Package org.utgenome.gwt.utgb.client.bio

Biological data objects for Google Web Toolkit RPC (Remote Procedure Call).

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  
 

Package org.utgenome.gwt.utgb.client.bio Description

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.

Author:
leo


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