Serialized Form

Package org.utgenome

Class org.utgenome.UTGBException extends Exception implements Serializable

Serialized Fields

errorCode

UTGBErrorCode errorCode

Package org.utgenome.format.bed

Class org.utgenome.format.bed.BEDEntry extends BEDGene implements Serializable

serialVersionUID: 1L

Class org.utgenome.format.bed.BEDTrack extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

name

String name

description

String description

visibility

int visibility

color

String color

itemRgb

String itemRgb

useScore

int useScore

group

String group

priority

String priority

db

String db

offset

long offset

url

String url

htmlUrl

String htmlUrl

Package org.utgenome.gwt.ribbon.client.model

Class org.utgenome.gwt.ribbon.client.model.GenomeCoordinate extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

group

String group

group name of this coordinate

sequence

String sequence

sequence id of this coordinate. e.g., hg19, oryLat2, etc.

chr

String chr

chromosome/contig/scaffold name. e.g., chr1, contig1, scaffold1, etc.

Class org.utgenome.gwt.ribbon.client.model.Ribbon extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

segment

ArrayList<E> segment

Package org.utgenome.gwt.utgb.client

Class org.utgenome.gwt.utgb.client.UTGBClientException extends Exception implements Serializable

serialVersionUID: 1L

Serialized Fields

errorCode

UTGBClientErrorCode errorCode

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

Class org.utgenome.gwt.utgb.client.bio.BEDGene extends Gene implements Serializable

serialVersionUID: 1L

Serialized Fields

chr

String chr

score

int score

Class org.utgenome.gwt.utgb.client.bio.BlastResult extends Read implements Serializable

serialVersionUID: 1L

Serialized Fields

seq

String seq

cigar

String cigar

bitScore

int bitScore

eValue

String eValue

identity

int identity

matchLength

int matchLength

tag

Properties tag

Class org.utgenome.gwt.utgb.client.bio.BSSRead extends Read implements Serializable

serialVersionUID: 1L

Serialized Fields

queryLength

int queryLength

similarity

double similarity

queryCoverage

double queryCoverage

evalue

String evalue

bitScore

int bitScore

targetSequence

String targetSequence

querySequence

String querySequence

alignment

String alignment

Class org.utgenome.gwt.utgb.client.bio.CDS extends Interval implements Serializable

serialVersionUID: 1L

Class org.utgenome.gwt.utgb.client.bio.ChrInterval extends Interval implements Serializable

serialVersionUID: 1L

Serialized Fields

chr

String chr

Class org.utgenome.gwt.utgb.client.bio.ChrLoc extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

start

int start

end

int end

chr

String chr

Class org.utgenome.gwt.utgb.client.bio.CIGAR extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

cigar

ArrayList<E> cigar

Class org.utgenome.gwt.utgb.client.bio.CIGAR.Element extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

type

CIGAR.Type type

length

int length

Class org.utgenome.gwt.utgb.client.bio.CompactWIGData extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

trackId

int trackId

maxValue

float maxValue

minValue

float minValue

browser

ArrayList<E> browser

track

HashMap<K,V> track

data

float[] data

start

int start

span

int span

Class org.utgenome.gwt.utgb.client.bio.CytoBand extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

chrom

String chrom

start

int start

end

int end

name

String name

gieStain

String gieStain

Class org.utgenome.gwt.utgb.client.bio.DASLocation extends GenomeDB implements Serializable

serialVersionUID: 1L

Serialized Fields

dasType

String dasType

Class org.utgenome.gwt.utgb.client.bio.DASResult extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

gff

DASResult.DASGFF gff

segment

DASResult.Segment segment

Class org.utgenome.gwt.utgb.client.bio.DASResult.DASFeature extends Read implements Serializable

serialVersionUID: 1L

Serialized Fields

id

String id

label

String label

score

String score

orientation

String orientation

phase

String phase

method

DASResult.DASFeature.Method method

type

DASResult.DASFeature.FeatureType type

group

DASResult.DASFeature.Group group

target

DASResult.DASFeature.Target target

Class org.utgenome.gwt.utgb.client.bio.DASResult.DASFeature.FeatureType extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

id

String id

category

String category

reference

String reference

value

String value

Class org.utgenome.gwt.utgb.client.bio.DASResult.DASFeature.Group extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

id

String id

type

String type

label

String label

link

DASResult.DASFeature.Group.Link link

target

DASResult.DASFeature.Target target

Class org.utgenome.gwt.utgb.client.bio.DASResult.DASFeature.Group.Link extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

href

String href

value

String value

Class org.utgenome.gwt.utgb.client.bio.DASResult.DASFeature.Method extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

id

String id

value

String value

Class org.utgenome.gwt.utgb.client.bio.DASResult.DASFeature.Target extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

id

String id

start

long start

stop

long stop

value

String value

Class org.utgenome.gwt.utgb.client.bio.DASResult.DASGFF extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

version

String version

href

String href

Class org.utgenome.gwt.utgb.client.bio.DASResult.Segment extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

id

String id

start

long start

stop

long stop

feature

List<E> feature

Class org.utgenome.gwt.utgb.client.bio.Exon extends Interval implements Serializable

serialVersionUID: 1L

Class org.utgenome.gwt.utgb.client.bio.Gap extends Interval implements Serializable

serialVersionUID: 1L

Class org.utgenome.gwt.utgb.client.bio.Gene extends Read implements Serializable

serialVersionUID: 1L

Serialized Fields

exonList

ArrayList<E> exonList

cdsList

ArrayList<E> cdsList

Class org.utgenome.gwt.utgb.client.bio.GenomeDB extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

path

String path

database path. When the path starts with "local:", it searches for locally stored database files.

ref

String ref

reference sequence name to which this genome DB is associated

type

GenomeDB.DBType type

database type

Class org.utgenome.gwt.utgb.client.bio.GenomeRangeDataSet extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

location

ChrLoc location

read

List<E> read

block

List<E> block

Class org.utgenome.gwt.utgb.client.bio.Interval extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

start

int start

end

int end

Class org.utgenome.gwt.utgb.client.bio.KeywordSearchResult extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

page

int page

count

int count

maxPage

int maxPage

result

List<E> result

Class org.utgenome.gwt.utgb.client.bio.KeywordSearchResult.Entry extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

name

String name

chr

String chr

start

int start

end

int end

ref

String ref

offsets

String offsets

id

int id

rowid

int rowid

Class org.utgenome.gwt.utgb.client.bio.OnGenomeDataSet extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

location

ChrLoc location

read

List<E> read

block

List<E> block

Class org.utgenome.gwt.utgb.client.bio.Read extends Interval implements Serializable

serialVersionUID: 1L

Serialized Fields

name

String name

color

String color

strand

byte strand

Class org.utgenome.gwt.utgb.client.bio.ReadCoverage extends Interval implements Serializable

serialVersionUID: 1L

Serialized Fields

name

String name

coverage

int[] coverage

Coverage of each pixel position

pixelWidth

int pixelWidth

maxHeight

int maxHeight

minHeight

int minHeight

Class org.utgenome.gwt.utgb.client.bio.ReadList extends Interval implements Serializable

serialVersionUID: 1L

Serialized Fields

read

ArrayList<E> read

name

String name

Class org.utgenome.gwt.utgb.client.bio.ReadQueryConfig extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

hasCanvasSupport

boolean hasCanvasSupport

layout

ReadQueryConfig.Layout layout

pixelWidth

int pixelWidth

maxmumNumberOfReadsToDisplay

int maxmumNumberOfReadsToDisplay

wigPath

String wigPath

Path to the WIG db file of the read depth

window

GraphWindow window

Class org.utgenome.gwt.utgb.client.bio.ReferenceSequence extends Interval implements Serializable

serialVersionUID: 1L

Serialized Fields

name

String name

sequence

String sequence

Class org.utgenome.gwt.utgb.client.bio.SAMRead extends SAMReadLight implements Serializable

serialVersionUID: 1L

Serialized Fields

rname

String rname

mapq

int mapq

mrnm

String mrnm

mStart

int mStart

seq

String seq

qual

String qual

tag

Properties tag

refSeq

String refSeq

Class org.utgenome.gwt.utgb.client.bio.SAMReadLight extends Interval implements Serializable

serialVersionUID: 1L

Serialized Fields

qname

String qname

flag

int flag

unclippedStart

int unclippedStart

unclippedEnd

int unclippedEnd

cigar

String cigar

iSize

int iSize

Class org.utgenome.gwt.utgb.client.bio.SAMReadPair extends Interval implements Serializable

serialVersionUID: 1L

Serialized Fields

first

SAMReadLight first

second

SAMReadLight second

Class org.utgenome.gwt.utgb.client.bio.SAMReadPairFragment extends Interval implements Serializable

serialVersionUID: 1L

Serialized Fields

oneEnd

SAMReadLight oneEnd

mateStart

int mateStart

Class org.utgenome.gwt.utgb.client.bio.WigGraphData extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

trackId

int trackId

maxValue

float maxValue

minValue

float minValue

browser

ArrayList<E> browser

track

HashMap<K,V> track

data

HashMap<K,V> data

Package org.utgenome.gwt.utgb.client.track

Class org.utgenome.gwt.utgb.client.track.TrackWindow extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

pixelWidth

int pixelWidth

startIndexOnGenome

int startIndexOnGenome

endIndexOnGenome

int endIndexOnGenome

Package org.utgenome.gwt.utgb.client.track.bean

Class org.utgenome.gwt.utgb.client.track.bean.LegacyTrackInformation extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

descriptionXML

String descriptionXML

name

String name

docURL

String docURL

species

String species

revision

String revision

Class org.utgenome.gwt.utgb.client.track.bean.SpeciesRevision extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

speciesRevisionTable

HashMap<K,V> speciesRevisionTable

Package org.utgenome.gwt.utgb.client.util

Class org.utgenome.gwt.utgb.client.util.CanonicalProperties extends HashMap<String,String> implements Serializable

serialVersionUID: 1L

Class org.utgenome.gwt.utgb.client.util.Properties extends HashMap<String,String> implements Serializable

serialVersionUID: 1L

Package org.utgenome.gwt.utgb.client.view

Class org.utgenome.gwt.utgb.client.view.TrackView extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

trackGroup

TrackView.TrackGroup trackGroup

track

ArrayList<E> track

Class org.utgenome.gwt.utgb.client.view.TrackView.Coordinate extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

species

String species

species name (optional)

ref

String ref

reference sequence name

chr

String chr

name of chromosome, contig, scaffold, etc.

start

int start

1-based start position (inclusive)

end

int end

1-based end position (inclusive)

ribbon

String ribbon

ribbon string showing in/del states

pixelWidth

int pixelWidth

pixel width of the track window

Class org.utgenome.gwt.utgb.client.view.TrackView.Track extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

trackGroup

TrackView.TrackGroup trackGroup

belonging track group

name

String name

height

int height

pack

boolean pack

class_

String class_

Java class name of this track. The underscore (_) is necessary to differentiate this parameter name from the same name Java keyword, class

property

CanonicalProperties property

Class org.utgenome.gwt.utgb.client.view.TrackView.TrackGroup extends Object implements Serializable

serialVersionUID: 1L

Serialized Fields

id

int id

ID of this track group

class_

String class_

Java class name of this track group. The underscore (_) is necessary to differentiate this parameter name from the Java keyword class

coordinate

TrackView.Coordinate coordinate

property

CanonicalProperties property

Package org.utgenome.gwt.utgb.server

Class org.utgenome.gwt.utgb.server.BrowserServiceImpl extends com.google.gwt.user.server.rpc.RemoteServiceServlet implements Serializable

serialVersionUID: 1L

Class org.utgenome.gwt.utgb.server.HelloServlet extends javax.servlet.http.HttpServlet implements Serializable

serialVersionUID: 1L

Class org.utgenome.gwt.utgb.server.RequestHandlerBase extends javax.servlet.http.HttpServlet implements Serializable

serialVersionUID: 1L

Class org.utgenome.gwt.utgb.server.WebTrackBase extends RequestHandlerBase implements Serializable

serialVersionUID: 1L

Package org.utgenome.gwt.utgb.server.app

Class org.utgenome.gwt.utgb.server.app.ACGT extends WebTrackBase implements Serializable

serialVersionUID: 1L

Serialized Fields

colorA

String colorA

colorC

String colorC

colorG

String colorG

colorT

String colorT

colorN

String colorN

colorO

String colorO

coloro

String coloro

fontWidth

int fontWidth

height

int height

Class org.utgenome.gwt.utgb.server.app.BEDViewer extends WebTrackBase implements Serializable

serialVersionUID: 1L

Serialized Fields

species

String species

revision

String revision

name

String name

start

int start

end

int end

width

int width

fileName

String fileName

Class org.utgenome.gwt.utgb.server.app.BSSReadView extends WebTrackBase implements Serializable

serialVersionUID: 1L

Serialized Fields

bssQuery

String bssQuery

name

String name

dbGroup

String dbGroup

dbName

String dbName

width

int width

Class org.utgenome.gwt.utgb.server.app.BSSReadView.BSSAlignment extends Read implements Serializable

serialVersionUID: 1L

Serialized Fields

similarity

double similarity

queryCoverage

double queryCoverage

queryLength

int queryLength

evalue

String evalue

bitScore

int bitScore

targetSequence

String targetSequence

querySequence

String querySequence

alignment

String alignment

target

String target

Class org.utgenome.gwt.utgb.server.app.ChromosomeMap extends WebTrackBase implements Serializable

serialVersionUID: 1L

Serialized Fields

species

String species

revision

String revision

displayType

String displayType

width

int width

start

long start

end

long end

dbGroup

String dbGroup

dbName

String dbName

bssQuery

String bssQuery

name

String name

chromWindows

HashMap<K,V> chromWindows

Class org.utgenome.gwt.utgb.server.app.ChromosomeMap.ReadLocus extends Read implements Serializable

serialVersionUID: 1L

Serialized Fields

target

String target

Class org.utgenome.gwt.utgb.server.app.CSEGViewer extends WebTrackBase implements Serializable

serialVersionUID: 1L

Serialized Fields

species

String species

revision

String revision

name

String name

start

long start

end

long end

fileName

String fileName

width

int width

Class org.utgenome.gwt.utgb.server.app.DASDsn extends WebTrackBase implements Serializable

serialVersionUID: 1L

Serialized Fields

dasDSNURL

String dasDSNURL

Class org.utgenome.gwt.utgb.server.app.DASViewer extends WebTrackBase implements Serializable

serialVersionUID: 1L

Serialized Fields

start

int start

end

int end

width

int width

name

String name

dasBaseURL

String dasBaseURL

dasType

String dasType

Class org.utgenome.gwt.utgb.server.app.DotPlot extends WebTrackBase implements Serializable

serialVersionUID: 1L

Class org.utgenome.gwt.utgb.server.app.EchoBackView extends WebTrackBase implements Serializable

serialVersionUID: 1L

Serialized Fields

view

String view

time

long time

Class org.utgenome.gwt.utgb.server.app.FontMetric extends WebTrackBase implements Serializable

serialVersionUID: 1L

Serialized Fields

fontSize

int fontSize

Class org.utgenome.gwt.utgb.server.app.FontPanel extends WebTrackBase implements Serializable

serialVersionUID: 1L

Serialized Fields

fontSize

float fontSize

color

String color

Class org.utgenome.gwt.utgb.server.app.GeneViewer extends WebTrackBase implements Serializable

serialVersionUID: 1L

Serialized Fields

url

String url

species

String species

revision

String revision

name

String name

start

long start

end

long end

width

int width

Class org.utgenome.gwt.utgb.server.app.Hello extends RequestHandlerBase implements Serializable

serialVersionUID: 1L

Serialized Fields

name

String name

year

int year

Class org.utgenome.gwt.utgb.server.app.KeywordSearch extends WebTrackBase implements Serializable

serialVersionUID: 1L

Serialized Fields

ref

String ref

Describe your web action parameters here. Public fields in this class will be set using the web request query parameters before calling handle().

page

int page

size

int size

Class org.utgenome.gwt.utgb.server.app.LoadView extends WebTrackBase implements Serializable

serialVersionUID: 1L

Class org.utgenome.gwt.utgb.server.app.MethylViewer extends WebTrackBase implements Serializable

serialVersionUID: 1L

Serialized Fields

species

String species

revision

String revision

name

String name

db

String db

start

long start

end

long end

width

int width

entryList

List<E> entryList

Class org.utgenome.gwt.utgb.server.app.MethylViewer.MethlEntry extends Read implements Serializable

Serialized Fields

scaffold

String scaffold

genome

String genome

tag

String tag

frequency

int frequency

numCtoT

int numCtoT

numOtherMismatch

int numOtherMismatch

Class org.utgenome.gwt.utgb.server.app.ReadView extends WebTrackBase implements Serializable

serialVersionUID: 1L

Serialized Fields

start

int start

end

int end

species

String species

ref

String ref

chr

String chr

width

int width

useCanvas

boolean useCanvas

layout

ReadQueryConfig.Layout layout

path

String path

Class org.utgenome.gwt.utgb.server.app.RoundCircle extends RequestHandlerBase implements Serializable

serialVersionUID: 19443895944286732L

Serialized Fields

color

String color

size

int size

opacity

float opacity

Class org.utgenome.gwt.utgb.server.app.SAMViewer extends WebTrackBase implements Serializable

serialVersionUID: 1L

Serialized Fields

species

String species

Predefined coordinate parameters for GenomeTrack. Uncomment the following lines if you want to receive these parameter values described in the request URL

revision

String revision

name

String name

start

int start

end

int end

width

int width

Class org.utgenome.gwt.utgb.server.app.ScaleBar extends WebTrackBase implements Serializable

serialVersionUID: 1L

Serialized Fields

range

long range

Predefined coordinate parameters for GenomeTrack. Uncomment the following lines if you want to receive these parameter values.

width

int width

height

int height

template

int[] template

image

BufferedImage image

g

Graphics2D g

Class org.utgenome.gwt.utgb.server.app.Sequence extends WebTrackBase implements Serializable

serialVersionUID: 1L

Serialized Fields

colorA

String colorA

colorC

String colorC

colorG

String colorG

colorT

String colorT

colorN

String colorN

dbGroup

String dbGroup

species

String species

revision

String revision

start

int start

end

int end

name

String name

width

int width

path

String path

Class org.utgenome.gwt.utgb.server.app.SnappyVersion extends WebTrackBase implements Serializable

serialVersionUID: 1L

Class org.utgenome.gwt.utgb.server.app.SQLiteAccessSample extends RequestHandlerBase implements Serializable

serialVersionUID: 1L

Class org.utgenome.gwt.utgb.server.app.TextLabel extends RequestHandlerBase implements Serializable

serialVersionUID: 1L

Serialized Fields

text

String text

width

int width

height

int height

size

int size

color

String color

Class org.utgenome.gwt.utgb.server.app.Transparent extends WebTrackBase implements Serializable

serialVersionUID: 1L

Serialized Fields

color

String color

opacity

float opacity

Package org.utgenome.gwt.utgb.server.app.example

Class org.utgenome.gwt.utgb.server.app.example.UsingTemplate extends WebTrackBase implements Serializable

serialVersionUID: 1L

Serialized Fields

name

String name

Use dbGroup, dbName parameters to specify database contents to be accessed

Package org.utgenome.shell

Class org.utgenome.shell.UTGBPortableWidget extends JFrame implements Serializable

serialVersionUID: 1L

Serialized Fields

config

UTGBPortableConfig config

serverLaunchPanel

org.utgenome.shell.UTGBPortableWidget.ServerLaunchPanel serverLaunchPanel

status

JLabel status

mainPanel

JPanel mainPanel

launcher

org.utgenome.shell.TomcatServerLauncher launcher

Class org.utgenome.shell.UTGBShellException extends Exception implements Serializable

Package org.utgenome.util.repeat

Class org.utgenome.util.repeat.RepeatChainFinder.FlippedInterval2D extends Interval implements Serializable

serialVersionUID: 1L

Serialized Fields

orig

RepeatChainFinder.Interval2D orig

Class org.utgenome.util.repeat.RepeatChainFinder.Interval2D extends Interval implements Serializable

serialVersionUID: 1L

Serialized Fields

y1

int y1

y2

int y2