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

Packages that use org.utgenome.gwt.utgb.client.bio
org.utgenome.core.cui CUI commands. 
org.utgenome.format.bed   
org.utgenome.format.fasta FASTA utilities 
org.utgenome.format.keyword   
org.utgenome.format.sam   
org.utgenome.format.wig   
org.utgenome.graphics Graphics drawing classes 
org.utgenome.gwt.utgb.client UTGB Browser interface & track implementations. 
org.utgenome.gwt.utgb.client.bio Biological data objects for Google Web Toolkit RPC (Remote Procedure Call). 
org.utgenome.gwt.utgb.client.canvas Browser-side graphic drawing libraries using HTML canvas (or VML in IE). 
org.utgenome.gwt.utgb.client.track   
org.utgenome.gwt.utgb.client.track.lib Standard track library for UTGB browser. 
org.utgenome.gwt.utgb.server UTGB's server-side libraries for supporting web request handling, managing database connections, initialization of UTGB web applications, etc. 
org.utgenome.gwt.utgb.server.app Contains sample codes of web actions. 
org.utgenome.util   
org.utgenome.util.repeat   
org.utgenome.util.sv   
 

Classes in org.utgenome.gwt.utgb.client.bio used by org.utgenome.core.cui
ChrLoc
           
 

Classes in org.utgenome.gwt.utgb.client.bio used by org.utgenome.format.bed
BEDGene
          Representing each gene line of BED format
ChrLoc
           
Gene
          Gene with Exon and CDS regions
GenomeRange
          A common interface for interval data mapped onto a genome sequence (e.g., Read, Gene, SAMRead, WigGraphData, etc.)
Interval
          An interval in a genome sequence.
Read
          An interval with starnd information
 

Classes in org.utgenome.gwt.utgb.client.bio used by org.utgenome.format.fasta
ChrLoc
           
CytoBand
          CytoBand
ReferenceSequence
          reference genome sequence to which genome reads are aligned
 

Classes in org.utgenome.gwt.utgb.client.bio used by org.utgenome.format.keyword
KeywordSearchResult
          keyword search result
 

Classes in org.utgenome.gwt.utgb.client.bio used by org.utgenome.format.sam
ChrLoc
           
GenomeRange
          A common interface for interval data mapped onto a genome sequence (e.g., Read, Gene, SAMRead, WigGraphData, etc.)
ReadQueryConfig
          Read query configuration
SAMRead
          Genome Read data
SAMReadLight
          Light weight SAMRead
 

Classes in org.utgenome.gwt.utgb.client.bio used by org.utgenome.format.wig
ChrLoc
           
CompactWIGData
           
GraphWindow
          Windowing type for graph data
WigGraphData
          wig format data
 

Classes in org.utgenome.gwt.utgb.client.bio used by org.utgenome.graphics
CDS
          Coding Sequence (CDS)
CytoBand
          CytoBand
Exon
          Exon
Gene
          Gene with Exon and CDS regions
GenomeRange
          A common interface for interval data mapped onto a genome sequence (e.g., Read, Gene, SAMRead, WigGraphData, etc.)
SAMReadLight
          Light weight SAMRead
 

Classes in org.utgenome.gwt.utgb.client.bio used by org.utgenome.gwt.utgb.client
ChrLoc
           
ChrRange
           
CompactWIGData
           
GenomeDB
          Database locator.
GenomeRange
          A common interface for interval data mapped onto a genome sequence (e.g., Read, Gene, SAMRead, WigGraphData, etc.)
GraphWindow
          Windowing type for graph data
KeywordSearchResult
          keyword search result
ReadQueryConfig
          Read query configuration
SAMRead
          Genome Read data
WigGraphData
          wig format data
 

Classes in org.utgenome.gwt.utgb.client.bio used by org.utgenome.gwt.utgb.client.bio
Alignment
          Alignment result
AminoAcid
          AminoAcid table
BEDGene
          Representing each gene line of BED format
CDS
          Coding Sequence (CDS)
ChrLoc
           
CIGAR.Element
           
CIGAR.Type
           
Coordinate
          Coordinate system
DASResult.DASFeature
           
DASResult.DASFeature.FeatureType
           
DASResult.DASFeature.Group
           
DASResult.DASFeature.Group.Link
           
DASResult.DASFeature.Method
           
DASResult.DASFeature.Target
           
DASResult.DASGFF
           
DASResult.Segment
           
Exon
          Exon
Gap
          Gap of paired-end, mate-pair reads
Gene
          Gene with Exon and CDS regions
GenomeDB
          Database locator.
GenomeDB.DBType
           
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
GenomeRangeVisitorBase
          Refereece implementation of the GenomeRangeVisitor.
GraphData
          A common interface for graph data
GraphWindow
          Windowing type for graph data
Interval
          An interval in a genome sequence.
IUPAC
          IUPAC: allele variation notation
KeywordSearchResult.Entry
           
Read
          An interval with starnd information
Read.ReadType
           
ReadCoverage
          Read coverage histogram
ReadList
          ReadList is a list of read objects, and used to draw a sequence of blocks on genome.
ReadQueryConfig.Layout
           
ReferenceSequence
          reference genome sequence to which genome reads are aligned
SAMRead
          Genome Read data
SAMReadLight
          Light weight SAMRead
SAMReadPair
          Mate pair (paired end) of SAMReads
SAMReadPairFragment
          Paired-end reads without the other mate data
 

Classes in org.utgenome.gwt.utgb.client.bio used by org.utgenome.gwt.utgb.client.canvas
CDS
          Coding Sequence (CDS)
CompactWIGData
           
Exon
          Exon
Gene
          Gene with Exon and CDS regions
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
GenomeRangeVisitorBase
          Refereece implementation of the GenomeRangeVisitor.
Interval
          An interval in a genome sequence.
ReadCoverage
          Read coverage histogram
SAMRead
          Genome Read data
SAMReadLight
          Light weight SAMRead
SAMReadPair
          Mate pair (paired end) of SAMReads
SAMReadPairFragment
          Paired-end reads without the other mate data
 

Classes in org.utgenome.gwt.utgb.client.bio used by org.utgenome.gwt.utgb.client.track
Coordinate
          Coordinate system
GenomeRange
          A common interface for interval data mapped onto a genome sequence (e.g., Read, Gene, SAMRead, WigGraphData, etc.)
 

Classes in org.utgenome.gwt.utgb.client.bio used by org.utgenome.gwt.utgb.client.track.lib
ChrRange
           
GenomeDB
          Database locator.
GenomeRange
          A common interface for interval data mapped onto a genome sequence (e.g., Read, Gene, SAMRead, WigGraphData, etc.)
 

Classes in org.utgenome.gwt.utgb.client.bio used by org.utgenome.gwt.utgb.server
ChrLoc
           
ChrRange
           
CompactWIGData
           
Gene
          Gene with Exon and CDS regions
GenomeDB
          Database locator.
GenomeRange
          A common interface for interval data mapped onto a genome sequence (e.g., Read, Gene, SAMRead, WigGraphData, etc.)
GraphWindow
          Windowing type for graph data
Interval
          An interval in a genome sequence.
KeywordSearchResult
          keyword search result
ReadQueryConfig
          Read query configuration
SAMRead
          Genome Read data
WigGraphData
          wig format data
 

Classes in org.utgenome.gwt.utgb.client.bio used by org.utgenome.gwt.utgb.server.app
ChrLoc
           
ChrRange
           
CytoBand
          CytoBand
DASResult
          DAS Result
GenomeDB
          Database locator.
GenomeRange
          A common interface for interval data mapped onto a genome sequence (e.g., Read, Gene, SAMRead, WigGraphData, etc.)
Interval
          An interval in a genome sequence.
Read
          An interval with starnd information
ReadCoverage
          Read coverage histogram
ReadQueryConfig
          Read query configuration
ReadQueryConfig.Layout
           
 

Classes in org.utgenome.gwt.utgb.client.bio used by org.utgenome.util
GenomeRange
          A common interface for interval data mapped onto a genome sequence (e.g., Read, Gene, SAMRead, WigGraphData, etc.)
 

Classes in org.utgenome.gwt.utgb.client.bio used by org.utgenome.util.repeat
GenomeRange
          A common interface for interval data mapped onto a genome sequence (e.g., Read, Gene, SAMRead, WigGraphData, etc.)
Interval
          An interval in a genome sequence.
 

Classes in org.utgenome.gwt.utgb.client.bio used by org.utgenome.util.sv
AminoAcid
          AminoAcid table
IUPAC
          IUPAC: allele variation notation
 



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