All Classes Class Summary Enum Summary Exception Summary
| Class |
Description |
| AbstractRegionExportService |
Base class for Biological region export services.
|
| AttributeLinksController |
Set up maps for attributeLinks.jsp
|
| BEDExporter |
Exports LocatedSequenceFeature objects in UCSC BED format.
|
| BEDExportForm |
Form for sequence export in BED format
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| BEDHttpExporter |
An implementation of TableHttpExporter that exports LocatedSequenceFeature
objects in BED format.
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| BEDQueryService |
A service for exporting query results in UCSC BED format.
|
| BEDQueryServlet |
A servlet to hand off to the UCSC BED query service.
|
| BioExportServlet |
A servlet to hand off to the GFF3-query-service.
|
| BioLinkRedirectManager |
Contructs an alternate object details link pointing to an external URL for use in results table.
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| BioQueryService |
A service for exporting query results as gff3.
|
| BioSequence |
An implementation of the BioJava Sequence interface that uses InterMine objects underneath.
|
| BioSequenceFactory |
A factory for creating BioSequence objects.
|
| BioSequenceFactory.SequenceType |
Type of sequences.
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| BioWidgetUtil |
Utility methods for the flymine package.
|
| ChromosomeInfo |
This Java bean stores the information for span validation use.
|
| ComplexDisplayer |
Displayer for gene/protein interactions using complex viewer
|
| CuratedProteinsDisplayer |
|
| CytoscapeNetworkDisplayer |
Displayer for gene/protein interactions using cytoscape plugin
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| DiseaseDisplayer |
For ratmine, display all disease ontology objects for orthologues
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| Engine |
An adaptor for running JBrowse queries against a genomic database.
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| EsynDisplayer |
displayer for esyn
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| EsynListDisplayer |
displayer for esyn on list analysis page
|
| ExportService |
Web service that produces JSON required by the complex viewer.
|
| ExternalLinksService |
Exports selected web.properties.
|
| ExternalLinksServlet |
Runs ExternalLinksService web service.
|
| FastaListService |
Export a list as FASTA.
|
| FastaListServlet |
|
| FastaQueryService |
A service for exporting query results as fasta.
|
| FastaQueryServlet |
A servlet to hand off to the FASTA-query-service.
|
| FlyBaseExpressionDisplayer |
FlyBase modENCODE expression data
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| FriendlyMineLinkController |
Gets list of friendly intermines to show on list analysis page.
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| FriendlyMineLinkGenerator |
Helper class for intermine links generated on report and lists pages
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| GalaxyExportAction |
Generate feature path query.
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| GalaxyExportForm |
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| GalaxyExportOptionsController |
Controller for galaxyExportOptions.tile.
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| GBrowseDisplayer |
Displayer for GBrowse
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| GeneExpressionAtlasDiseasesDisplayer |
Gene Expression Atlas Displayer (Blue/Green)
|
| GeneExpressionAtlasDiseasesExpressions |
Gene Expression Atlas Tissues Expressions
|
| GeneExpressionAtlasTissuesDisplayer |
Gene Expression Atlas Displayer (Blue/Green)
|
| GeneExpressionAtlasTissuesExpressions |
Gene Expression Atlas Tissues Expressions
|
| GeneIdentifiersDisplayer |
|
| GeneLengthCorrectionCoefficient |
Implementation of the gene length coefficient
|
| GeneModel |
Representation of a gene model - being one transcript of a gene and including exons, introns,
UTRs and CDSs where data are available.
|
| GeneModelCache |
A cache for gene models by Gene object id.
|
| GeneModelSettings |
|
| GeneOntologyDisplayer |
Builds datastructure from go parent id to go term id.
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| GeneStructureDisplayer |
Custom displayer for gene structure.
|
| GenomicRegion |
This Java bean represents one record of Chromosome coordinates from user input
The record should be in BED format: "chr\tstart\tend".
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| GenomicRegionBedService |
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| GenomicRegionBedServlet |
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| GenomicRegionFastaService |
A class for exposing the region search as a FASTA resource.
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| GenomicRegionFastaServlet |
|
| GenomicRegionGFF3Service |
|
| GenomicRegionGFF3Servlet |
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| GenomicRegionSearchAction |
For genomic region search.
|
| GenomicRegionSearchAjaxAction |
Genomic region search ajax calls.
|
| GenomicRegionSearchConstraint |
A class to represent the constraints a user selected including a list of features and genomic
regions, etc.
|
| GenomicRegionSearchForm |
This ActionForm represents the form elements on the genomicRegionSearchOptionsBase.jsp
|
| GenomicRegionSearchListInput |
|
| GenomicRegionSearchOptionsController |
Class to prepare data for genomicRegionSeachOptions.jsp.
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| GenomicRegionSearchQueryRunner |
This class has all database query logics for genomic region search.
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| GenomicRegionSearchService |
A class to provide genomic region search services in general.
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| GenomicRegionSearchService |
A web service resource to expose the Region Search functionality.
|
| GenomicRegionSearchServlet |
|
| GenomicRegionSearchUtil |
This utility class instance a GenomicRegionSearchService object based on mine's setting.
|
| GenomicRegionSequenceExporter |
Exports DNA sequences of given genomic regions in FASTA format.
|
| GFF3Exporter |
Exports LocatedSequenceFeature objects in GFF3 format.
|
| GFF3ExportForm |
Form for sequence export (FASTA probably)
|
| GFF3HttpExporter |
An implementation of TableHttpExporter that exports LocatedSequenceFeature
objects in GFF3 format.
|
| GFF3ListService |
Export a List as GFF3.
|
| GFF3ListServlet |
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| GFF3QueryServlet |
A servlet to hand off to the GFF3-query-service.
|
| GFFQueryService |
A service for exporting query results as gff3.
|
| HomologueDisplayer |
Displayer for Homology
|
| JBrowseDisplayer |
Displayer for JBrowse
|
| JMOLDisplayer |
displayer for protein structures.
|
| LiftOverService |
Communication between intermine and liftover server in a way as
posting http request from the webapp, avoiding cross-domian issue.
|
| MetabolicGeneSummaryDisplayer |
|
| MinePathwaysDisplayer |
For all friendly mines, query for pathways
|
| MouseAllelesDisplayer |
If we are mouse, fetch results straight off of us, otherwise create a PathQuery from other
organisms.
|
| OrganismGenomeBuildLookup |
An util class to help looking up genome build by a given organism id.
|
| OrganismInfo |
Bean to store organism information for Galaxy use.
|
| OrthologueConverter |
|
| OtherMinesLinkController |
Show Other Mines Links on "Gene" page
|
| OverlappingFeaturesDisplayer |
Displayer for features overlapping a particular SequenceFeature using the overlappingFeatures
collection.
|
| PathwayDescriptionDisplayer |
|
| PathwaysDisplayer |
Display pathway for this gene, plus the count of the other genes on this pathway
|
| ProteinAtlasDisplayer |
Protein Atlas Tissue Expression Displayer, showing antibody staining per organ group etc.
|
| ProteinAtlasExpressions |
Protein Atlas Expressions
|
| ProteinSequenceDisplayer |
Displayer for protein sequence
|
| ProteinStructureATMDisplayer |
Protein Structure ATM Displayer turning the field into a link that shows the shebang in new
window.
|
| PublicationAnnotationsDisplayer |
Display all objects mentioned by publication
|
| PublicationCountsDisplayer |
Display publication and number of genes annotated by that publication.
|
| RegionParseException |
|
| RegulatoryRegionsDisplayer |
TODO: merge this with OverlappingFeaturesDisplayer to reuse common functionality (preferrably wo/
creating another table type on a report page
|
| ReportWidgetDisplayer |
|
| ResidueFieldExporter |
ResidueFieldExporter class
|
| SequenceExportAction |
Exports sequence.
|
| SequenceExporter |
Export data in FASTA format.
|
| SequenceExportForm |
Form for sequence export (FASTA etc.)
|
| SequenceExportOptionsController |
Controller for sequence export tile.
|
| SequenceFeatureDisplayer |
Displayer for gene sequence feature
|
| SequenceFeatureExportOptionsController |
Controller for sequence, gff3 and bed format tiles.
|
| SequenceFeatureExportUtil |
Utility methods for LocatedSequenceFeature exporting.
|
| SequenceFeatureExportUtil.InvalidQueryException |
|
| SequenceHttpExporter |
Obsoleted - replaced by new results table
An implementation of TableExporter that exports sequence objects using the BioJava sequence and
feature writers.
|
| SnpToGeneDisplayer |
SNPs to nearby Genes displayer for metabolicMine report page
|
| UniProtCommentsDisplayer |
metabolicMine UniProt curated comments displayer on Gene report page
|
| XRef |
This is a bean to store cross-reference data
This class is half finished, more fields may be added
|