Serialized Form
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Package uk.ac.sanger.cgp.standalonecsa.beans |
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).
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.
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Package uk.ac.sanger.cgp.standalonecsa.exceptions |
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Package uk.ac.sanger.cgp.standalonecsa.gui |
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