Serialized Form

Package jaligner

Class jaligner.Sequence extends java.lang.Object implements Serializable

serialVersionUID: 3256721801357898297l

Serialized Fields

sequence

java.lang.String sequence

Sequence

id

java.lang.String id

Sequence id.

description

java.lang.String description

Sequence description.

type

int type

Sequence type.

Package jaligner.matrix

Class jaligner.matrix.Matrix extends java.lang.Object implements Serializable

serialVersionUID: 3833742170619524400l

Serialized Fields

id

java.lang.String id

Matrix id (or name)

scores

float[][] scores

Scores

Class jaligner.matrix.MatrixLoaderException extends java.lang.Exception implements Serializable

serialVersionUID: 3906364935142586680l

Package jaligner.ui

Class jaligner.ui.AlignWindow extends javax.swing.JFrame implements Serializable

serialVersionUID: 3257844376876364850l

Serialized Fields

clipboardPoller

ClipboardPoller clipboardPoller

Clipboard poller thread

matrices

java.util.HashMap matrices

Loaded scoring matrices

currentTextComponent

javax.swing.text.JTextComponent currentTextComponent

Current text component

nextFocusAction

javax.swing.Action nextFocusAction

prevFocusAction

javax.swing.Action prevFocusAction

buttonGroupSequences

javax.swing.ButtonGroup buttonGroupSequences

jButtonCopy

javax.swing.JButton jButtonCopy

jButtonCut

javax.swing.JButton jButtonCut

jButtonDelete

javax.swing.JButton jButtonDelete

jButtonExit

javax.swing.JButton jButtonExit

jButtonGo

javax.swing.JButton jButtonGo

jButtonOpen

javax.swing.JButton jButtonOpen

jButtonPaste

javax.swing.JButton jButtonPaste

jButtonPrint

javax.swing.JButton jButtonPrint

jButtonSave

javax.swing.JButton jButtonSave

jComboBoxOutputFormat

javax.swing.JComboBox jComboBoxOutputFormat

jComboBoxScoringMatrix

javax.swing.JComboBox jComboBoxScoringMatrix

jFormattedTextFieldGapExtend

javax.swing.JFormattedTextField jFormattedTextFieldGapExtend

jFormattedTextFieldGapOpen

javax.swing.JFormattedTextField jFormattedTextFieldGapOpen

jLabelExtendGapPenalty

javax.swing.JLabel jLabelExtendGapPenalty

jLabelOpenGapPenalty

javax.swing.JLabel jLabelOpenGapPenalty

jLabelOutputFormat

javax.swing.JLabel jLabelOutputFormat

jLabelScoringMatrix

javax.swing.JLabel jLabelScoringMatrix

jMenuBar

javax.swing.JMenuBar jMenuBar

jMenuEdit

javax.swing.JMenu jMenuEdit

jMenuFile

javax.swing.JMenu jMenuFile

jMenuHelp

javax.swing.JMenu jMenuHelp

jMenuItemAbout

javax.swing.JMenuItem jMenuItemAbout

jMenuItemEditCopy

javax.swing.JMenuItem jMenuItemEditCopy

jMenuItemEditCut

javax.swing.JMenuItem jMenuItemEditCut

jMenuItemEditDelete

javax.swing.JMenuItem jMenuItemEditDelete

jMenuItemEditPaste

javax.swing.JMenuItem jMenuItemEditPaste

jMenuItemEditSelectAll

javax.swing.JMenuItem jMenuItemEditSelectAll

jMenuItemFileExit

javax.swing.JMenuItem jMenuItemFileExit

jMenuItemFileLoadMatrix

javax.swing.JMenuItem jMenuItemFileLoadMatrix

jMenuItemFileLoadSequence1

javax.swing.JMenuItem jMenuItemFileLoadSequence1

jMenuItemFileLoadSequence2

javax.swing.JMenuItem jMenuItemFileLoadSequence2

jMenuItemFileOpen

javax.swing.JMenuItem jMenuItemFileOpen

jMenuItemFilePrint

javax.swing.JMenuItem jMenuItemFilePrint

jMenuItemToolsRunExample

javax.swing.JMenuItem jMenuItemToolsRunExample

jMenuTools

javax.swing.JMenu jMenuTools

jPanelAlignment

javax.swing.JPanel jPanelAlignment

jPanelConsole

javax.swing.JPanel jPanelConsole

jPanelControls

javax.swing.JPanel jPanelControls

jPanelGapExtend

javax.swing.JPanel jPanelGapExtend

jPanelGapOpen

javax.swing.JPanel jPanelGapOpen

jPanelGo

javax.swing.JPanel jPanelGo

jPanelOutputFormat

javax.swing.JPanel jPanelOutputFormat

jPanelScoringMatrix

javax.swing.JPanel jPanelScoringMatrix

jPanelSequence1

javax.swing.JPanel jPanelSequence1

jPanelSequence2

javax.swing.JPanel jPanelSequence2

jPopup

javax.swing.JPopupMenu jPopup

jPopupCopy

javax.swing.JMenuItem jPopupCopy

jPopupCut

javax.swing.JMenuItem jPopupCut

jPopupDelete

javax.swing.JMenuItem jPopupDelete

jPopupOpen

javax.swing.JMenuItem jPopupOpen

jPopupPaste

javax.swing.JMenuItem jPopupPaste

jPopupPrint

javax.swing.JMenuItem jPopupPrint

jPopupSave

javax.swing.JMenuItem jPopupSave

jPopupSelectAll

javax.swing.JMenuItem jPopupSelectAll

jPopupSeparator1

javax.swing.JSeparator jPopupSeparator1

jPopupSeparator2

javax.swing.JSeparator jPopupSeparator2

jPopupSeparator3

javax.swing.JSeparator jPopupSeparator3

jRadioButtonAlignment

javax.swing.JRadioButton jRadioButtonAlignment

jRadioButtonConsole

javax.swing.JRadioButton jRadioButtonConsole

jRadioButtonSequence1

javax.swing.JRadioButton jRadioButtonSequence1

jRadioButtonSequence2

javax.swing.JRadioButton jRadioButtonSequence2

jScrollPaneAlignment

javax.swing.JScrollPane jScrollPaneAlignment

jScrollPaneConsole

javax.swing.JScrollPane jScrollPaneConsole

jScrollPaneSequence1

javax.swing.JScrollPane jScrollPaneSequence1

jScrollPaneSequence2

javax.swing.JScrollPane jScrollPaneSequence2

jSeparatorFile

javax.swing.JSeparator jSeparatorFile

jSplitPaneBody

javax.swing.JSplitPane jSplitPaneBody

jSplitPaneIO

javax.swing.JSplitPane jSplitPaneIO

jSplitPaneSequences

javax.swing.JSplitPane jSplitPaneSequences

jTextAreaAlignment

javax.swing.JTextArea jTextAreaAlignment

jTextAreaSequence1

javax.swing.JTextArea jTextAreaSequence1

jTextAreaSequence2

javax.swing.JTextArea jTextAreaSequence2

jTextPaneConsole

javax.swing.JTextPane jTextPaneConsole

jToolBar

javax.swing.JToolBar jToolBar

Package jaligner.ui.filechooser

Class jaligner.ui.filechooser.FileChooserException extends java.lang.Exception implements Serializable

serialVersionUID: 3258408434931086648l

Class jaligner.ui.filechooser.NamedInputStream extends java.lang.Object implements Serializable

serialVersionUID: 3256441404384686387l

Serialized Fields

name

java.lang.String name

Name.

inputStream

java.io.InputStream inputStream

Input stream.

Package jaligner.ui.util

Class jaligner.ui.util.TextComponentUtilException extends java.lang.Exception implements Serializable

serialVersionUID: 4050763797251567922l

Package jaligner.util

Class jaligner.util.SequenceParserException extends java.lang.Exception implements Serializable

serialVersionUID: 3258417248288191543l