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Package apollo.datamodel

Interface Summary
AssemblyFeatureI  
Comparable  
EvidenceConstants  
ExonI  
FeaturePairI  
FeatureSetI  
GenericAnnotationI  
GenericAnnotationSetI Extends FeatureSetI as a GenericAnnotationSetI is always going to be a FeatureSetI, isnt it? Thats what the "Set" means isnt it?
LazySequenceI  
RangeI  
SeqFeatureI  
SequenceI  
StrandedFeatureSetI  
 

Class Summary
AbstractLazySequence  
AbstractSequence  
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.
CacheSeqIdLoader  
CacheSequenceLoader  
Chromosome  
ChromosomeBand  
Comment  
CurationSet I am the central holder of renderable data - results, annotations etc.
DbXref  
DebugLazySequence  
EnsCGISequence EnsCGISequence:
Evidence  
EvidenceFinder  
EvidenceSet  
Exon  
FeaturePair  
FeatureSet what is a FeatureSet - does it have biological meaning it seems to have biological methods - is it a scandal to use a FeatureSet to hold a bunch of graphical features - meaning like a set of features held together because they are all visible and on the same row - not necasarily having the whole gene as a normal FeatureSet might - should there be a superclass and subclass - FeatureSet, GeneFeatureSet? Yes! FeatureSet should just be an object that holds Features, GeneFeatureSet should subclass that and adds all the gene functions (eg setTranslationStart, setTranslationEnd...) I'm a little scared as A LOT of things use FeatureSet - or the gene fuctions could get put in a static util class (or non static) FeatureSet should NOT subclass SeqFeature.
GAMESequence  
Gene  
GenericAnnotation  
GenericAnnotationSet  
GenomicRange  
Identifier  
Karyotype  
PFetchSequence  
Range  
Score  
SeqFeature A class to represent a basic sequence feature, such as a result span.
Sequence  
SortedFeatureSet  
SRSSequence  
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
SyntenyRegion  
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