ScriptNode _node
Token currentToken
int[][] expectedTokenSequences
java.lang.String[] tokenImage
int kind
int beginLine
int beginColumn
int endLine
int endColumn
java.lang.String image
Token next
Token specialToken
int errorCode
AppLog log
javax.swing.JMenuBar menuBar
javax.swing.JToolBar toolBar
javax.swing.JPanel statusBar
javax.swing.JLabel infoLabel
javax.swing.JDesktopPane desktop
MenuList mainMenus
ur_rna.Utilities.swing.MergeManager menuMerger
java.util.function.Consumer<T> InfoLabelConsumer
java.awt.Component[] keepToolBarItems
javax.swing.event.InternalFrameListener frameListener
MenuList customMenus
java.lang.String error
java.lang.String file
javax.swing.JLabel label
javax.swing.JPanel legendGrid
javax.swing.JPanel mainPanel
double imgSizeX
double imgSizeY
java.awt.print.PrinterJob job
int preferredDialogWidth
double scale
DotPlotBackend backend
int strand
int plotLength
int drawOptions
StructureBackend backend
java.lang.String[] data
boolean hasPairs
int number
java.lang.String[] regex
StructureDialog dialog
PlotDialog dialog
PlotDialog dialog
StructureDialog dialog
ur_rna.Utilities.swing.CheckMergeItem circular
ur_rna.Utilities.swing.CheckMergeItem flat
ur_rna.Utilities.swing.CheckMergeItem flipped
ur_rna.Utilities.swing.CheckMergeItem circled
RNAstructureBackendCalculator backend
int str
ur_rna.Utilities.swing.MergeMenu drawOptionMenu
java.awt.event.MouseAdapter guiInfoListener
AppMainFrame mainFrame
java.awt.event.ActionListener menuListener
int subItemMergePos
java.util.HashMap<K,V> rollovers
java.util.function.Consumer<T> rolloverHandler
java.lang.String acidName
java.util.function.Consumer<T> handler
java.lang.String text
boolean verifyType
java.io.File file
javax.swing.JButton btnExtract
javax.swing.JPanel mainPanel
javax.swing.JButton btnClose
javax.swing.JLabel lblWebsite
javax.swing.JLabel lblHelp
javax.swing.JLabel lblLogo
boolean disableClose
AppMainFrame mainFrame
MenuList customMenus
AppLog log
java.util.HashSet<E> warnings
java.awt.event.ActionListener commandListener
javax.swing.event.InternalFrameListener frameListener
java.beans.VetoableChangeListener changeListener
ur_rna.RNAstructureUI.ui.NumberField.DoubleField maxdefect
ur_rna.RNAstructureUI.ui.NumberField.IntegerField maxdepth
ur_rna.RNAstructureUI.ui.NumberField.IntegerField maxmutate
ur_rna.RNAstructureUI.ui.NumberField.IntegerField maxleaf
ur_rna.RNAstructureUI.ui.NumberField.IntegerField maxredesign
ImageDialog dialog
boolean error
int strand
AppMainFrame mainFrame
javax.swing.JDesktopPane desktop
boolean disableClose
AppLog log
RNAstructureBackendCalculator backend
MenuList customMenus
java.util.HashSet<E> warnings
javax.swing.event.InternalFrameListener frameListener
java.beans.VetoableChangeListener changeListener
ModuleWindow self
java.awt.GridBagConstraints constraints
java.awt.GridBagLayout layout
boolean isRNA
java.awt.Component progressIndicator
java.lang.Thread mainCalcThread
javax.swing.JButton startButton
java.awt.event.ActionListener calcCancelListener
long calcCompleted
java.awt.event.ActionListener calcProgressListener
long lastUpdate
boolean calcCanceled
java.util.HashMap<K,V> enabledState
int columnWidth
java.util.ArrayList<E> imageDialogs
javax.swing.Box options
ur_rna.RNAstructureUI.ui.ScrollerPane scroll
boolean isInputWindow
javax.swing.JPanel panelInput
javax.swing.JPanel panelResults
javax.swing.JSpinner spinner
javax.swing.JPanel contentPanel
javax.swing.JTextField txtSeqFile1
javax.swing.JTabbedPane tabControls
javax.swing.JSpinner spnMaxEnergyDiff
javax.swing.JSpinner spnWindowSize
javax.swing.JSpinner spnMaxStructs
javax.swing.JTextField txtConFile1
javax.swing.JButton btnStartCalc
javax.swing.JTextField txtOutputFile1
javax.swing.JTextField txtOutputFile2
javax.swing.JButton btnResetOptions
javax.swing.JLabel lblOptionWarning
javax.swing.JButton btnCancelTask
javax.swing.JProgressBar prgTaskProgress
javax.swing.JLabel lblTaskStatus
javax.swing.JPanel pnlTaskStatus
javax.swing.JCheckBox chkShowDescription
javax.swing.JLabel lblToolDescription
javax.swing.JTextField txtSeqFile2
javax.swing.JTextField txtConFile2
javax.swing.JPanel pnlOutput
javax.swing.JPanel pnlSequences
javax.swing.JPanel pnlOptions
javax.swing.JPanel pnlConstraints
javax.swing.JButton btnResetAll
javax.swing.JLabel lblProgressPercent
javax.swing.JRadioButton optRNA
javax.swing.JRadioButton optDNA
javax.swing.JSpinner spnMaxLoopSize
javax.swing.JSpinner spnTemperature
java.util.HashMap<K,V> defaultOptionValues
java.util.ArrayList<E> optionsControls
java.util.ArrayList<E> settingsControls
java.lang.String settingsNodeName
java.lang.String lastSeqFile1
java.lang.String lastOutFile1
java.lang.String lastSeqFile2
java.lang.String lastOutFile2
javax.swing.JPanel pnlFiles
javax.swing.JLabel lblResults
javax.swing.JButton btnClose
javax.swing.JPanel pnlDrawings
javax.swing.JPanel pnlContent
javax.swing.JLabel lblFile
javax.swing.JButton btnShowAbbreviations
javax.swing.JPanel pnlClient
java.util.HashMap<K,V> plotResults
int fileCount
int plotRow
int plotCol
java.awt.Font headerFont
javax.swing.JPanel contentPanel
javax.swing.JTabbedPane tabControls
javax.swing.JSpinner spnTemperature
javax.swing.JButton btnStartCalc
javax.swing.JTextField txtOutputFile
javax.swing.JButton btnResetOptions
javax.swing.JLabel lblOptionWarning
javax.swing.JButton btnCancelTask
javax.swing.JProgressBar prgTaskProgress
javax.swing.JLabel lblTaskStatus
javax.swing.JPanel pnlTaskStatus
javax.swing.JCheckBox chkShowDescription
javax.swing.JLabel lblToolDescription
javax.swing.JComboBox<E> cmbTurboMode
javax.swing.JPanel pnlOutput
javax.swing.JPanel pnlSequences
javax.swing.JPanel pnlOptions
javax.swing.JPanel pnlTurboOptions
javax.swing.JButton btnResetAll
javax.swing.JButton btnResetTurboOptions
javax.swing.JList<E> lstSeqs
javax.swing.JSpinner spnTurboGamma
javax.swing.JSpinner spnTurboIterations
javax.swing.JSpinner spnTurboMaxEnergyDiff
javax.swing.JSpinner spnTurboWindowSize
javax.swing.JSpinner spnTurboMEAGamma
javax.swing.JSpinner spnTurboThreshold
javax.swing.JSpinner spnTurboMinHelix
javax.swing.JSpinner spnTurboPKIterations
javax.swing.JSpinner spnMultiIterations
javax.swing.JSpinner spnMultiDsvChange
javax.swing.JSpinner spnMultiGapPenalty
javax.swing.JSpinner spnMultiAlnSize
javax.swing.JSpinner spnMultiWindowSize
javax.swing.JSpinner spnMultiMaxStructures
javax.swing.JSpinner spnMultiMaxEnergyDiff
javax.swing.JCheckBox chkAllowBaseInserts
javax.swing.JPanel pnlMultiOptions
javax.swing.JButton btnMoveUp
javax.swing.JButton btnMoveDn
javax.swing.JButton btnRemove
javax.swing.JButton btnClearList
javax.swing.JSpinner spnTurboMaxStructures
javax.swing.JLabel lblBaseInserts
javax.swing.JButton btnResetMultiOptions
javax.swing.JPanel pnlSeqInfo
javax.swing.JSpinner spnMultiMaxPairs
javax.swing.JLabel lblProgressPercent
javax.swing.JTextField txtSeqFile
javax.swing.JTextField txtMSeqFile
java.util.HashMap<K,V> defaultOptionValues
java.util.ArrayList<E> optionsControls
java.util.ArrayList<E> settingsControls
java.lang.String settingsNodeName
boolean _seqInfoUpdating
java.util.ArrayList<E> seqList
javax.swing.JPanel contentPanel
javax.swing.JTextField txtSeqFile
javax.swing.JRadioButton optSeqFile
javax.swing.JButton btnBrowseSeq
javax.swing.JTextArea txtSequence
javax.swing.JTextField txtSeqTitle
javax.swing.JRadioButton optRNA
javax.swing.JSpinner spnTemperature
javax.swing.JTabbedPane tabControls
javax.swing.JSpinner spnMaxLoopSize
javax.swing.JSpinner spnMaxEnergyDiff
javax.swing.JSpinner spnMinHelixLen
javax.swing.JSpinner spnIterations
javax.swing.JSpinner spnGamma
javax.swing.JSpinner spnWindowSize
javax.swing.JSpinner spnMaxStructs
javax.swing.JRadioButton optDNA
javax.swing.JRadioButton optEnterSeq
javax.swing.JTextField txtConFile
javax.swing.JButton btnBrowseCon
javax.swing.JTextField txtShapeFile
javax.swing.JButton btnBrowseShape
javax.swing.JSpinner spnShapeIntercept
javax.swing.JSpinner spnShapeSlope
javax.swing.JButton btnStartCalc
javax.swing.JTextField txtOutputFile
javax.swing.JButton btnBrowseOutput
javax.swing.JButton btnRecentSeq
javax.swing.JButton btnRecentOutput
javax.swing.JButton btnRecentCon
javax.swing.JButton btnRecentShape
javax.swing.JButton btnResetOptions
javax.swing.JLabel lblOptionWarning
javax.swing.JScrollPane scrlSequence
javax.swing.JButton btnCancelTask
javax.swing.JProgressBar prgTaskProgress
javax.swing.JLabel lblTaskStatus
javax.swing.JPanel pnlTaskStatus
javax.swing.JCheckBox chkShowDescription
javax.swing.JLabel lblToolDescription
javax.swing.JPanel pnlOutput
javax.swing.JLabel lblProgressPercent
java.util.HashMap<K,V> defaultOptionValues
java.util.ArrayList<E> optionsControls
java.util.ArrayList<E> settingsControls
java.lang.String settingsNodeName
java.lang.String lastSeqFile
java.lang.String lastOutFile
javax.swing.JPanel contentPanel
javax.swing.JTextField txtSeqFile1
javax.swing.JTabbedPane tabControls
javax.swing.JSpinner spnMaxEnergyDiff
javax.swing.JSpinner spnWindowSize
javax.swing.JSpinner spnMaxStructs
javax.swing.JTextField txtConFile1
javax.swing.JButton btnStartCalc
javax.swing.JTextField txtOutputFile1
javax.swing.JTextField txtOutputFile2
javax.swing.JButton btnResetOptions
javax.swing.JLabel lblOptionWarning
javax.swing.JButton btnCancelTask
javax.swing.JProgressBar prgTaskProgress
javax.swing.JLabel lblTaskStatus
javax.swing.JPanel pnlTaskStatus
javax.swing.JCheckBox chkShowDescription
javax.swing.JLabel lblToolDescription
javax.swing.JTextField txtSeqFile2
javax.swing.JSpinner spnAlnWindowSize
javax.swing.JSpinner spnGapPenalty
javax.swing.JCheckBox chkBaseInserts
javax.swing.JComboBox<E> cmbPartsMode
javax.swing.JLabel lblBaseInserts
javax.swing.JSpinner spnStochasticSamples
javax.swing.JTextField txtConFile2
javax.swing.JPanel pnlOutput
javax.swing.JPanel pnlSequences
javax.swing.JPanel pnlOptions
javax.swing.JPanel pnlPartsOptions
javax.swing.JPanel pnlConstraints
javax.swing.JButton btnResetAll
javax.swing.JButton btnResetPartsOptions
javax.swing.JLabel lblProgressPercent
java.util.HashMap<K,V> defaultOptionValues
java.util.ArrayList<E> optionsControls
java.util.ArrayList<E> settingsControls
java.lang.String settingsNodeName
java.lang.String lastSeqFile1
java.lang.String lastOutFile1
java.lang.String lastSeqFile2
java.lang.String lastOutFile2
javax.swing.Timer uiUpdateTimer
javax.swing.JPanel pnlClient
javax.swing.JPanel pnlContent
java.util.HashMap<K,V> fileFields
java.util.HashMap<K,V> fields
PredictWindowBase.BackgroundTask runningTask
java.text.DecimalFormat numberFormatter
java.awt.Font defaultFont
javax.swing.JTextArea titleBox
javax.swing.JTextArea commentBox
javax.swing.JTextPane sequenceBox
javax.swing.text.StyledDocument sequenceDoc
boolean edited
boolean userAcceptedInvalidSequence
int speakPosition
javax.swing.JButton speakButton
boolean speakWhileTyping
boolean speakingFullSequence
javax.swing.Timer speakTimer
javax.swing.Timer styleTimer
javax.swing.text.Style styleStandardBase
javax.swing.text.Style styleInvalidChar
javax.swing.text.Style styleUnpairedBase
javax.swing.text.Style styleUnspecifiedBase
javax.swing.text.Style styleIgnoredChar
SequenceDisplayWindow.SoundPlayer _speakPlayer
java.util.HashMap<K,V> _speakStreams
java.io.InputStream invalidSoundClip
SequenceDisplayWindow.SpeakMenu speakMenu
java.awt.CardLayout cards
javax.swing.JPanel specificPanel
java.lang.String updatedMessage
java.util.HashMap<K,V> data
java.util.Map<K,V> readOnlyData
java.lang.Object existingKey
java.lang.Object existingValue
java.lang.StringBuilder _sb
java.lang.String errorDescription
java.lang.String offendingText
java.lang.String location
SyntaxErrorException.getLocation()
.int lineOffset
int columnOffset