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See:
Description
| Interface Summary | |
|---|---|
| GenomeRange | A common interface for interval data mapped onto a genome sequence (e.g., Read, Gene, SAMRead, WigGraphData, etc.) |
| GenomeRangeVisitor | Visitor interface for traversing data mapped onto a genome sequence |
| GraphData | A common interface for graph data |
| Class Summary | |
|---|---|
| ACGTEncoder | Nucleotide ACGT <-> 2bit code conversion utility |
| Alignment | Alignment result |
| AlignmentResult | |
| BEDGene | Representing each gene line of BED format |
| BlastResult | Read with cigar and sequence information |
| BSSRead | BSS read data object |
| CDS | Coding Sequence (CDS) |
| ChrInterval | Interval in a chromosome |
| ChrLoc | |
| ChrRange | |
| CIGAR | CIGAR string (in SAM format) management utility |
| CIGAR.Element | |
| CodonTable | Codon table |
| CompactWIGData | |
| Coordinate | Coordinate system |
| CytoBand | CytoBand |
| DASLocation | DAS information |
| DASResult | DAS Result |
| DASResult.DASFeature | |
| DASResult.DASFeature.FeatureType | |
| DASResult.DASFeature.Group | |
| DASResult.DASFeature.Group.Link | |
| DASResult.DASFeature.Method | |
| DASResult.DASFeature.Target | |
| DASResult.DASGFF | |
| DASResult.Segment | |
| Exon | Exon |
| FASTASequence | Genome sequence |
| Gap | Gap of paired-end, mate-pair reads |
| Gene | Gene with Exon and CDS regions |
| GenomeDB | Database locator. |
| GenomeRangeDataSet | A set of on-genome data used for transferring genome data between server and client (GWT) |
| GenomeRangeVisitorBase | Refereece implementation of the GenomeRangeVisitor. |
| InfoSilkGenerator | Generating read information in Silk format, which is used for displaying mouse over message |
| Interval | An interval in a genome sequence. |
| KeywordSearchResult | keyword search result |
| KeywordSearchResult.Entry | |
| Read | An interval with starnd information |
| ReadCoverage | Read coverage histogram |
| ReadList | ReadList is a list of read objects, and used to draw a sequence of blocks on genome. |
| ReadQueryConfig | Read query configuration |
| ReferenceSequence | reference genome sequence to which genome reads are aligned |
| SAMRead | Genome Read data |
| SAMReadFlag | Flag bits of SAM reads |
| SAMReadLight | Light weight SAMRead |
| SAMReadPair | Mate pair (paired end) of SAMReads |
| SAMReadPairFragment | Paired-end reads without the other mate data |
| WigGraphData | wig format data |
| Enum Summary | |
|---|---|
| AminoAcid | AminoAcid table |
| CIGAR.Type | |
| GenomeDB.DBType | |
| GraphWindow | Windowing type for graph data |
| IUPAC | IUPAC: allele variation notation |
| Read.ReadType | |
| ReadQueryConfig.Layout | |
Biological data objects for Google Web Toolkit RPC (Remote Procedure Call). This package includes standard biological data objects, such as Gene, Exon, Locus on genomes, etc. The objects defined in this package is used as data structure for manipulating biological data through web actions, objects stored in databases, etc.
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