Uses of Class
uk.ac.roslin.ensembl.exception.RangeException

Packages that use RangeException

Package	Description
uk.ac.roslin.ensembl.datasourceaware.core
uk.ac.roslin.ensembl.model.core

Uses of RangeException in uk.ac.roslin.ensembl.datasourceaware.core

Methods in uk.ac.roslin.ensembl.datasourceaware.core that throw RangeException

Modifier and Type	Method and Description
Coordinate	DATranslation.getChromosomePositionFromAA(Integer aminoAcidPosition) Returns the mapped chromosomal coordinates of an amino acid position.
String	DAFeature.getFlankingTargetSequenceAsString(Integer start, Integer stop) Retrieves the String representation of the target (genomic) sequence that this feature is annotated upon, for the given range.
String	DAAssembledDNASequence.getPaddedReverseComplementSequenceAsString(Integer begin, Integer end)
Coordinate	DATranslation.getPrimaryTranscriptPositionFromAA(Integer aminoAcidPosition) Returns the mapped coordinates of an amino acid position on the unprocessed primary transcript that provides this translation.
String	DATranscript.getPrimaryTranscriptRNASequenceAsString(Integer start, Integer stop) Preferred method to explicitly get a String representing the RNA sequence of the PrimaryTranscript, for the given range.
Coordinate	DATranslation.getProcessedTranscriptPositionFromAA(Integer aminoAcidPosition) Returns the mapped coordinates of an amino acid position on the (spliced) processed transcript that provides this translation.
String	DATranscript.getProcessedTranscriptRNASequenceAsString(Integer start, Integer stop) Returns a String representing the RNA sequence of the Processed (RNA spliced) Transcript, for the given range.
String	GapSequence.getReverseComplementSequenceAsString(Integer start, Integer stop)
String	DADNASequence.getReverseComplementSequenceAsString(Integer begin, Integer end) Method to get a string representation of the reverse complement of the sequence for the given range.
String	DAAssembly.getReverseComplementSequenceAsString(Integer start, Integer stop) Returns a String representation of the reverse complement of the assembly sequence for the given range.
String	DAAssembledDNASequence.getReverseComplementSequenceAsString(Integer begin, Integer end)
String	GapSequence.getRNASequenceAsString(Integer start, Integer stop)
String	DATranscript.getRNASequenceAsString(Integer start, Integer stop) Deprecated.
String	DAFeature.getRNASequenceAsString(Integer start, Integer stop) Returns a string representation for the given range of the RNASequence object trancribed from the DNASequence representing the extent of this annotation.
String	GapSequence.getSequenceAsString(Integer start, Integer stop)
String	DAFeature.getSequenceAsString(Integer start, Integer stop) Returns the string representation of the (genomic) sequence that this feature is annotated upon (at 'top level'), for the specified range.
String	DADNASequence.getSequenceAsString(Integer begin, Integer end) Method to get a string representation of the sequence for the given range.
String	DAAssembly.getSequenceAsString(Integer start, Integer stop) Returns a String representation of the assembly sequence for the given range.
String	DAAssembledDNASequence.getSequenceAsString(Integer begin, Integer end) Method to get a string representation for the given range of the assembled sequence.
String	DAAssembledDNASequence.getSequenceAsString(Integer begin, Integer end, Strand strand) Deprecated.
MappingSet	DAAssembly.getStitchedMappings(Integer start, Integer stop) For a given range, returns a subset of the MappingSet 'stitchedComponentMappings' of all of the mappings of all of the DNASequences that make up this assembly, that have been 'edited', i.e. stitched together into a single continuous gap free assembly.
String	DATranslation.getTranslatedSequenceAsString(Integer start, Integer stop) Returns a String representation of this Translation for the given range (i.e. the DNA Sequence...).

Uses of RangeException in uk.ac.roslin.ensembl.model.core

Methods in uk.ac.roslin.ensembl.model.core that throw RangeException

Modifier and Type	Method and Description
String	DNASequence.getReverseComplementSequenceAsString(Integer begin, Integer end)
String	DNASequence.getSequenceAsString(Integer begin, Integer end)
MappingSet	Assembly.getStitchedMappings()