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Class Summary |
| AbstractSequence |
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| AnnotatedFeature |
One thought Im having is that annotation stuff would be a HASA instead
of a ISA for SeqFeatureI. |
| AssemblyFeature |
A class to represent SeqFeatures which have been mapped to a static golden path-
the usual start/end is assumed to be in chromosome coords, but the assembly
start/end specific to this subclass are in coords relative to the feature. |
| Chromosome |
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| ChromosomeBand |
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| Comment |
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| CompositeDataHolder |
Holds multiple curation sets for synteny. |
| CurationSet |
I am the central holder of renderable data - results, annotations etc. |
| DbXref |
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| Evidence |
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| EvidenceFinder |
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| EvidenceSet |
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| Exon |
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| FeaturePair |
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| FeatureSet |
I think SeqFeature should implement all the functions of FeatureSet, so its
polymorphic, so when you have a SeqFeatureI you dont have to care whether its
a SeqFeature or a FeatureSet, so you dont have to keep downcasting to descend
the datamodel (or do any other feature set functionality)
As now you go through the Vector of SeqFeatures, cast to SeqFeature,
then ask instanceof FeatureSetI and cast to FeatureSetI, which
is potentially confusing. |
| GenomicRange |
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| Identifier |
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| Karyotype |
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| Link |
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| LinkSet |
Set of links for synteny view |
| Protein |
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| Range |
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| Score |
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| SeqFeature |
A class to represent a basic sequence feature, such as a result span. |
| Sequence |
Update this to take to use Range - used to ignore Range and use residueOffset,
which was redundat with using Range. |
| SequenceEdit |
seq edits are really seq features (very tiny ones) arent they
so subclass seq feature? do we still need seq edit? or seq edit has
a seq feature? chado models indels as features which makes
sense so why not apollo? needs to be annotated feat for chado
transaction transformer sake - to be consistent with other annots |
| SpeciesComparison |
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| StrandedFeatureSet |
It may well be that any FeatureSet for which the
strand is not explicitly set to either 1 or -1
(in other words the strand is 0) should be treated
as a mixed set of features that may be on either
strand |
| Synonym |
In Apollo, synonyms used to be strings, but in the ChadoXML data, synonyms
have other fields (pub_id, is_current), so this new datamodel allows us to
capture those fields (and any others that may come up) as properties. |
| SyntenyRegion |
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| Transcript |
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