collection<String>, String, Integer, Boolean) - Static method in class org.intermine.bio.web.logic.GenomicRegionSearchUtil

Create a list of GenomicRegion objects from a collection of region strings

createQueries(GenomicRegionSearchListInput.GenomicRegionSearchInfo) - Method in class org.intermine.bio.webservice.GenomicRegionSearchService

Create the queries used to run the genomic region search.

createQueryList() - Method in class org.intermine.bio.web.logic.GenomicRegionSearchService

To prepare queries for genomic regions

createQueryList(Collection<GenomicRegion>, int, String, Set<Class<?>>, boolean) - Static method in class org.intermine.bio.web.logic.GenomicRegionSearchUtil

Create a list of queries from user regions.

createRegionListQueries(Collection<GenomicRegion>, int, Map<String, ChromosomeInfo>, String, Set<Class<?>>, boolean) - Static method in class org.intermine.bio.web.logic.GenomicRegionSearchUtil

Create a list of queries from user regions.

CuratedProteinsDisplayer - Class in org.intermine.bio.web.displayer

CuratedProteinsDisplayer(ReportDisplayerConfig, InterMineAPI) - Constructor for class org.intermine.bio.web.displayer.CuratedProteinsDisplayer

Construct with config and the InterMineAPI.

CytoscapeNetworkDisplayer - Class in org.intermine.bio.web.displayer

Displayer for gene/protein interactions using cytoscape plugin

CytoscapeNetworkDisplayer(ReportDisplayerConfig, InterMineAPI) - Constructor for class org.intermine.bio.web.displayer.CytoscapeNetworkDisplayer

Construct with config and the InterMineAPI.

D

DEFAULT_REGION_INIT_BATCH_SIZE - Static variable in class org.intermine.bio.web.logic.GenomicRegionSearchService

Default batch size to be used for region search initialisation queries.

densities(Command) - Method in class org.intermine.webservice.server.jbrowse.genomic.Engine

DiseaseDisplayer - Class in org.intermine.bio.web.displayer

For ratmine, display all disease ontology objects for orthologues

DiseaseDisplayer(ReportDisplayerConfig, InterMineAPI) - Constructor for class org.intermine.bio.web.displayer.DiseaseDisplayer

Construct with config and the InterMineAPI.

display(HttpServletRequest, ReportObject) - Method in class org.intermine.bio.web.displayer.ComplexDisplayer

display(HttpServletRequest, ReportObject) - Method in class org.intermine.bio.web.displayer.CuratedProteinsDisplayer

display(HttpServletRequest, ReportObject) - Method in class org.intermine.bio.web.displayer.CytoscapeNetworkDisplayer

display(HttpServletRequest, ReportObject) - Method in class org.intermine.bio.web.displayer.DiseaseDisplayer

display(HttpServletRequest, ReportObject) - Method in class org.intermine.bio.web.displayer.EsynDisplayer

display(HttpServletRequest, ReportObject) - Method in class org.intermine.bio.web.displayer.FlyBaseExpressionDisplayer

display(HttpServletRequest, ReportObject) - Method in class org.intermine.bio.web.displayer.GBrowseDisplayer

display(HttpServletRequest, ReportObject) - Method in class org.intermine.bio.web.displayer.GeneExpressionAtlasDiseasesDisplayer

display(HttpServletRequest, ReportObject) - Method in class org.intermine.bio.web.displayer.GeneExpressionAtlasTissuesDisplayer

display(HttpServletRequest, ReportObject) - Method in class org.intermine.bio.web.displayer.GeneIdentifiersDisplayer

display(HttpServletRequest, ReportObject) - Method in class org.intermine.bio.web.displayer.GeneOntologyDisplayer

display(HttpServletRequest, ReportObject) - Method in class org.intermine.bio.web.displayer.GeneStructureDisplayer

display(HttpServletRequest, ReportObject) - Method in class org.intermine.bio.web.displayer.HomologueDisplayer

display(HttpServletRequest, ReportObject) - Method in class org.intermine.bio.web.displayer.JBrowseDisplayer

display(HttpServletRequest, ReportObject) - Method in class org.intermine.bio.web.displayer.JMOLDisplayer

display(HttpServletRequest, ReportObject) - Method in class org.intermine.bio.web.displayer.MetabolicGeneSummaryDisplayer

display(HttpServletRequest, ReportObject) - Method in class org.intermine.bio.web.displayer.MinePathwaysDisplayer

display(HttpServletRequest, ReportObject) - Method in class org.intermine.bio.web.displayer.MouseAllelesDisplayer

display(HttpServletRequest, ReportObject) - Method in class org.intermine.bio.web.displayer.OverlappingFeaturesDisplayer

display(HttpServletRequest, ReportObject) - Method in class org.intermine.bio.web.displayer.PathwayDescriptionDisplayer

display(HttpServletRequest, ReportObject) - Method in class org.intermine.bio.web.displayer.PathwaysDisplayer

display(HttpServletRequest, ReportObject) - Method in class org.intermine.bio.web.displayer.ProteinAtlasDisplayer

display(HttpServletRequest, ReportObject) - Method in class org.intermine.bio.web.displayer.ProteinSequenceDisplayer

display(HttpServletRequest, ReportObject) - Method in class org.intermine.bio.web.displayer.ProteinStructureATMDisplayer

display(HttpServletRequest, ReportObject) - Method in class org.intermine.bio.web.displayer.PublicationAnnotationsDisplayer

display(HttpServletRequest, ReportObject) - Method in class org.intermine.bio.web.displayer.PublicationCountsDisplayer

display(HttpServletRequest, ReportObject) - Method in class org.intermine.bio.web.displayer.RegulatoryRegionsDisplayer

display(HttpServletRequest, ReportObject) - Method in class org.intermine.bio.web.displayer.ReportWidgetDisplayer

display(HttpServletRequest, ReportObject) - Method in class org.intermine.bio.web.displayer.SequenceFeatureDisplayer

display(HttpServletRequest, ReportObject) - Method in class org.intermine.bio.web.displayer.SnpToGeneDisplayer

display(HttpServletRequest, ReportObject) - Method in class org.intermine.bio.web.displayer.UniProtCommentsDisplayer

DNA - org.intermine.bio.web.biojava.BioSequenceFactory.SequenceType

DNA sequence

doGet(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.bio.webservice.ExternalLinksServlet

}

doLiftOver(GenomicRegionSearchConstraint, String, String, String, String) - Method in class org.intermine.bio.web.logic.LiftOverService

Send a HTTP POST request to liftOver service.

doListCreation(GenomicRegionSearchListInput, Profile, String) - Method in class org.intermine.bio.webservice.GenomicRegionSearchService

Create the list specified by the region search input.

doPost(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.bio.webservice.ExternalLinksServlet

}

E

Engine - Class in org.intermine.webservice.server.jbrowse.genomic

An adaptor for running JBrowse queries against a genomic database.

Engine(InterMineAPI) - Constructor for class org.intermine.webservice.server.jbrowse.genomic.Engine

constructor

equals(Object) - Method in class org.intermine.bio.web.model.GenomicRegion

equals(Object) - Method in class org.intermine.bio.web.model.GenomicRegionSearchConstraint

EsynDisplayer - Class in org.intermine.bio.web.displayer

displayer for esyn

EsynDisplayer(ReportDisplayerConfig, InterMineAPI) - Constructor for class org.intermine.bio.web.displayer.EsynDisplayer

Construct with config and the InterMineAPI.

EsynListDisplayer - Class in org.intermine.bio.web

displayer for esyn on list analysis page

EsynListDisplayer() - Constructor for class org.intermine.bio.web.EsynListDisplayer

evaluate(String) - Method in class org.intermine.bio.web.model.ProteinAtlasExpressions.StainingLevelEvaluator

String representing the level to integer conversion

execute() - Method in class org.intermine.bio.webservice.BioQueryService

execute() - Method in class org.intermine.bio.webservice.ExternalLinksService

execute() - Method in class org.intermine.webservice.server.complexes.ExportService

execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.bio.web.struts.GalaxyExportAction

execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.bio.web.struts.GenomicRegionSearchAction

execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.bio.web.struts.GenomicRegionSearchAjaxAction

execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.bio.web.struts.SequenceExportAction

This action is invoked directly to export SequenceFeatures.

execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.bio.web.AttributeLinksController

execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.bio.web.EsynListDisplayer

execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.bio.web.FriendlyMineLinkController

execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.bio.web.OtherMinesLinkController

execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.bio.web.struts.GalaxyExportOptionsController

execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.bio.web.struts.GenomicRegionSearchOptionsController

execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.bio.web.struts.SequenceExportOptionsController

execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.bio.web.struts.SequenceFeatureExportOptionsController

export(Iterator<? extends List<ResultElement>>) - Method in class org.intermine.bio.web.export.BEDExporter

export(Iterator<? extends List<ResultElement>>) - Method in class org.intermine.bio.web.export.GFF3Exporter

export(Iterator<? extends List<ResultElement>>) - Method in class org.intermine.bio.web.export.SequenceExporter

export(Iterator<? extends List<ResultElement>>, Collection<Path>, Collection<Path>) - Method in class org.intermine.bio.web.export.BEDExporter

export(Iterator<? extends List<ResultElement>>, Collection<Path>, Collection<Path>) - Method in class org.intermine.bio.web.export.GFF3Exporter

export(Iterator<? extends List<ResultElement>>, Collection<Path>, Collection<Path>) - Method in class org.intermine.bio.web.export.SequenceExporter

Lines are always separated with \n because third party tool writeFasta is used for writing sequence.

export(List<GenomicRegion>) - Method in class org.intermine.bio.web.export.GenomicRegionSequenceExporter

DO export

export(PathQuery, Profile) - Method in class org.intermine.bio.webservice.AbstractRegionExportService

Method that carries out the logic for this exporter.

export(PagedTable, HttpServletRequest, HttpServletResponse, TableExportForm, Collection<Path>, Collection<Path>) - Method in class org.intermine.bio.web.export.BEDHttpExporter

Method called to export a PagedTable object as BED.

export(PagedTable, HttpServletRequest, HttpServletResponse, TableExportForm, Collection<Path>, Collection<Path>) - Method in class org.intermine.bio.web.export.GFF3HttpExporter

Method called to export a PagedTable object as GFF3.

export(PagedTable, HttpServletRequest, HttpServletResponse, TableExportForm, Collection<Path>, Collection<Path>) - Method in class org.intermine.bio.web.export.SequenceHttpExporter

Method called to export a PagedTable object using the BioJava sequence and feature writers.

exportField(InterMineObject, String, ObjectStore, HttpServletResponse) - Method in class org.intermine.bio.web.export.ResidueFieldExporter

Export a field containing residues in FASTA format.

ExportService - Class in org.intermine.webservice.server.complexes

Web service that produces JSON required by the complex viewer.

ExportService(InterMineAPI) - Constructor for class org.intermine.webservice.server.complexes.ExportService

Default constructor.

ExportService.FeatureHolder - Class in org.intermine.webservice.server.complexes

hold the feature / linked feature relationships here

ExpressionList() - Constructor for class org.intermine.bio.web.model.GeneExpressionAtlasDiseasesExpressions.ExpressionList

Constructor

ExpressionList() - Constructor for class org.intermine.bio.web.model.GeneExpressionAtlasTissuesExpressions.ExpressionList

Constructor

ExpressionList(Comparator<String>) - Constructor for class org.intermine.bio.web.model.ProteinAtlasExpressions.ExpressionList

Constructor

ExternalLinksService - Class in org.intermine.bio.webservice

Exports selected web.properties.

ExternalLinksService(InterMineAPI) - Constructor for class org.intermine.bio.webservice.ExternalLinksService

ExternalLinksServlet - Class in org.intermine.bio.webservice

Runs ExternalLinksService web service.

ExternalLinksServlet() - Constructor for class org.intermine.bio.webservice.ExternalLinksServlet

F

FastaListService - Class in org.intermine.bio.webservice

Export a list as FASTA.

FastaListService(InterMineAPI) - Constructor for class org.intermine.bio.webservice.FastaListService

FastaListServlet - Class in org.intermine.bio.webservice

FastaListServlet() - Constructor for class org.intermine.bio.webservice.FastaListServlet

FastaQueryService - Class in org.intermine.bio.webservice

A service for exporting query results as fasta.

FastaQueryService(InterMineAPI) - Constructor for class org.intermine.bio.webservice.FastaQueryService

Constructor.

FastaQueryServlet - Class in org.intermine.bio.webservice

A servlet to hand off to the FASTA-query-service.

FastaQueryServlet() - Constructor for class org.intermine.bio.webservice.FastaQueryServlet

FeatureHolder(String, DefaultModelledParticipant) - Constructor for class org.intermine.webservice.server.complexes.ExportService.FeatureHolder

features(Command) - Method in class org.intermine.webservice.server.jbrowse.genomic.Engine

fetchGeneModels(Gene, Model) - Static method in class org.intermine.bio.web.model.GeneModelCache

Look up gene models for a particular gene, either fetch from cache or create new gene models for each transcript.

FLY_LINK - Static variable in class org.intermine.bio.web.export.GFF3Exporter

for the gff header, link to taxomony

FlyBaseExpressionDisplayer - Class in org.intermine.bio.web.displayer

FlyBase modENCODE expression data

FlyBaseExpressionDisplayer(ReportDisplayerConfig, InterMineAPI) - Constructor for class org.intermine.bio.web.displayer.FlyBaseExpressionDisplayer

Constructor

FriendlyMineLinkController - Class in org.intermine.bio.web

Gets list of friendly intermines to show on list analysis page.

FriendlyMineLinkController() - Constructor for class org.intermine.bio.web.FriendlyMineLinkController

FriendlyMineLinkGenerator - Class in org.intermine.bio.web.displayer

Helper class for intermine links generated on report and lists pages

FriendlyMineLinkGenerator() - Constructor for class org.intermine.bio.web.displayer.FriendlyMineLinkGenerator

Constructor

G

GalaxyExportAction - Class in org.intermine.bio.web.struts

Generate feature path query.

GalaxyExportAction() - Constructor for class org.intermine.bio.web.struts.GalaxyExportAction

GalaxyExportForm - Class in org.intermine.bio.web.struts

GalaxyExportForm() - Constructor for class org.intermine.bio.web.struts.GalaxyExportForm

GalaxyExportOptionsController - Class in org.intermine.bio.web.struts

Controller for galaxyExportOptions.tile.

GalaxyExportOptionsController() - Constructor for class org.intermine.bio.web.struts.GalaxyExportOptionsController

GBrowseDisplayer - Class in org.intermine.bio.web.displayer

Displayer for GBrowse

GBrowseDisplayer(ReportDisplayerConfig, InterMineAPI) - Constructor for class org.intermine.bio.web.displayer.GBrowseDisplayer

Construct with config and the InterMineAPI.

GeneExpressionAtlasDiseasesDisplayer - Class in org.intermine.bio.web.displayer

Gene Expression Atlas Displayer (Blue/Green)

GeneExpressionAtlasDiseasesDisplayer(ReportDisplayerConfig, InterMineAPI) - Constructor for class org.intermine.bio.web.displayer.GeneExpressionAtlasDiseasesDisplayer

Constructor

GeneExpressionAtlasDiseasesExpressions - Class in org.intermine.bio.web.model

Gene Expression Atlas Tissues Expressions

GeneExpressionAtlasDiseasesExpressions(ExportResultsIterator) - Constructor for class org.intermine.bio.web.model.GeneExpressionAtlasDiseasesExpressions

Convert Path results into a List (ProteinAtlasDisplayer.java)

GeneExpressionAtlasDiseasesExpressions.ByPValueComparator - Class in org.intermine.bio.web.model

Sort by p-value inversely

GeneExpressionAtlasDiseasesExpressions.ByTStatisticComparator - Class in org.intermine.bio.web.model

Sort by t-statistic

GeneExpressionAtlasDiseasesExpressions.CaseInsensitiveComparator - Class in org.intermine.bio.web.model

Comparator used on "conditions" to sort them (their keys) case insensitively

GeneExpressionAtlasDiseasesExpressions.ExpressionList - Class in org.intermine.bio.web.model

Represents a list of expressions (taken from multiple probe sets) for a given tissue type

GeneExpressionAtlasTissuesDisplayer - Class in org.intermine.bio.web.displayer

Gene Expression Atlas Displayer (Blue/Green)

GeneExpressionAtlasTissuesDisplayer(ReportDisplayerConfig, InterMineAPI) - Constructor for class org.intermine.bio.web.displayer.GeneExpressionAtlasTissuesDisplayer

Constructor

GeneExpressionAtlasTissuesExpressions - Class in org.intermine.bio.web.model

Gene Expression Atlas Tissues Expressions

GeneExpressionAtlasTissuesExpressions(ExportResultsIterator) - Constructor for class org.intermine.bio.web.model.GeneExpressionAtlasTissuesExpressions

Convert Path results into a List (ProteinAtlasDisplayer.java)

GeneExpressionAtlasTissuesExpressions.ByPValueComparator - Class in org.intermine.bio.web.model

Sort by p-value inversely

GeneExpressionAtlasTissuesExpressions.ByTStatisticComparator - Class in org.intermine.bio.web.model

Sort by t-statistic

GeneExpressionAtlasTissuesExpressions.CaseInsensitiveComparator - Class in org.intermine.bio.web.model

Comparator used on "conditions" to sort them (their keys) case insensitively

GeneExpressionAtlasTissuesExpressions.ExpressionList - Class in org.intermine.bio.web.model

Represents a list of expressions (taken from multiple probe sets) for a given tissue type

GeneIdentifiersDisplayer - Class in org.intermine.bio.web.displayer

GeneIdentifiersDisplayer(ReportDisplayerConfig, InterMineAPI) - Constructor for class org.intermine.bio.web.displayer.GeneIdentifiersDisplayer

Construct with config and the InterMineAPI.

GeneLengthCorrectionCoefficient - Class in org.intermine.bio.web.widget

Implementation of the gene length coefficient

GeneLengthCorrectionCoefficient(WidgetConfig, ObjectStore, InterMineBag, String) - Constructor for class org.intermine.bio.web.widget.GeneLengthCorrectionCoefficient

GeneModel - Class in org.intermine.bio.web.model

Representation of a gene model - being one transcript of a gene and including exons, introns, UTRs and CDSs where data are available.

GeneModel(Model, Gene, InterMineObject) - Constructor for class org.intermine.bio.web.model.GeneModel

Construct a new gene model for the given transcript and gene.

GeneModelCache - Class in org.intermine.bio.web.model

A cache for gene models by Gene object id.

GeneModelSettings - Class in org.intermine.bio.web.model

GeneModelSettings(String) - Constructor for class org.intermine.bio.web.model.GeneModelSettings

GeneOntologyDisplayer - Class in org.intermine.bio.web.displayer

Builds datastructure from go parent id to go term id.

GeneOntologyDisplayer(ReportDisplayerConfig, InterMineAPI) - Constructor for class org.intermine.bio.web.displayer.GeneOntologyDisplayer

Construct with config and the InterMineAPI.

generateCreateListHtml(Map<GenomicRegion, List<List<String>>>) - Method in class org.intermine.bio.web.logic.GenomicRegionSearchService

Generate a html string with all feature type for list creation.

generateGenomicRegions(Collection<String>) - Static method in class org.intermine.bio.web.logic.GenomicRegionSearchUtil

Generate a GenomicRegion object from region strings and relevant information

generateJBrowseURL(GenomicRegion) - Method in class org.intermine.bio.web.logic.GenomicRegionSearchService

A wrapper of generateJBrowseURL(GenomicRegion s, List featureTypes)

generateJBrowseURL(GenomicRegion, List<String>) - Method in class org.intermine.bio.web.logic.GenomicRegionSearchService

Generated a jbrowse url

generateLink(InterMineAPI, InterMineObject) - Method in class org.intermine.bio.web.BioLinkRedirectManager

GeneStructureDisplayer - Class in org.intermine.bio.web.displayer

Custom displayer for gene structure.

GeneStructureDisplayer(ReportDisplayerConfig, InterMineAPI) - Constructor for class org.intermine.bio.web.displayer.GeneStructureDisplayer

Construct with config and the InterMineAPI.

GeneSummary(InterMineObject, HttpServletRequest) - Constructor for class org.intermine.bio.web.displayer.MetabolicGeneSummaryDisplayer.GeneSummary

GenomicRegion - Class in org.intermine.bio.web.model

This Java bean represents one record of Chromosome coordinates from user input The record should be in BED format: "chr\tstart\tend".

GenomicRegion() - Constructor for class org.intermine.bio.web.model.GenomicRegion

Default constructor a new GenomicRegion must use setters to set start, end, extendedRegionSize

GenomicRegionBedService - Class in org.intermine.bio.webservice

GenomicRegionBedService(InterMineAPI) - Constructor for class org.intermine.bio.webservice.GenomicRegionBedService

Constructor.

GenomicRegionBedServlet - Class in org.intermine.bio.webservice

GenomicRegionBedServlet() - Constructor for class org.intermine.bio.webservice.GenomicRegionBedServlet

GenomicRegionFastaService - Class in org.intermine.bio.webservice

A class for exposing the region search as a FASTA resource.

GenomicRegionFastaService(InterMineAPI) - Constructor for class org.intermine.bio.webservice.GenomicRegionFastaService

Constructor.

GenomicRegionFastaServlet - Class in org.intermine.bio.webservice

GenomicRegionFastaServlet() - Constructor for class org.intermine.bio.webservice.GenomicRegionFastaServlet

GenomicRegionGFF3Service - Class in org.intermine.bio.webservice

GenomicRegionGFF3Service(InterMineAPI) - Constructor for class org.intermine.bio.webservice.GenomicRegionGFF3Service

Constructor.

GenomicRegionGFF3Servlet - Class in org.intermine.bio.webservice

GenomicRegionGFF3Servlet() - Constructor for class org.intermine.bio.webservice.GenomicRegionGFF3Servlet

GenomicRegionSearchAction - Class in org.intermine.bio.web.struts

For genomic region search.

GenomicRegionSearchAction() - Constructor for class org.intermine.bio.web.struts.GenomicRegionSearchAction

GenomicRegionSearchAjaxAction - Class in org.intermine.bio.web.struts

Genomic region search ajax calls.

GenomicRegionSearchAjaxAction() - Constructor for class org.intermine.bio.web.struts.GenomicRegionSearchAjaxAction

GenomicRegionSearchConstraint - Class in org.intermine.bio.web.model

A class to represent the constraints a user selected including a list of features and genomic regions, etc.

GenomicRegionSearchConstraint() - Constructor for class org.intermine.bio.web.model.GenomicRegionSearchConstraint

GenomicRegionSearchForm - Class in org.intermine.bio.web.struts

This ActionForm represents the form elements on the genomicRegionSearchOptionsBase.jsp

GenomicRegionSearchForm() - Constructor for class org.intermine.bio.web.struts.GenomicRegionSearchForm

GenomicRegionSearchInfo() - Constructor for class org.intermine.bio.webservice.GenomicRegionSearchListInput.GenomicRegionSearchInfo

GenomicRegionSearchListInput - Class in org.intermine.bio.webservice

GenomicRegionSearchListInput(HttpServletRequest, BagManager, Profile, InterMineAPI) - Constructor for class org.intermine.bio.webservice.GenomicRegionSearchListInput

A representation of a request to a region based web service.

GenomicRegionSearchListInput.GenomicRegionSearchInfo - Class in org.intermine.bio.webservice

GenomicRegionSearchOptionsController - Class in org.intermine.bio.web.struts

Class to prepare data for genomicRegionSeachOptions.jsp.

GenomicRegionSearchOptionsController() - Constructor for class org.intermine.bio.web.struts.GenomicRegionSearchOptionsController

GenomicRegionSearchQueryRunner - Class in org.intermine.bio.web.logic

This class has all database query logics for genomic region search.

GenomicRegionSearchQueryRunner(HttpServletRequest, String, GenomicRegionSearchConstraint, Map<GenomicRegion, Query>) - Constructor for class org.intermine.bio.web.logic.GenomicRegionSearchQueryRunner

Constructor

GenomicRegionSearchService - Class in org.intermine.bio.web.logic

A class to provide genomic region search services in general.

GenomicRegionSearchService - Class in org.intermine.bio.webservice

A web service resource to expose the Region Search functionality.

GenomicRegionSearchService() - Constructor for class org.intermine.bio.web.logic.GenomicRegionSearchService

Constructor

GenomicRegionSearchService(InterMineAPI) - Constructor for class org.intermine.bio.webservice.GenomicRegionSearchService

Constructor.

GenomicRegionSearchServlet - Class in org.intermine.bio.webservice

GenomicRegionSearchServlet() - Constructor for class org.intermine.bio.webservice.GenomicRegionSearchServlet

GenomicRegionSearchUtil - Class in org.intermine.bio.web.logic

This utility class instance a GenomicRegionSearchService object based on mine's setting.

GenomicRegionSequenceExporter - Class in org.intermine.bio.web.export

Exports DNA sequences of given genomic regions in FASTA format.

GenomicRegionSequenceExporter(ObjectStore, OutputStream) - Constructor for class org.intermine.bio.web.export.GenomicRegionSequenceExporter

Instructor

getActionMessage(String, int, String, String) - Method in class org.intermine.bio.web.logic.OrthologueConverter

getAllGenomicRegionOverlapFeaturesByType(Map<GenomicRegion, List<List<String>>>, String) - Method in class org.intermine.bio.web.logic.GenomicRegionSearchService

Get a set of ids of all span's overlap features by given feature type.

getAnnotation() - Method in class org.intermine.bio.web.biojava.BioSequence

getByCells() - Method in class org.intermine.bio.web.model.ProteinAtlasExpressions

getByLevel() - Method in class org.intermine.bio.web.model.ProteinAtlasExpressions

getByName() - Method in class org.intermine.bio.web.model.GeneExpressionAtlasDiseasesExpressions

getByName() - Method in class org.intermine.bio.web.model.GeneExpressionAtlasTissuesExpressions

getByOrgan() - Method in class org.intermine.bio.web.model.ProteinAtlasExpressions

getByPValue() - Method in class org.intermine.bio.web.model.GeneExpressionAtlasDiseasesExpressions

getByPValue() - Method in class org.intermine.bio.web.model.GeneExpressionAtlasTissuesExpressions

getByTStatistic() - Method in class org.intermine.bio.web.model.GeneExpressionAtlasDiseasesExpressions

getByTStatistic() - Method in class org.intermine.bio.web.model.GeneExpressionAtlasTissuesExpressions

getCDSs() - Method in class org.intermine.bio.web.model.GeneModel

Get the CDSs if present.

getChr() - Method in class org.intermine.bio.web.model.GenomicRegion

getChrLength() - Method in class org.intermine.bio.web.model.ChromosomeInfo

getChromosomeInfo(InterMineAPI) - Static method in class org.intermine.bio.web.logic.GenomicRegionSearchQueryRunner

Query the information of all the organisms and their chromosomes' names and length.

getChromosomeInfo(InterMineAPI, int) - Static method in class org.intermine.bio.web.logic.GenomicRegionSearchQueryRunner

Query the information of all the organisms and their chromosomes' names and length.

getChromosomeInfomationMap() - Method in class org.intermine.bio.web.logic.GenomicRegionSearchService

Get chromosome information as in a map, keys are lowercased chromosome ids

getChrPID() - Method in class org.intermine.bio.web.model.ChromosomeInfo

getChrPIDLowerCase() - Method in class org.intermine.bio.web.model.ChromosomeInfo

getComplex(String) - Method in class org.intermine.webservice.server.complexes.ExportService

getConstraint() - Method in class org.intermine.bio.web.logic.GenomicRegionSearchService

getContentType() - Method in class org.intermine.bio.webservice.AbstractRegionExportService

getContentType() - Method in class org.intermine.bio.webservice.BEDQueryService

getContentType() - Method in class org.intermine.bio.webservice.BioQueryService

getContentType() - Method in class org.intermine.bio.webservice.FastaQueryService

getContentType() - Method in class org.intermine.bio.webservice.GenomicRegionBedService

getContentType() - Method in class org.intermine.bio.webservice.GenomicRegionFastaService

getContentType() - Method in class org.intermine.bio.webservice.GenomicRegionGFF3Service

getContentType() - Method in class org.intermine.bio.webservice.GFFQueryService

getConvertedObjectIds(Profile, String, List<Integer>, String) - Method in class org.intermine.bio.web.logic.OrthologueConverter

runs the orthologue conversion pathquery and returns list of intermine IDs used in the portal

getCounts(Profile, InterMineBag) - Method in class org.intermine.bio.web.logic.OrthologueConverter

getDefaultFileName() - Method in class org.intermine.bio.webservice.AbstractRegionExportService

getDefaultFileName() - Method in class org.intermine.bio.webservice.BioQueryService

getDefaultFormat() - Method in class org.intermine.bio.webservice.AbstractRegionExportService

getDefaultFormat() - Method in class org.intermine.bio.webservice.BioQueryService

getDefaultOutput(PrintWriter, OutputStream, String) - Method in class org.intermine.bio.webservice.AbstractRegionExportService

getDefaultOutput(PrintWriter, OutputStream, String) - Method in class org.intermine.bio.webservice.BioQueryService

getEnd() - Method in class org.intermine.bio.web.model.GenomicRegion

getExecutor() - Method in class org.intermine.bio.web.displayer.MetabolicGeneSummaryDisplayer.GeneSummary

getExons() - Method in class org.intermine.bio.web.model.GeneModel

Get the exons if present.

getExportClassPaths(PathQuery) - Static method in class org.intermine.bio.web.logic.SequenceFeatureExportUtil

From the view elements of a PathQuery, return a List of the Paths that this exporter will use to find sequences to export.

getExportClassPaths(PagedTable) - Method in class org.intermine.bio.web.export.BEDHttpExporter

getExportClassPaths(PagedTable) - Method in class org.intermine.bio.web.export.GFF3HttpExporter

getExportClassPaths(PagedTable) - Static method in class org.intermine.bio.web.struts.GalaxyExportOptionsController

From the columns of the PagedTable, return a List of the Paths that this exporter will use to find sequences to export.

getExporter(PathQuery) - Method in class org.intermine.bio.webservice.AbstractRegionExportService

getExporter(PathQuery) - Method in class org.intermine.bio.webservice.BEDQueryService

getExporter(PathQuery) - Method in class org.intermine.bio.webservice.BioQueryService

getExporter(PathQuery) - Method in class org.intermine.bio.webservice.FastaQueryService

getExporter(PathQuery) - Method in class org.intermine.bio.webservice.GenomicRegionBedService

getExporter(PathQuery) - Method in class org.intermine.bio.webservice.GenomicRegionFastaService

getExporter(PathQuery) - Method in class org.intermine.bio.webservice.GenomicRegionGFF3Service

getExporter(PathQuery) - Method in class org.intermine.bio.webservice.GFFQueryService

getExportFeaturesQuery(Set<Integer>, String, Set<String>, List<String>) - Method in class org.intermine.bio.web.logic.GenomicRegionSearchService

A flexiable way of setting query fields.

getExtendedEnd() - Method in class org.intermine.bio.web.model.GenomicRegion

getExtendedRegion() - Method in class org.intermine.bio.web.model.GenomicRegion

getExtendedRegionSize() - Method in class org.intermine.bio.web.model.GenomicRegion

getExtendedRegionSize() - Method in class org.intermine.bio.web.model.GenomicRegionSearchConstraint

getExtendedStart() - Method in class org.intermine.bio.web.model.GenomicRegion

getExtension() - Method in class org.intermine.bio.webservice.GenomicRegionSearchListInput.GenomicRegionSearchInfo

getExtraAttributes(ObjectStore, InterMineBag) - Method in class org.intermine.bio.web.widget.BioWidgetUtil

getFeatureAndSOInfo(InterMineAPI, Map<String, String>, int) - Static method in class org.intermine.bio.web.logic.GenomicRegionSearchQueryRunner

Query the information of all feature types and their according so terms.

getFeatureCds() - Method in class org.intermine.bio.webservice.GenomicRegionSearchListInput.GenomicRegionSearchInfo

Returns an unmodifiable set of the classdescriptors corresponding to the feature types in this query.

getFeatureClasses() - Method in class org.intermine.bio.webservice.GenomicRegionSearchListInput.GenomicRegionSearchInfo

getFeatureTypes() - Method in class org.intermine.bio.web.model.GenomicRegionSearchConstraint

getFeatureTypes() - Method in class org.intermine.bio.webservice.GenomicRegionSearchListInput.GenomicRegionSearchInfo

getFeatureTypeSetInAlphabeticalOrder(Set<String>) - Method in class org.intermine.bio.web.logic.GenomicRegionSearchService

Get all feature types in a TresSet

getFeatureTypeToSOTermMap() - Method in class org.intermine.bio.web.logic.GenomicRegionSearchService

getFields() - Method in class org.intermine.bio.web.displayer.MetabolicGeneSummaryDisplayer.GeneSummary

getFivePrimeUTR() - Method in class org.intermine.bio.web.model.GeneModel

Get the fivePrimeUTR if present.

getFormatter() - Method in class org.intermine.bio.webservice.AbstractRegionExportService

getFullRegionInfo() - Method in class org.intermine.bio.web.model.GenomicRegion

getGene() - Method in class org.intermine.bio.web.model.GeneModel

The parent gene for this gene model.

getGeneModelIds(InterMineObject, Model) - Static method in class org.intermine.bio.web.model.GeneModelCache

Look up the gene models for a given gene or gene model component and return the ids of all objects involved.

getGeneModelOrganismSettings(String, ObjectStore) - Static method in class org.intermine.bio.web.model.GeneModelCache

getGeneModels(InterMineObject, Model) - Static method in class org.intermine.bio.web.model.GeneModelCache

Fetch a list of gene models for a gene.

getGenomeBuild() - Method in class org.intermine.bio.web.model.OrganismInfo

getGenomeBuildbyOrgansimAbbreviation(String) - Static method in class org.intermine.bio.web.logic.OrganismGenomeBuildLookup

Get genome build by organism short name such as "D.

getGenomeBuildByOrgansimCollection(Collection<String>) - Static method in class org.intermine.bio.web.logic.OrganismGenomeBuildLookup

Get genome build by a collection of ids

getGenomeBuildbyOrgansimFullName(String) - Static method in class org.intermine.bio.web.logic.OrganismGenomeBuildLookup

Get genome build by organism full name such as "Drosophila melanogaster"

getGenomeBuildbyOrgansimId(String) - Static method in class org.intermine.bio.web.logic.OrganismGenomeBuildLookup

Get genome build by any id

getGenomeBuildbyOrgansimTaxon(Integer) - Static method in class org.intermine.bio.web.logic.OrganismGenomeBuildLookup

Get genome build by organism taxon such as 7227

getGenomicRegionExtendedSizeConstraint(String, Map<GenomicRegionSearchConstraint, String>) - Method in class org.intermine.bio.web.logic.GenomicRegionSearchService

Get flanking size for GenomicRegionSearchAjaxAction use.

getGenomicRegionList() - Method in class org.intermine.bio.web.model.GenomicRegionSearchConstraint

getGenomicRegionOrganismConstraint(String, Map<GenomicRegionSearchConstraint, String>) - Method in class org.intermine.bio.web.logic.GenomicRegionSearchService

Get organism for GenomicRegionSearchAjaxAction use.

getGenomicRegionOverlapFeaturesAsSet(String, Map<GenomicRegion, List<List<String>>>) - Method in class org.intermine.bio.web.logic.GenomicRegionSearchService

Get a set of ids of a span's overlap features.

getGenomicRegionOverlapFeaturesAsString(String, Map<GenomicRegion, List<List<String>>>) - Method in class org.intermine.bio.web.logic.GenomicRegionSearchService

Get a comma separated string of a span's overlap features.

getGenomicRegionOverlapFeaturesByType(String, Map<GenomicRegion, List<List<String>>>, String) - Method in class org.intermine.bio.web.logic.GenomicRegionSearchService

Get a set of ids of a span's overlap features by given feature type.

getGenomicRegions() - Method in class org.intermine.bio.webservice.GenomicRegionSearchListInput.GenomicRegionSearchInfo

getGenomicRegionSearchService(HttpServletRequest) - Static method in class org.intermine.bio.web.logic.GenomicRegionSearchUtil

Generate GenomicRegionSearchService object by using Java reflection

getHasCDSs() - Method in class org.intermine.bio.web.model.GeneModelSettings

getHasExons() - Method in class org.intermine.bio.web.model.GeneModelSettings

getHasFivePrimeUTRs() - Method in class org.intermine.bio.web.model.GeneModelSettings

getHasGenes() - Method in class org.intermine.bio.web.model.GeneModelSettings

getHasIntrons() - Method in class org.intermine.bio.web.model.GeneModelSettings

getHasThreePrimeUTRs() - Method in class org.intermine.bio.web.model.GeneModelSettings

getHasTranscripts() - Method in class org.intermine.bio.web.model.GeneModelSettings

getHeaderAttributes() - Method in class org.intermine.bio.webservice.GenomicRegionSearchService

Gets the header attributes on the output object.

getIds() - Method in class org.intermine.bio.web.model.GeneModel

Return the ids of all objects represented in this gene model including the gene itself.

getIdx() - Method in class org.intermine.bio.web.model.OrganismInfo

getImageName() - Method in class org.intermine.bio.web.XRef

getIMObjectForSequence(ObjectStore, Class, Sequence) - Static method in class org.intermine.bio.web.export.ResidueFieldExporter

Find the IntermineObject that references the given Sequence.

getInitialExportPaths(PagedTable) - Method in class org.intermine.bio.web.export.BEDHttpExporter

The intial export path list is just the paths from the columns of the PagedTable.

getInitialExportPaths(PagedTable) - Method in class org.intermine.bio.web.export.GFF3HttpExporter

The intial export path list is just the paths from the columns of the PagedTable.

getInitialExportPaths(PagedTable) - Method in class org.intermine.bio.web.export.SequenceHttpExporter

The intial export path list is just the paths from the columns of the PagedTable with chromosomeLocation added (if appropriate)

getInput() - Method in class org.intermine.bio.webservice.GenomicRegionSearchService

getIntrons() - Method in class org.intermine.bio.web.model.GeneModel

Get the introns if present.

getInvalidSpans() - Method in class org.intermine.bio.webservice.GenomicRegionSearchListInput.GenomicRegionSearchInfo

getJBrowseTracks() - Method in class org.intermine.bio.web.logic.GenomicRegionSearchService

Get jbrowse track information from web.properties

getLevelClass() - Method in class org.intermine.bio.web.model.ProteinAtlasExpressions.ExpressionList.StainingLevel

Convert the overall staining level of all Expressions into an average (ceiled/floored) value

getLevelValue() - Method in class org.intermine.bio.web.model.ProteinAtlasExpressions.ExpressionList.StainingLevel

Get the float value representing the average Expression level

getLinkedFeature(String) - Method in class org.intermine.webservice.server.complexes.ExportService.FeatureHolder

getLinks(Mine, Mine, ObjectRequest) - Method in class org.intermine.bio.web.displayer.FriendlyMineLinkGenerator

getMakeUcscCompatible() - Method in class org.intermine.bio.web.struts.BEDExportForm

Return whether to make exported BED compatible with UCSC genome browser.

getMatchedBaseCount(GenomicRegion, List<String>) - Method in class org.intermine.bio.web.logic.GenomicRegionSearchService

Calculate the number of matched bases.

getMinusStrand() - Method in class org.intermine.bio.web.model.GenomicRegion

getNewListType(ListInput) - Method in class org.intermine.bio.webservice.GenomicRegionSearchService

getObjectId() - Method in class org.intermine.bio.web.displayer.MetabolicGeneSummaryDisplayer.GeneSummary

getOptionsCss() - Method in class org.intermine.bio.web.logic.GenomicRegionSearchService

Get the name of customized options CSS

getOptionsJavascript() - Method in class org.intermine.bio.web.logic.GenomicRegionSearchService

Get the name of customized options javascript, by default, it is named "genomic_region_search_options_default.js"

getOrganism() - Method in class org.intermine.bio.web.model.GeneModelSettings

getOrganism() - Method in class org.intermine.bio.web.model.GenomicRegion

getOrganism() - Method in class org.intermine.bio.webservice.GenomicRegionSearchListInput.GenomicRegionSearchInfo

getOrganisms() - Method in class org.intermine.bio.web.struts.GFF3ExportForm

Get the organisms set

getOrganisms(PathQuery, HttpSession) - Static method in class org.intermine.bio.web.logic.SequenceFeatureExportUtil

Get organism info from PathQuery

getOrganisms(PathQuery, InterMineAPI, Profile) - Static method in class org.intermine.bio.web.logic.SequenceFeatureExportUtil

getOrganismToTaxonMap() - Method in class org.intermine.bio.web.logic.GenomicRegionSearchService

getOrganName() - Method in class org.intermine.bio.web.model.ProteinAtlasExpressions.ExpressionList

getOrgansimString() - Method in class org.intermine.bio.web.struts.BEDExportForm

getOrgList() - Method in class org.intermine.bio.web.model.OrganismInfo

getOrgName() - Method in class org.intermine.bio.web.model.ChromosomeInfo

getOrgName() - Method in class org.intermine.bio.web.model.GenomicRegionSearchConstraint

getOriginalRegion() - Method in class org.intermine.bio.web.model.GenomicRegion

Make a string of orginal region if extended

getOutputInfo(String) - Method in class org.intermine.bio.web.widget.GeneLengthCorrectionCoefficient

getOutputStream() - Method in class org.intermine.bio.webservice.AbstractRegionExportService

getOutputStream() - Method in class org.intermine.bio.webservice.BioQueryService

getParticipant() - Method in class org.intermine.webservice.server.complexes.ExportService.FeatureHolder

getPathQueryViews(String[]) - Static method in class org.intermine.bio.webservice.BioQueryService

Parse path query views from request parameter "view" comma-separated

getPrimaryId() - Method in class org.intermine.bio.web.displayer.MetabolicGeneSummaryDisplayer.GeneSummary

getPrintWriter() - Method in class org.intermine.bio.webservice.AbstractRegionExportService

getPrintWriter() - Method in class org.intermine.bio.webservice.BioQueryService

getProteinForSequence(ObjectStore, Sequence) - Static method in class org.intermine.bio.web.export.ResidueFieldExporter

Find the Protein that references the given Sequence.

getQuery() - Method in class org.intermine.bio.webservice.BioQueryService

Return the query specified in the request, shorn of all duplicate classes in the view.

getQuery() - Method in class org.intermine.bio.webservice.FastaListService

getQuery() - Method in class org.intermine.bio.webservice.FastaQueryService

Make the path-query to run, and check it has the right number of columns.

getQuery() - Method in class org.intermine.bio.webservice.GFF3ListService

getQueryPaths(PathQuery) - Method in class org.intermine.bio.webservice.BioQueryService

Parse view strings to Path objects

getRegions() - Method in class org.intermine.bio.webservice.GenomicRegionSearchListInput.GenomicRegionSearchInfo

getRegionStringFromPathQuery(PathQuery, InterMineAPI, Profile) - Static method in class org.intermine.bio.web.logic.GenomicRegionSearchQueryRunner

query chromosome locations by a ready-to-use pathquery, return region string as chr:start..end

getRegionStringFromSequenceFeatureList(Collection<SequenceFeature>, InterMineAPI, Profile) - Static method in class org.intermine.bio.web.logic.GenomicRegionSearchQueryRunner

query chromosome locations by a list of sequence features, return region string as chr:start..end

getReliability() - Method in class org.intermine.bio.web.model.ProteinAtlasExpressions

getResultsCss() - Method in class org.intermine.bio.web.logic.GenomicRegionSearchService

Get the name of customized results CSS

getResultsJavascript() - Method in class org.intermine.bio.web.logic.GenomicRegionSearchService

Get the name of customized results javascript

getSearchInfo() - Method in class org.intermine.bio.webservice.GenomicRegionSearchListInput

getSelectionInformation() - Method in class org.intermine.bio.web.logic.GenomicRegionSearchService

The message passed to results page

getSequenceFeatureForSequence(ObjectStore, Sequence) - Static method in class org.intermine.bio.web.export.ResidueFieldExporter

Find the SequenceFeature that references the given Sequence.

getSequencePath() - Method in class org.intermine.bio.web.struts.SequenceExportForm

Gets the selected path

getService() - Method in class org.intermine.bio.webservice.BEDQueryServlet

getService() - Method in class org.intermine.bio.webservice.BioExportServlet

getService() - Method in class org.intermine.bio.webservice.FastaListServlet

getService() - Method in class org.intermine.bio.webservice.FastaQueryServlet

getService() - Method in class org.intermine.bio.webservice.GenomicRegionBedServlet

getService() - Method in class org.intermine.bio.webservice.GenomicRegionFastaServlet

getService() - Method in class org.intermine.bio.webservice.GenomicRegionGFF3Servlet

getService() - Method in class org.intermine.bio.webservice.GenomicRegionSearchServlet

getService() - Method in class org.intermine.bio.webservice.GFF3ListServlet

getService() - Method in class org.intermine.bio.webservice.GFF3QueryServlet

getService(WebServiceServlet.Method) - Method in class org.intermine.bio.webservice.BioExportServlet

getSourceName() - Method in class org.intermine.bio.web.XRef

getStainingLevel() - Method in class org.intermine.bio.web.model.ProteinAtlasExpressions.ExpressionList

getStart() - Method in class org.intermine.bio.web.model.GenomicRegion

getStrandSpecific() - Method in class org.intermine.bio.web.model.GenomicRegionSearchConstraint

getStrandSpecific() - Method in class org.intermine.bio.webservice.GenomicRegionSearchListInput.GenomicRegionSearchInfo

getSuffix() - Method in class org.intermine.bio.webservice.AbstractRegionExportService

getSuffix() - Method in class org.intermine.bio.webservice.BEDQueryService

getSuffix() - Method in class org.intermine.bio.webservice.BioQueryService

getSuffix() - Method in class org.intermine.bio.webservice.FastaQueryService

getSuffix() - Method in class org.intermine.bio.webservice.GenomicRegionBedService

getSuffix() - Method in class org.intermine.bio.webservice.GenomicRegionFastaService

getSuffix() - Method in class org.intermine.bio.webservice.GenomicRegionGFF3Service

getSuffix() - Method in class org.intermine.bio.webservice.GFFQueryService

getTag() - Method in class org.intermine.bio.web.model.GenomicRegion

getTaxonIds(Set<String>) - Method in class org.intermine.bio.web.logic.GenomicRegionSearchService

getTaxonIds(PathQuery, HttpSession) - Static method in class org.intermine.bio.web.logic.SequenceFeatureExportUtil

Get organism taxon ids info from PathQuery

getTaxonIds(PathQuery, InterMineAPI, Profile) - Static method in class org.intermine.bio.web.logic.SequenceFeatureExportUtil

getTaxonInfo(InterMineAPI, int) - Static method in class org.intermine.bio.web.logic.GenomicRegionSearchQueryRunner

Query the information of all organisms and their taxon ids.

getThreePrimeUTR() - Method in class org.intermine.bio.web.model.GeneModel

Get the threePrimeUTR if present.

getTrackDescription() - Method in class org.intermine.bio.web.struts.BEDExportForm

getTranscript() - Method in class org.intermine.bio.web.model.GeneModel

Get the transcript this gene model represents

getUcscCompatibleCheck() - Method in class org.intermine.bio.web.struts.BEDExportForm

getUrl() - Method in class org.intermine.bio.web.XRef

getValues() - Method in class org.intermine.bio.web.model.GeneExpressionAtlasDiseasesExpressions.ExpressionList

Get the internal list of expressions

getValues() - Method in class org.intermine.bio.web.model.GeneExpressionAtlasTissuesExpressions.ExpressionList

Get the internal list of expressions

getValues() - Method in class org.intermine.bio.web.model.ProteinAtlasExpressions.ExpressionList

Get the internal map of expressions

getWrittenResultsCount() - Method in class org.intermine.bio.web.export.BEDExporter

getWrittenResultsCount() - Method in class org.intermine.bio.web.export.GFF3Exporter

getWrittenResultsCount() - Method in class org.intermine.bio.web.export.SequenceExporter

GFF_FIELDS - Static variable in class org.intermine.bio.web.export.GFF3Exporter

the fields we don't want to display as attributes

GFF3Exporter - Class in org.intermine.bio.web.export

Exports LocatedSequenceFeature objects in GFF3 format.

GFF3Exporter(PrintWriter, List<Integer>, Map<String, String>, List<String>, String, Set<String>, boolean) - Constructor for class org.intermine.bio.web.export.GFF3Exporter

Constructor.

GFF3Exporter(PrintWriter, List<Integer>, Map<String, String>, List<String>, String, Set<String>, boolean, List<Path>) - Constructor for class org.intermine.bio.web.export.GFF3Exporter

Constructor.

GFF3ExportForm - Class in org.intermine.bio.web.struts

Form for sequence export (FASTA probably)

GFF3ExportForm() - Constructor for class org.intermine.bio.web.struts.GFF3ExportForm

GFF3HttpExporter - Class in org.intermine.bio.web.export

An implementation of TableHttpExporter that exports LocatedSequenceFeature objects in GFF3 format.

GFF3HttpExporter() - Constructor for class org.intermine.bio.web.export.GFF3HttpExporter

GFF3ListService - Class in org.intermine.bio.webservice

Export a List as GFF3.

GFF3ListService(InterMineAPI) - Constructor for class org.intermine.bio.webservice.GFF3ListService

GFF3ListServlet - Class in org.intermine.bio.webservice

GFF3ListServlet() - Constructor for class org.intermine.bio.webservice.GFF3ListServlet

GFF3QueryServlet - Class in org.intermine.bio.webservice

A servlet to hand off to the GFF3-query-service.

GFF3QueryServlet() - Constructor for class org.intermine.bio.webservice.GFF3QueryServlet

GFFQueryService - Class in org.intermine.bio.webservice

A service for exporting query results as gff3.

GFFQueryService(InterMineAPI) - Constructor for class org.intermine.bio.webservice.GFFQueryService

Constructor.

groupGenomicRegionByInterval(String, Set<GenomicRegion>) - Static method in class org.intermine.bio.web.logic.GenomicRegionSearchUtil

Look for genomic regions within or overlap an interval.

H

hashCode() - Method in class org.intermine.bio.web.model.GenomicRegion

hashCode() - Method in class org.intermine.bio.web.model.GenomicRegionSearchConstraint

hasJBrowseTrack(String) - Method in class org.intermine.bio.web.logic.GenomicRegionSearchService

Test if jbrowse has a track regards to a feature type

HomologueDisplayer - Class in org.intermine.bio.web.displayer

Displayer for Homology

HomologueDisplayer(ReportDisplayerConfig, InterMineAPI) - Constructor for class org.intermine.bio.web.displayer.HomologueDisplayer

Construct with config information read from webconfig-model.xml and the API.

I

init() - Method in class org.intermine.bio.webservice.BioExportServlet

init(HttpServletRequest) - Method in class org.intermine.bio.web.logic.GenomicRegionSearchService

To set globally used variables.

initialise() - Method in class org.intermine.bio.web.struts.SequenceExportForm

Initialiser

isApplicable() - Method in class org.intermine.bio.web.widget.GeneLengthCorrectionCoefficient

isAuthenticated() - Method in class org.intermine.bio.webservice.AbstractRegionExportService

isEmptyFeature(Map<GenomicRegion, List<List<String>>>) - Method in class org.intermine.bio.web.logic.GenomicRegionSearchService

Check whether the results have empty features.

isInterbase() - Method in class org.intermine.bio.webservice.GenomicRegionSearchListInput.GenomicRegionSearchInfo

isJBrowseEnabled() - Method in class org.intermine.bio.web.logic.GenomicRegionSearchService

Test if jbrowse is enabled

isOverlapped(GenomicRegion) - Method in class org.intermine.bio.web.model.GenomicRegion

Test if two regions are overlapped.

isSelected(String) - Method in class org.intermine.bio.web.widget.GeneLengthCorrectionCoefficient

isThisAHuman() - Method in class org.intermine.bio.web.displayer.MetabolicGeneSummaryDisplayer.GeneSummary

isThisAMouser() - Method in class org.intermine.bio.web.displayer.MetabolicGeneSummaryDisplayer.GeneSummary

isValidFastaQuery(PathQuery) - Static method in class org.intermine.bio.web.logic.SequenceFeatureExportUtil

isValidSequenceFeatureQuery(PathQuery) - Static method in class org.intermine.bio.web.logic.SequenceFeatureExportUtil

true if valid feature

J

JBrowseDisplayer - Class in org.intermine.bio.web.displayer

Displayer for JBrowse

JBrowseDisplayer(ReportDisplayerConfig, InterMineAPI) - Constructor for class org.intermine.bio.web.displayer.JBrowseDisplayer

Construct with config and the InterMineAPI.

JMOLDisplayer - Class in org.intermine.bio.web.displayer

displayer for protein structures.

JMOLDisplayer(ReportDisplayerConfig, InterMineAPI) - Constructor for class org.intermine.bio.web.displayer.JMOLDisplayer

Construct with config and the InterMineAPI.

L

LiftOverService - Class in org.intermine.bio.web.logic

Communication between intermine and liftover server in a way as posting http request from the webapp, avoiding cross-domian issue.

LiftOverService() - Constructor for class org.intermine.bio.web.logic.LiftOverService

LOG - Static variable in class org.intermine.bio.web.AttributeLinksController

LOG - Static variable in class org.intermine.bio.web.BioLinkRedirectManager

LOG - Static variable in class org.intermine.bio.web.displayer.CuratedProteinsDisplayer

LOG - Static variable in class org.intermine.bio.web.displayer.DiseaseDisplayer

LOG - Static variable in class org.intermine.bio.web.displayer.EsynDisplayer

LOG - Static variable in class org.intermine.bio.web.displayer.GeneIdentifiersDisplayer

LOG - Static variable in class org.intermine.bio.web.displayer.HomologueDisplayer

LOG - Static variable in class org.intermine.bio.web.displayer.JMOLDisplayer

LOG - Static variable in class org.intermine.bio.web.displayer.MetabolicGeneSummaryDisplayer

LOG - Static variable in class org.intermine.bio.web.displayer.MinePathwaysDisplayer

LOG - Static variable in class org.intermine.bio.web.displayer.MouseAllelesDisplayer

LOG - Static variable in class org.intermine.bio.web.displayer.OverlappingFeaturesDisplayer

LOG - Static variable in class org.intermine.bio.web.displayer.PublicationAnnotationsDisplayer

LOG - Static variable in class org.intermine.bio.web.displayer.PublicationCountsDisplayer

LOG - Static variable in class org.intermine.bio.web.displayer.RegulatoryRegionsDisplayer

LOG - Static variable in class org.intermine.bio.web.displayer.SnpToGeneDisplayer

LOG - Static variable in class org.intermine.bio.web.displayer.UniProtCommentsDisplayer

LOG - Static variable in class org.intermine.bio.web.export.ResidueFieldExporter

LOG - Static variable in class org.intermine.bio.web.export.SequenceHttpExporter

LOG - Static variable in class org.intermine.bio.web.model.GeneModel

LOG - Static variable in class org.intermine.bio.web.model.GeneModelCache

LOG - Static variable in class org.intermine.bio.webservice.ExternalLinksService

M

make(BioEntity, BioSequenceFactory.SequenceType) - Static method in class org.intermine.bio.web.biojava.BioSequenceFactory

Create a new BioSequence from a BioEntity, given its SequenceType

make(Protein) - Static method in class org.intermine.bio.web.biojava.BioSequenceFactory

Create a new BioSequence from a Protein

make(SequenceFeature) - Static method in class org.intermine.bio.web.biojava.BioSequenceFactory

Create a new BioSequence from a SequenceFeature

makeList(ListInput, String, Profile, Set<String>) - Method in class org.intermine.bio.webservice.AbstractRegionExportService

makeList(ListInput, String, Profile, Set<String>) - Method in class org.intermine.bio.webservice.GenomicRegionSearchService

makePathQuery(String, Collection<Integer>) - Method in class org.intermine.bio.webservice.AbstractRegionExportService

Make a path-query from a bag.

makeUcscCompatible() - Method in class org.intermine.bio.web.struts.GFF3ExportForm

Return whether to make exported GFF3 compatible with UCSC genome browser.

makeWithTranslation(SequenceFeature) - Static method in class org.intermine.bio.web.biojava.BioSequenceFactory

Create a new BioSequence from a SequenceFeature

MetabolicGeneSummaryDisplayer - Class in org.intermine.bio.web.displayer

MetabolicGeneSummaryDisplayer(ReportDisplayerConfig, InterMineAPI) - Constructor for class org.intermine.bio.web.displayer.MetabolicGeneSummaryDisplayer

Construct with config and the InterMineAPI.

MetabolicGeneSummaryDisplayer.GeneSummary - Class in org.intermine.bio.web.displayer

Internal wrapper.

MinePathwaysDisplayer - Class in org.intermine.bio.web.displayer

For all friendly mines, query for pathways

MinePathwaysDisplayer(ReportDisplayerConfig, InterMineAPI) - Constructor for class org.intermine.bio.web.displayer.MinePathwaysDisplayer

Construct with config and the InterMineAPI.

MouseAllelesDisplayer - Class in org.intermine.bio.web.displayer

If we are mouse, fetch results straight off of us, otherwise create a PathQuery from other organisms.

MouseAllelesDisplayer(ReportDisplayerConfig, InterMineAPI) - Constructor for class org.intermine.bio.web.displayer.MouseAllelesDisplayer

Construct with config and the InterMineAPI.

O

ONTOLOGIES - Static variable in class org.intermine.bio.web.displayer.GeneOntologyDisplayer

The names of ontology root terms.

org.intermine.bio.web - package org.intermine.bio.web

org.intermine.bio.web.biojava - package org.intermine.bio.web.biojava

org.intermine.bio.web.displayer - package org.intermine.bio.web.displayer

org.intermine.bio.web.export - package org.intermine.bio.web.export

org.intermine.bio.web.logic - package org.intermine.bio.web.logic

org.intermine.bio.web.model - package org.intermine.bio.web.model

org.intermine.bio.web.struts - package org.intermine.bio.web.struts

org.intermine.bio.web.widget - package org.intermine.bio.web.widget

org.intermine.bio.webservice - package org.intermine.bio.webservice

org.intermine.webservice.server.complexes - package org.intermine.webservice.server.complexes

org.intermine.webservice.server.jbrowse.genomic - package org.intermine.webservice.server.jbrowse.genomic

OrganismGenomeBuildLookup - Class in org.intermine.bio.web.logic

An util class to help looking up genome build by a given organism id.

OrganismInfo - Class in org.intermine.bio.web.model

Bean to store organism information for Galaxy use.

OrganismInfo(int, String, String) - Constructor for class org.intermine.bio.web.model.OrganismInfo

Constructor

OrthologueConverter - Class in org.intermine.bio.web.logic

OrthologueConverter(InterMineAPI, WebConfig) - Constructor for class org.intermine.bio.web.logic.OrthologueConverter

OtherMinesLinkController - Class in org.intermine.bio.web

Show Other Mines Links on "Gene" page

OtherMinesLinkController() - Constructor for class org.intermine.bio.web.OtherMinesLinkController

OverlappingFeaturesDisplayer - Class in org.intermine.bio.web.displayer

Displayer for features overlapping a particular SequenceFeature using the overlappingFeatures collection.

OverlappingFeaturesDisplayer(ReportDisplayerConfig, InterMineAPI) - Constructor for class org.intermine.bio.web.displayer.OverlappingFeaturesDisplayer

Construct with config and the InterMineAPI.

P

parseBasicInput(GenomicRegionSearchForm) - Method in class org.intermine.bio.web.logic.GenomicRegionSearchService

parseExtension(String) - Static method in class org.intermine.bio.webservice.FastaQueryService

A method for parsing the value of the extension parameter.

parseGenomicRegionSearchForm(GenomicRegionSearchForm) - Method in class org.intermine.bio.web.logic.GenomicRegionSearchService

To parse form data

parseRegion(String, boolean, Map<String, ChromosomeInfo>) - Static method in class org.intermine.bio.web.logic.GenomicRegionSearchUtil

Parse region from string to GenomicRegion object

participant - Variable in class org.intermine.webservice.server.complexes.ExportService.FeatureHolder

PathwayDescriptionDisplayer - Class in org.intermine.bio.web.displayer

PathwayDescriptionDisplayer(ReportDisplayerConfig, InterMineAPI) - Constructor for class org.intermine.bio.web.displayer.PathwayDescriptionDisplayer

PathwaysDisplayer - Class in org.intermine.bio.web.displayer

Display pathway for this gene, plus the count of the other genes on this pathway

PathwaysDisplayer(ReportDisplayerConfig, InterMineAPI) - Constructor for class org.intermine.bio.web.displayer.PathwaysDisplayer

Construct with config and the InterMineAPI.

primaryIdentifier - Variable in class org.intermine.webservice.server.complexes.ExportService.FeatureHolder

produceName() - Method in class org.intermine.bio.webservice.GenomicRegionSearchListInput

PROPERTY_DESCRIPTIONLINE - Static variable in class org.intermine.bio.web.export.ResidueFieldExporter

PROTEIN - org.intermine.bio.web.biojava.BioSequenceFactory.SequenceType

PROTEIN sequence

ProteinAtlasDisplayer - Class in org.intermine.bio.web.displayer

Protein Atlas Tissue Expression Displayer, showing antibody staining per organ group etc.

ProteinAtlasDisplayer(ReportDisplayerConfig, InterMineAPI) - Constructor for class org.intermine.bio.web.displayer.ProteinAtlasDisplayer

ProteinAtlasExpressions - Class in org.intermine.bio.web.model

Protein Atlas Expressions

ProteinAtlasExpressions(ExportResultsIterator) - Constructor for class org.intermine.bio.web.model.ProteinAtlasExpressions

Convert Path results into a List (ProteinAtlasDisplayer.java)

ProteinAtlasExpressions.ByCellCountComparator - Class in org.intermine.bio.web.model

Reorder a TreeMap based on the number of cells contained in Expressions

ProteinAtlasExpressions.ByLevelComparator - Class in org.intermine.bio.web.model

Comparator used on Expressions to order them by staining level

ProteinAtlasExpressions.ByOverallLevelComparator - Class in org.intermine.bio.web.model

Reorder a TreeMap based on the overall staining level of the Expressions

ProteinAtlasExpressions.ExpressionList - Class in org.intermine.bio.web.model

Represents a treemap structure of maps of expressions

ProteinAtlasExpressions.ExpressionList.StainingLevel - Class in org.intermine.bio.web.model

Gives us 'stats' on the overall staining level of the Expressions

ProteinAtlasExpressions.StainingLevelEvaluator - Class in org.intermine.bio.web.model

Determines the "points" staining levels will get

ProteinSequenceDisplayer - Class in org.intermine.bio.web.displayer

Displayer for protein sequence

ProteinSequenceDisplayer(ReportDisplayerConfig, InterMineAPI) - Constructor for class org.intermine.bio.web.displayer.ProteinSequenceDisplayer

Construct with config and the InterMineAPI.

ProteinStructureATMDisplayer - Class in org.intermine.bio.web.displayer

Protein Structure ATM Displayer turning the field into a link that shows the shebang in new window.

ProteinStructureATMDisplayer(ReportDisplayerConfig, InterMineAPI) - Constructor for class org.intermine.bio.web.displayer.ProteinStructureATMDisplayer

PublicationAnnotationsDisplayer - Class in org.intermine.bio.web.displayer

Display all objects mentioned by publication

PublicationAnnotationsDisplayer(ReportDisplayerConfig, InterMineAPI) - Constructor for class org.intermine.bio.web.displayer.PublicationAnnotationsDisplayer

Construct with config and the InterMineAPI.

PublicationCountsDisplayer - Class in org.intermine.bio.web.displayer

Display publication and number of genes annotated by that publication.

PublicationCountsDisplayer(ReportDisplayerConfig, InterMineAPI) - Constructor for class org.intermine.bio.web.displayer.PublicationCountsDisplayer

Construct with config and the InterMineAPI.

R

reference(Command) - Method in class org.intermine.webservice.server.jbrowse.genomic.Engine

RegionParseException - Exception in org.intermine.bio.web.logic

RegionParseException(String) - Constructor for exception org.intermine.bio.web.logic.RegionParseException

RegulatoryRegionsDisplayer - Class in org.intermine.bio.web.displayer

TODO: merge this with OverlappingFeaturesDisplayer to reuse common functionality (preferrably wo/ creating another table type on a report page

RegulatoryRegionsDisplayer(ReportDisplayerConfig, InterMineAPI) - Constructor for class org.intermine.bio.web.displayer.RegulatoryRegionsDisplayer

Construct with config and the InterMineAPI.

ReportWidgetDisplayer - Class in org.intermine.bio.web.displayer

ReportWidgetDisplayer(ReportDisplayerConfig, InterMineAPI) - Constructor for class org.intermine.bio.web.displayer.ReportWidgetDisplayer

reset(ActionMapping, HttpServletRequest) - Method in class org.intermine.bio.web.struts.SequenceExportForm

Reset the form to the initial state

ResidueFieldExporter - Class in org.intermine.bio.web.export

ResidueFieldExporter class

ResidueFieldExporter() - Constructor for class org.intermine.bio.web.export.ResidueFieldExporter

reverseEvaluate(Integer) - Method in class org.intermine.bio.web.model.ProteinAtlasExpressions.StainingLevelEvaluator

Integer value to string conversion

RNA - org.intermine.bio.web.biojava.BioSequenceFactory.SequenceType

RNA sequence

run() - Method in class org.intermine.bio.web.logic.GenomicRegionSearchQueryRunner

S

search() - Method in class org.intermine.bio.web.logic.GenomicRegionSearchQueryRunner

Main body of db search

SequenceExportAction - Class in org.intermine.bio.web.struts

Exports sequence.

SequenceExportAction() - Constructor for class org.intermine.bio.web.struts.SequenceExportAction

SequenceExporter - Class in org.intermine.bio.web.export

Export data in FASTA format.

SequenceExporter(ObjectStore, OutputStream, int, Map<String, List<FieldDescriptor>>, int, String) - Constructor for class org.intermine.bio.web.export.SequenceExporter

Constructor.

SequenceExporter(ObjectStore, OutputStream, int, Map<String, List<FieldDescriptor>>, int, String, List<Path>) - Constructor for class org.intermine.bio.web.export.SequenceExporter

Constructor.

SequenceExportForm - Class in org.intermine.bio.web.struts

Form for sequence export (FASTA etc.)

SequenceExportForm() - Constructor for class org.intermine.bio.web.struts.SequenceExportForm

Constructor

SequenceExportOptionsController - Class in org.intermine.bio.web.struts

Controller for sequence export tile.

SequenceExportOptionsController() - Constructor for class org.intermine.bio.web.struts.SequenceExportOptionsController

SequenceFeatureDisplayer - Class in org.intermine.bio.web.displayer

Displayer for gene sequence feature

SequenceFeatureDisplayer(ReportDisplayerConfig, InterMineAPI) - Constructor for class org.intermine.bio.web.displayer.SequenceFeatureDisplayer

Construct with config and the InterMineAPI.

SequenceFeatureExportOptionsController - Class in org.intermine.bio.web.struts

Controller for sequence, gff3 and bed format tiles.

SequenceFeatureExportOptionsController() - Constructor for class org.intermine.bio.web.struts.SequenceFeatureExportOptionsController

SequenceFeatureExportUtil - Class in org.intermine.bio.web.logic

Utility methods for LocatedSequenceFeature exporting.

SequenceFeatureExportUtil.InvalidQueryException - Exception in org.intermine.bio.web.logic

SequenceHttpExporter - Class in org.intermine.bio.web.export

Obsoleted - replaced by new results table An implementation of TableExporter that exports sequence objects using the BioJava sequence and feature writers.

SequenceHttpExporter() - Constructor for class org.intermine.bio.web.export.SequenceHttpExporter

setChr(String) - Method in class org.intermine.bio.web.model.GenomicRegion

setChrLength(Integer) - Method in class org.intermine.bio.web.model.ChromosomeInfo

setChrPID(String) - Method in class org.intermine.bio.web.model.ChromosomeInfo

setEnd(Integer) - Method in class org.intermine.bio.web.model.GenomicRegion

setExtendedEnd(Integer) - Method in class org.intermine.bio.web.model.GenomicRegion

setExtendedRegionSize(int) - Method in class org.intermine.bio.web.model.GenomicRegion

setExtendedRegionSize(int) - Method in class org.intermine.bio.web.model.GenomicRegionSearchConstraint

setExtendedStart(Integer) - Method in class org.intermine.bio.web.model.GenomicRegion

setExtension(int) - Method in class org.intermine.bio.webservice.GenomicRegionSearchListInput.GenomicRegionSearchInfo

setFeatureTypes(Collection<String>) - Method in class org.intermine.bio.webservice.GenomicRegionSearchListInput.GenomicRegionSearchInfo

Set the feature types for this request.

setFeatureTypes(Set<Class<?>>) - Method in class org.intermine.bio.web.model.GenomicRegionSearchConstraint

setGenomeBuild(String) - Method in class org.intermine.bio.web.model.OrganismInfo

setGenomicRegionList(List<GenomicRegion>) - Method in class org.intermine.bio.web.model.GenomicRegionSearchConstraint

setIdx(int) - Method in class org.intermine.bio.web.model.OrganismInfo

setImageName(String) - Method in class org.intermine.bio.web.XRef

setInterbase(boolean) - Method in class org.intermine.bio.webservice.GenomicRegionSearchListInput.GenomicRegionSearchInfo

setMakeUcscCompatible(boolean) - Method in class org.intermine.bio.web.struts.BEDExportForm

Set whether to make exported BED compatible with UCSC genome browser.

setMakeUcscCompatible(boolean) - Method in class org.intermine.bio.web.struts.GFF3ExportForm

Set whether to make exported GFF3 compatible with UCSC genome browser.

setMinusStrand(boolean) - Method in class org.intermine.bio.web.model.GenomicRegion

setMinusStrand(Boolean) - Method in class org.intermine.bio.web.model.GenomicRegion

setOrganism(String) - Method in class org.intermine.bio.web.model.GenomicRegion

setOrganism(String) - Method in class org.intermine.bio.webservice.GenomicRegionSearchListInput.GenomicRegionSearchInfo

setOrganisms(Set<String>) - Method in class org.intermine.bio.web.struts.GFF3ExportForm

Set the organisms

setOrganName(String) - Method in class org.intermine.bio.web.model.ProteinAtlasExpressions.ExpressionList

setOrgansimString(String) - Method in class org.intermine.bio.web.struts.BEDExportForm

setOrgList(String) - Method in class org.intermine.bio.web.model.OrganismInfo

setOrgName(String) - Method in class org.intermine.bio.web.model.ChromosomeInfo

setOrgName(String) - Method in class org.intermine.bio.web.model.GenomicRegionSearchConstraint

setRegions(List<String>) - Method in class org.intermine.bio.webservice.GenomicRegionSearchListInput.GenomicRegionSearchInfo

setSequenceExportHeader(HttpServletResponse, boolean) - Static method in class org.intermine.bio.web.export.SequenceHttpExporter

Set response proper header.

setSequencePath(String) - Method in class org.intermine.bio.web.struts.SequenceExportForm

Sets the selected sequence path.

setSourceName(String) - Method in class org.intermine.bio.web.XRef

setStart(Integer) - Method in class org.intermine.bio.web.model.GenomicRegion

setStrandSpecific(boolean) - Method in class org.intermine.bio.web.model.GenomicRegionSearchConstraint

setStrandSpecific(boolean) - Method in class org.intermine.bio.webservice.GenomicRegionSearchListInput.GenomicRegionSearchInfo

setTag(Integer) - Method in class org.intermine.bio.web.model.GenomicRegion

setTrackDescription(String) - Method in class org.intermine.bio.web.struts.BEDExportForm

setUcscCompatibleCheck(String) - Method in class org.intermine.bio.web.struts.BEDExportForm

setupWebData() - Method in class org.intermine.bio.web.logic.GenomicRegionSearchService

To call the queryOrganismAndSequenceFeatureTypes method in GenomicRegionSearchQueryRunner.

setUrl(String) - Method in class org.intermine.bio.web.XRef

SnpToGeneDisplayer - Class in org.intermine.bio.web.displayer

SNPs to nearby Genes displayer for metabolicMine report page

SnpToGeneDisplayer(ReportDisplayerConfig, InterMineAPI) - Constructor for class org.intermine.bio.web.displayer.SnpToGeneDisplayer

Construct with config and the InterMineAPI.

SO_CLASS_NAMES - Static variable in class org.intermine.bio.webservice.BioExportServlet

so class names

StainingLevel(ProteinAtlasExpressions.ByLevelComparator) - Constructor for class org.intermine.bio.web.model.ProteinAtlasExpressions.ExpressionList.StainingLevel

StainingLevelEvaluator() - Constructor for class org.intermine.bio.web.model.ProteinAtlasExpressions.StainingLevelEvaluator

stats(Command) - Method in class org.intermine.webservice.server.jbrowse.genomic.Engine

SUFFIX - Static variable in class org.intermine.bio.webservice.GenomicRegionBedService

SUFFIX - Static variable in class org.intermine.bio.webservice.GenomicRegionFastaService

T

toString() - Method in class org.intermine.bio.web.model.GenomicRegion

TYPES - Static variable in class org.intermine.bio.web.model.GeneModel

The unqualified class names of types that comprise a gene model.

U

UniProtCommentsDisplayer - Class in org.intermine.bio.web.displayer

metabolicMine UniProt curated comments displayer on Gene report page

UniProtCommentsDisplayer(ReportDisplayerConfig, InterMineAPI) - Constructor for class org.intermine.bio.web.displayer.UniProtCommentsDisplayer

Construct with config and the InterMineAPI.

updatePopulationQuery(Query, Query, QueryField) - Method in class org.intermine.bio.web.widget.GeneLengthCorrectionCoefficient

updateQueryWithCorrectionCoefficient(Query, QueryClass) - Method in class org.intermine.bio.web.widget.GeneLengthCorrectionCoefficient

V

validateGenomicRegions() - Method in class org.intermine.bio.web.logic.GenomicRegionSearchService

Validate input genomic regions

validateState() - Method in class org.intermine.bio.webservice.AbstractRegionExportService

valueOf(String) - Static method in enum org.intermine.bio.web.biojava.BioSequenceFactory.SequenceType

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

values() - Static method in enum org.intermine.bio.web.biojava.BioSequenceFactory.SequenceType

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

W

WORM_LINK - Static variable in class org.intermine.bio.web.export.GFF3Exporter

for the gff header, link to taxomony

X

XRef - Class in org.intermine.bio.web

This is a bean to store cross-reference data This class is half finished, more fields may be added

XRef() - Constructor for class org.intermine.bio.web.XRef

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