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