Serialized Form

Package phylosort

Class phylosort.Path extends java.util.ArrayList<java.lang.Integer> implements Serializable

serialVersionUID: -3219999536658557694L

Package phylosort.ui

Class phylosort.ui.MutableList extends javax.swing.JList implements Serializable

serialVersionUID: -213214033062865966L

Serialized Fields

target

MutableList target

Another MutableList that is a target for moving an element from this list when this list is double clicked

Class phylosort.ui.PhyloSortWindow extends javax.swing.JFrame implements Serializable

serialVersionUID: 3257844376876364850L

Serialized Fields

sourceList

MutableList sourceList

configFile

java.lang.String configFile

treeWindow

TreeWindow treeWindow

Reference tree frame

groupIndex

int groupIndex

nextFocusAction

javax.swing.Action nextFocusAction

prevFocusAction

javax.swing.Action prevFocusAction

buttonGroupTaxaSource

javax.swing.ButtonGroup buttonGroupTaxaSource

jButtonCancel

javax.swing.JButton jButtonCancel

jButtonConsoleClear

javax.swing.JButton jButtonConsoleClear

jButtonExecute

javax.swing.JButton jButtonExecute

jButtonExit

javax.swing.JButton jButtonExit

jButtonGroupAdd

javax.swing.JButton jButtonGroupAdd

jButtonGroupRemove

javax.swing.JButton jButtonGroupRemove

jButtonInputDirectory

javax.swing.JButton jButtonInputDirectory

jButtonOK

javax.swing.JButton jButtonOK

jButtonOutputDirectory

javax.swing.JButton jButtonOutputDirectory

jButtonTaxaAdd

javax.swing.JButton jButtonTaxaAdd

jButtonTaxaOpen

javax.swing.JButton jButtonTaxaOpen

jButtonTaxaReload

javax.swing.JButton jButtonTaxaReload

jButtonTaxaRemove

javax.swing.JButton jButtonTaxaRemove

jButtonTreeClusterCancel

javax.swing.JButton jButtonTreeClusterCancel

jButtonTreeClusterGo

javax.swing.JButton jButtonTreeClusterGo

jButtonTreeClusterInput

javax.swing.JButton jButtonTreeClusterInput

jButtonTreeClusterOutput

javax.swing.JButton jButtonTreeClusterOutput

jCheckBoxExclusive

javax.swing.JCheckBox jCheckBoxExclusive

jCheckBoxReference

javax.swing.JCheckBox jCheckBoxReference

jCheckBoxRoot

javax.swing.JCheckBox jCheckBoxRoot

jComboBoxOnMatch

javax.swing.JComboBox jComboBoxOnMatch

jComboBoxRegexp

javax.swing.JComboBox jComboBoxRegexp

jDialogTreeBrowser

javax.swing.JDialog jDialogTreeBrowser

jDialogTreeCluster

javax.swing.JDialog jDialogTreeCluster

jFileChooserTrees

javax.swing.JFileChooser jFileChooserTrees

jLabelConsole

javax.swing.JLabel jLabelConsole

jLabelGroups

javax.swing.JLabel jLabelGroups

jLabelInputTaxa

javax.swing.JLabel jLabelInputTaxa

jLabelMaxTaxa

javax.swing.JLabel jLabelMaxTaxa

jLabelMaximumNumberOfCopies

javax.swing.JLabel jLabelMaximumNumberOfCopies

jLabelMinBootstrap

javax.swing.JLabel jLabelMinBootstrap

jLabelMinTaxa

javax.swing.JLabel jLabelMinTaxa

jLabelOnMatch

javax.swing.JLabel jLabelOnMatch

jLabelRegexp

javax.swing.JLabel jLabelRegexp

jLabelTreeClusterInput

javax.swing.JLabel jLabelTreeClusterInput

jLabelTreeClusterMinimum

javax.swing.JLabel jLabelTreeClusterMinimum

jLabelTreeClusterOutput

javax.swing.JLabel jLabelTreeClusterOutput

jMenuBar

javax.swing.JMenuBar jMenuBar

jMenuFile

javax.swing.JMenu jMenuFile

jMenuHelp

javax.swing.JMenu jMenuHelp

jMenuItemAbout

javax.swing.JMenuItem jMenuItemAbout

jMenuItemFileExit

javax.swing.JMenuItem jMenuItemFileExit

jMenuItemFileLoadConfig

javax.swing.JMenuItem jMenuItemFileLoadConfig

jMenuItemFileSaveConfig

javax.swing.JMenuItem jMenuItemFileSaveConfig

jMenuItemTreeBrowser

javax.swing.JMenuItem jMenuItemTreeBrowser

jMenuItemTreeCluster

javax.swing.JMenuItem jMenuItemTreeCluster

jMenuTools

javax.swing.JMenu jMenuTools

jPanelBody

javax.swing.JPanel jPanelBody

jPanelButtonsAcceptReject

javax.swing.JPanel jPanelButtonsAcceptReject

jPanelCluster

javax.swing.JPanel jPanelCluster

jPanelConsole

javax.swing.JPanel jPanelConsole

jPanelConsoleEdit

javax.swing.JPanel jPanelConsoleEdit

jPanelControls

javax.swing.JPanel jPanelControls

jPanelExecute

javax.swing.JPanel jPanelExecute

jPanelExit

javax.swing.JPanel jPanelExit

jPanelGroupButtons

javax.swing.JPanel jPanelGroupButtons

jPanelInputDirectory

javax.swing.JPanel jPanelInputDirectory

jPanelInputTaxa

javax.swing.JPanel jPanelInputTaxa

jPanelMaxNumGenes

javax.swing.JPanel jPanelMaxNumGenes

jPanelMaxTaxa

javax.swing.JPanel jPanelMaxTaxa

jPanelMinBootstrap

javax.swing.JPanel jPanelMinBootstrap

jPanelMinTaxa

javax.swing.JPanel jPanelMinTaxa

jPanelMode

javax.swing.JPanel jPanelMode

jPanelOnMatch

javax.swing.JPanel jPanelOnMatch

jPanelOutputDirectory

javax.swing.JPanel jPanelOutputDirectory

jPanelQueryTaxa

javax.swing.JPanel jPanelQueryTaxa

jPanelReferenceTaxonomy

javax.swing.JPanel jPanelReferenceTaxonomy

jPanelRootByOutgroup

javax.swing.JPanel jPanelRootByOutgroup

jPanelSettings

javax.swing.JPanel jPanelSettings

jPanelTaxaButtons

javax.swing.JPanel jPanelTaxaButtons

jPanelTaxaRegexp

javax.swing.JPanel jPanelTaxaRegexp

jPanelTaxaSource

javax.swing.JPanel jPanelTaxaSource

jPanelTaxaSourceButtons

javax.swing.JPanel jPanelTaxaSourceButtons

jPanelTreeClusterButtons

javax.swing.JPanel jPanelTreeClusterButtons

jRadioButtonForest

javax.swing.JRadioButton jRadioButtonForest

jRadioButtonPlain

javax.swing.JRadioButton jRadioButtonPlain

jRadioButtonTree

javax.swing.JRadioButton jRadioButtonTree

jScrollPaneConsole

javax.swing.JScrollPane jScrollPaneConsole

jSeparatorFile

javax.swing.JSeparator jSeparatorFile

jSpinnerTreeClusterMinimum

javax.swing.JSpinner jSpinnerTreeClusterMinimum

jSplitPaneTop

javax.swing.JSplitPane jSplitPaneTop

jTabbedPaneGroups

javax.swing.JTabbedPane jTabbedPaneGroups

jTextFieldInputDirectory

javax.swing.JTextField jTextFieldInputDirectory

jTextFieldMaxTaxa

javax.swing.JTextField jTextFieldMaxTaxa

jTextFieldMaximumNumberOfCopies

javax.swing.JTextField jTextFieldMaximumNumberOfCopies

jTextFieldMinBoot

javax.swing.JTextField jTextFieldMinBoot

jTextFieldMinTaxa

javax.swing.JTextField jTextFieldMinTaxa

jTextFieldOutputDirectory

javax.swing.JTextField jTextFieldOutputDirectory

jTextFieldTaxaOpen

javax.swing.JTextField jTextFieldTaxaOpen

jTextFieldTreeClusterInput

javax.swing.JTextField jTextFieldTreeClusterInput

jTextFieldTreeClusterOutput

javax.swing.JTextField jTextFieldTreeClusterOutput

jTextPaneConsole

javax.swing.JTextPane jTextPaneConsole

taxaScrollPane

javax.swing.JScrollPane taxaScrollPane

Class phylosort.ui.TabbedList extends javax.swing.JScrollPane implements Serializable

serialVersionUID: -9190081312999593352L

Serialized Fields

list

MutableList list

MutableList inside the tab

Class phylosort.ui.TaxaRegexpExamples extends java.util.HashMap<java.lang.String,java.lang.String> implements Serializable

serialVersionUID: 4941186521009996141L

Serialized Fields

expressions

java.util.List<E> expressions

List of available regular expression examples

Class phylosort.ui.TreeWindow extends javax.swing.JFrame implements Serializable

serialVersionUID: 1L

Serialized Fields

rootNode

javax.swing.tree.DefaultMutableTreeNode rootNode

Root node

model

javax.swing.tree.DefaultTreeModel model

Tree model

tree

javax.swing.JTree tree

JTree

toolkit

java.awt.Toolkit toolkit

Toolkit

toolBar

javax.swing.JToolBar toolBar

JToolBar

buttonExpand

javax.swing.JButton buttonExpand

Button to Expand all nodes

buttonCollapse

javax.swing.JButton buttonCollapse

Button to collapse all nodes

listeners

java.util.Set<E> listeners

Nodes selection listener