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Packages that use org.utgenome.gwt.utgb.client.bio | |
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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 | |
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ChrLoc
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Classes in org.utgenome.gwt.utgb.client.bio used by org.utgenome.format.bed | |
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BEDGene
Representing each gene line of BED format |
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ChrLoc
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Gene
Gene with Exon and CDS regions |
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GenomeRange
A common interface for interval data mapped onto a genome sequence (e.g., Read, Gene, SAMRead, WigGraphData, etc.) |
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Interval
An interval in a genome sequence. |
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Read
An interval with starnd information |
Classes in org.utgenome.gwt.utgb.client.bio used by org.utgenome.format.fasta | |
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ChrLoc
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CytoBand
CytoBand |
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ReferenceSequence
reference genome sequence to which genome reads are aligned |
Classes in org.utgenome.gwt.utgb.client.bio used by org.utgenome.format.keyword | |
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KeywordSearchResult
keyword search result |
Classes in org.utgenome.gwt.utgb.client.bio used by org.utgenome.format.sam | |
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ChrLoc
|
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GenomeRange
A common interface for interval data mapped onto a genome sequence (e.g., Read, Gene, SAMRead, WigGraphData, etc.) |
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ReadQueryConfig
Read query configuration |
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SAMRead
Genome Read data |
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SAMReadLight
Light weight SAMRead |
Classes in org.utgenome.gwt.utgb.client.bio used by org.utgenome.format.wig | |
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ChrLoc
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CompactWIGData
|
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GraphWindow
Windowing type for graph data |
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WigGraphData
wig format data |
Classes in org.utgenome.gwt.utgb.client.bio used by org.utgenome.graphics | |
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CDS
Coding Sequence (CDS) |
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CytoBand
CytoBand |
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Exon
Exon |
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Gene
Gene with Exon and CDS regions |
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GenomeRange
A common interface for interval data mapped onto a genome sequence (e.g., Read, Gene, SAMRead, WigGraphData, etc.) |
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SAMReadLight
Light weight SAMRead |
Classes in org.utgenome.gwt.utgb.client.bio used by org.utgenome.gwt.utgb.client | |
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ChrLoc
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ChrRange
|
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CompactWIGData
|
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GenomeDB
Database locator. |
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GenomeRange
A common interface for interval data mapped onto a genome sequence (e.g., Read, Gene, SAMRead, WigGraphData, etc.) |
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GraphWindow
Windowing type for graph data |
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KeywordSearchResult
keyword search result |
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ReadQueryConfig
Read query configuration |
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SAMRead
Genome Read data |
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WigGraphData
wig format data |
Classes in org.utgenome.gwt.utgb.client.bio used by org.utgenome.gwt.utgb.client.bio | |
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Alignment
Alignment result |
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AminoAcid
AminoAcid table |
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BEDGene
Representing each gene line of BED format |
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CDS
Coding Sequence (CDS) |
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ChrLoc
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CIGAR.Element
|
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CIGAR.Type
|
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Coordinate
Coordinate system |
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DASResult.DASFeature
|
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DASResult.DASFeature.FeatureType
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DASResult.DASFeature.Group
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DASResult.DASFeature.Group.Link
|
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DASResult.DASFeature.Method
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DASResult.DASFeature.Target
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DASResult.DASGFF
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DASResult.Segment
|
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Exon
Exon |
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Gap
Gap of paired-end, mate-pair reads |
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Gene
Gene with Exon and CDS regions |
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GenomeDB
Database locator. |
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GenomeDB.DBType
|
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GenomeRange
A common interface for interval data mapped onto a genome sequence (e.g., Read, Gene, SAMRead, WigGraphData, etc.) |
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GenomeRangeVisitor
Visitor interface for traversing data mapped onto a genome sequence |
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GenomeRangeVisitorBase
Refereece implementation of the GenomeRangeVisitor . |
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GraphData
A common interface for graph data |
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GraphWindow
Windowing type for graph data |
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Interval
An interval in a genome sequence. |
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IUPAC
IUPAC: allele variation notation |
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KeywordSearchResult.Entry
|
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Read
An interval with starnd information |
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Read.ReadType
|
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ReadCoverage
Read coverage histogram |
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ReadList
ReadList is a list of read objects, and used to draw a sequence of blocks on genome. |
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ReadQueryConfig.Layout
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ReferenceSequence
reference genome sequence to which genome reads are aligned |
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SAMRead
Genome Read data |
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SAMReadLight
Light weight SAMRead |
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SAMReadPair
Mate pair (paired end) of SAMReads |
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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 | |
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CDS
Coding Sequence (CDS) |
|
CompactWIGData
|
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Exon
Exon |
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Gene
Gene with Exon and CDS regions |
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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 . |
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Interval
An interval in a genome sequence. |
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ReadCoverage
Read coverage histogram |
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SAMRead
Genome Read data |
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SAMReadLight
Light weight SAMRead |
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SAMReadPair
Mate pair (paired end) of SAMReads |
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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 | |
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Coordinate
Coordinate system |
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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 | |
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ChrRange
|
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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 | |
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ChrLoc
|
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ChrRange
|
|
CompactWIGData
|
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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 |
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SAMRead
Genome Read data |
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WigGraphData
wig format data |
Classes in org.utgenome.gwt.utgb.client.bio used by org.utgenome.gwt.utgb.server.app | |
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ChrLoc
|
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ChrRange
|
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CytoBand
CytoBand |
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DASResult
DAS Result |
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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 | |
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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 | |
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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 | |
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AminoAcid
AminoAcid table |
|
IUPAC
IUPAC: allele variation notation |
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