| ArrayDesignMapResultServiceImpl |
Supports obtaining detailed information about the sequence analysis of probes on microarrays.
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| BlatAssociationScorer |
Given a set of BlatAssociations that might be redundant, clean them up and score them.
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| BlatResult2Psl |
Used to convert BlatResult objects into PSL lines that can be displayed in the UCSC Genome Browser.
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| CompositeSequenceMapSummary |
This is a convenience object to hold the results of CompositeSequence mapping results.
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| CompositeSequenceMapValueObject |
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| GeneMappingSummary |
This is a convenience value object to hold a BlatResult and its associated gene products and genes.
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| ProbeMapperConfig |
Holds parameters for how mapping should be done.
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| ProbeMapperImpl |
Provides methods for mapping sequences to genes and gene products.
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| ProbeMapUtils |
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| RepeatScan |
Scan sequences for repeats
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| SequenceBinUtils |
Used to assign a bin to a chromosome location, identify bins for a range, or to generate SQL to add to a query on a
GoldenPath database.
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| SequenceManipulation |
Convenient methods for manipulating BioSequences and PhysicalLocations
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| SequenceWriter |
Tools for writing biosequences to files so they can be analyzed by external tools, and then read back into Gemma.
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| ShellDelegatingBlat |
Class to manage the gfServer and run BLAT searches.
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