Serialized Form


Package uk.ac.sanger.cgp.standalonecsa.beans

Class uk.ac.sanger.cgp.standalonecsa.beans.AmplimerBean extends java.lang.Object implements Serializable

Serialized Fields

amplimerName

java.lang.String amplimerName
holds the amplimer name


amplimer

java.lang.String amplimer
holds the amplimer


ampLength

java.lang.Integer ampLength
holds the length of the amplimer


roiStart

java.lang.Integer roiStart
holds the start position of the region of interest with respect to the amplimer sequence (indexed from 1)


roiStop

java.lang.Integer roiStop
holds the stop position of the region of interest with respect to the amplimer sequence (indexed from 1)


codingStartIndex

java.lang.Integer codingStartIndex
holds the start position of the region of the amplimer that was mapped to the CDS (indexed from 0)


codingStopIndex

java.lang.Integer codingStopIndex
holds the stop position of the region of the amplimer that was mapped to the CDS (indexed from 0)


mapsToCds

java.lang.String mapsToCds
The name of the CDS that this amplimer is expected to map to


cdsStartIndex

java.lang.Integer cdsStartIndex
The point in the CDS that the amplimer starts to match at (indexed from 0).


amplimerReversed

java.lang.Boolean amplimerReversed
Indicates if the amplimer required reverse complimenting for mapping to the CDS


cds

CdsBean cds
The CDS object


codingStart

java.lang.Integer codingStart
holds the start position of the region of the amplimer that was mapped to the CDS (indexed from 1)


codingStop

java.lang.Integer codingStop
holds the stop position of the region of the amplimer that was mapped to the CDS (indexed from 1)


cdsStart

java.lang.Integer cdsStart
The point in the CDS that the amplimer starts to match at (indexed from 1).

Class uk.ac.sanger.cgp.standalonecsa.beans.CdsBean extends java.lang.Object implements Serializable

Serialized Fields

name

java.lang.String name
Holds the name of this CDS.


cdsSeq

java.lang.String cdsSeq
Holds the dna sequence of this CDS.


senseTranslated

boolean senseTranslated
Boolean to indicate if this CDS translates in the sense direction.


proteinSeq

java.lang.String proteinSeq
Holds the translated protein sequence of this CDS.


Package uk.ac.sanger.cgp.standalonecsa.exceptions

Class uk.ac.sanger.cgp.standalonecsa.exceptions.CsaRenderException extends java.lang.Exception implements Serializable

Class uk.ac.sanger.cgp.standalonecsa.exceptions.CsaRuntimeAlignmentException extends java.lang.RuntimeException implements Serializable

Class uk.ac.sanger.cgp.standalonecsa.exceptions.CsaRuntimeException extends java.lang.RuntimeException implements Serializable


Package uk.ac.sanger.cgp.standalonecsa.gui

Class uk.ac.sanger.cgp.standalonecsa.gui.SetupBase extends javax.swing.JDialog implements Serializable

Serialized Fields

currentDisplayNum

int currentDisplayNum

addAmpButton

javax.swing.JButton addAmpButton

ampField

javax.swing.JTextField ampField

ampInfoTextPanel

javax.swing.JTextPane ampInfoTextPanel

ampLabel

javax.swing.JLabel ampLabel

ampNameField

javax.swing.JTextField ampNameField

ampNameLabel

javax.swing.JLabel ampNameLabel

ampPropText

javax.swing.JTextArea ampPropText

ampSeqField

javax.swing.JTextField ampSeqField

amplimerInfoPane

javax.swing.JScrollPane amplimerInfoPane

amplimerPanel

javax.swing.JPanel amplimerPanel

amplimerPropPanel

javax.swing.JPanel amplimerPropPanel

answerButton

javax.swing.JButton answerButton

answerField

javax.swing.JTextField answerField

answerLabel

javax.swing.JLabel answerLabel

antiField

javax.swing.JTextField antiField

antiLabel

javax.swing.JLabel antiLabel

backRootButton

javax.swing.JButton backRootButton

cancelRootButton

javax.swing.JButton cancelRootButton

componentTextPane

javax.swing.JTextPane componentTextPane

delimField

javax.swing.JTextField delimField

delimLabel

javax.swing.JLabel delimLabel

directField

javax.swing.JTextField directField

directLabel

javax.swing.JLabel directLabel

dnaField

javax.swing.JTextField dnaField

dnaLabel

javax.swing.JLabel dnaLabel

exampleField

javax.swing.JTextField exampleField

exampleLabel

javax.swing.JLabel exampleLabel

extField

javax.swing.JTextField extField

extLabel

javax.swing.JLabel extLabel

fieldHelpPane

javax.swing.JTextArea fieldHelpPane

fileChooserInfoLable

javax.swing.JLabel fileChooserInfoLable

fileConventionPanel

javax.swing.JPanel fileConventionPanel

fileInfoPane

javax.swing.JEditorPane fileInfoPane

fileSelLabel

javax.swing.JLabel fileSelLabel

grpField

javax.swing.JTextField grpField

grpLabel

javax.swing.JLabel grpLabel

helpPanel

javax.swing.JPanel helpPanel

inDirButton

javax.swing.JButton inDirButton

inDirField

javax.swing.JTextField inDirField

inDirLabel

javax.swing.JLabel inDirLabel

inputOutputPanel

javax.swing.JPanel inputOutputPanel

jLabel1

javax.swing.JLabel jLabel1

jLabel3

javax.swing.JLabel jLabel3

jPanel1

javax.swing.JPanel jPanel1

jPanel2

javax.swing.JPanel jPanel2

jPanel3

javax.swing.JPanel jPanel3

jScrollPane1

javax.swing.JScrollPane jScrollPane1

jScrollPane2

javax.swing.JScrollPane jScrollPane2

jScrollPane3

javax.swing.JScrollPane jScrollPane3

jScrollPane4

javax.swing.JScrollPane jScrollPane4

jScrollPane6

javax.swing.JScrollPane jScrollPane6

mainPanel

javax.swing.JPanel mainPanel

mainPanelSeperator

javax.swing.JSeparator mainPanelSeperator

newAmplimerPanel

javax.swing.JPanel newAmplimerPanel

nextRootButton

javax.swing.JButton nextRootButton

outDirButton

javax.swing.JButton outDirButton

outDirField

javax.swing.JTextField outDirField

outDirLabel

javax.swing.JLabel outDirLabel

questionTextPane

javax.swing.JTextPane questionTextPane

roiStartField

javax.swing.JTextField roiStartField

roiStartLabel

javax.swing.JLabel roiStartLabel

roiStopField

javax.swing.JTextField roiStopField

roiStopLabel

javax.swing.JLabel roiStopLabel

senseField

javax.swing.JTextField senseField

senseLabel

javax.swing.JLabel senseLabel

seqFileBrowseButton

javax.swing.JButton seqFileBrowseButton

seqFileField

javax.swing.JTextField seqFileField

seqLabel

javax.swing.JLabel seqLabel

welcomePanel

javax.swing.JPanel welcomePanel

welcomeScrollPane

javax.swing.JScrollPane welcomeScrollPane

welcomeTextPane

javax.swing.JTextPane welcomeTextPane

wtField

javax.swing.JTextField wtField

wtLabel

javax.swing.JLabel wtLabel

wtPosField

javax.swing.JTextField wtPosField

wtPosLabel

javax.swing.JLabel wtPosLabel