A B C D E F G H I J K L M N O P R S T U V W Z

S

safeCheck() - Static method in class gui.GuiManager
 
save(Container, Workspace) - Static method in class gui.workSpace.WorkspaceSaver
That function generates the dialog needed to prompt information about the place to export and calls a lower layer class to do that
saveMatrix(Matrix, String) - Static method in class data.SerialManager
Saves a matrix object with the given name
saveObject(Object, String, String, String) - Static method in class data.SerialManager
Saves any object in disk.
saveProps() - Static method in class data.PropsManager
Saves the current Properties
saveWorkspace(Workspace, String) - Static method in class data.SerialManager
Saves a Workspace object with the given name
scrollDesc - Variable in class gui.myWindows.PanelMatrixInfo
 
scrollDesc - Variable in class gui.workSpace.PanelWSCreate
 
scrollList - Variable in class gui.workSpace.WorkspaceLoader
 
scrollMatrix - Variable in class gui.matrixLibrary.PanelLibrary
 
scrollMatrix - Variable in class gui.workSpace.PanelWSCreate
 
scrollTable - Variable in class gui.workSpace.PanelWSEnterResults
 
scrollTaxa - Variable in class gui.myWindows.PanelMatrixInfo
 
scrollTest - Variable in class gui.myWindows.PanelMatrixInfo
 
secondValue - Variable in class data.IndexedItem
Additional Float value
sendMessage(String) - Static method in class gui.myClasses.MessageCenter
 
separator - Variable in class gui.workSpace.PanelWSShowInfo
 
SerialManager - Class in data
Low layer class to interact with the data in disk
SerialManager() - Constructor for class data.SerialManager
 
SerialManager.MyFilter - Class in data
It allows to create a custom FilenameFilter in an easy way
SerialManager.MyFilter(String) - Constructor for class data.SerialManager.MyFilter
Constructs a FilenameFilter that accepts files with the desired extension
serialVersionUID - Static variable in exception core.CoreException
 
serialVersionUID - Static variable in class data.Configuration
 
serialVersionUID - Static variable in exception data.DataException
 
serialVersionUID - Static variable in class data.Matrix
 
serialVersionUID - Static variable in class data.Workspace
 
serialVersionUID - Static variable in exception gui.GuiException
 
serialVersionUID - Static variable in class gui.MainBar
 
serialVersionUID - Static variable in class gui.MainFrame
 
serialVersionUID - Static variable in class gui.matrixLibrary.DialogMatrixImport
 
serialVersionUID - Static variable in class gui.matrixLibrary.DialogTree.MenuTree
 
serialVersionUID - Static variable in class gui.matrixLibrary.DialogTree
 
serialVersionUID - Static variable in class gui.matrixLibrary.PanelLibrary
 
serialVersionUID - Static variable in class gui.matrixLibrary.PanelTree
 
serialVersionUID - Static variable in class gui.matrixLibrary.TreeManager
 
serialVersionUID - Static variable in class gui.matrixLibrary.TreeView
 
serialVersionUID - Static variable in class gui.myClasses.CellEditorRadioButton
 
serialVersionUID - Static variable in class gui.myClasses.EventDoneTest
 
serialVersionUID - Static variable in class gui.myClasses.EventTaxaFound
 
serialVersionUID - Static variable in class gui.myClasses.JListMatrix
 
serialVersionUID - Static variable in class gui.myClasses.JListWorkspace
 
serialVersionUID - Static variable in class gui.myClasses.JPanelBackground
 
serialVersionUID - Static variable in class gui.myClasses.JRadioButtonTest
 
serialVersionUID - Static variable in class gui.myClasses.JTableRadioButtons
 
serialVersionUID - Static variable in class gui.myClasses.JTableTransparentBg
 
serialVersionUID - Static variable in class gui.myClasses.NonEditTableModel
 
serialVersionUID - Static variable in class gui.myWindows.DialogFirstRun
 
serialVersionUID - Static variable in class gui.myWindows.DialogMatrixInfo
 
serialVersionUID - Static variable in class gui.myWindows.DialogSetConfig
 
serialVersionUID - Static variable in class gui.myWindows.DialogTextArea
 
serialVersionUID - Static variable in class gui.myWindows.PanelConfig
 
serialVersionUID - Static variable in class gui.myWindows.PanelMatrixInfo
 
serialVersionUID - Static variable in class gui.PanelWelcome
 
serialVersionUID - Static variable in class gui.workSpace.DialogWSCreate
 
serialVersionUID - Static variable in class gui.workSpace.PanelWSCreate
 
serialVersionUID - Static variable in class gui.workSpace.PanelWSEnterResults
 
serialVersionUID - Static variable in class gui.workSpace.PanelWSMain
 
serialVersionUID - Static variable in class gui.workSpace.PanelWSShowInfo
 
serialVersionUID - Static variable in class gui.workSpace.PanelWSTaxaFound
 
serialVersionUID - Static variable in class gui.workSpace.WorkspaceLoader
 
setBestScoredCount(int) - Method in class data.Configuration
 
setFoundValue(float) - Method in class data.Configuration
 
setMinUnexpectedScore(float) - Method in class data.Configuration
 
setProp(String, String) - Static method in class data.PropsManager
Sets a key with a value in the Props.
setReadOnly(boolean) - Method in class gui.myClasses.NonEditTableModel
Sets all the columns of the table as non-editable (read-only table)
setSignalScoreLimitLow(float) - Method in class data.Configuration
 
setSignalScoreLimitUpp(float) - Method in class data.Configuration
 
setUnsavedChanges(boolean) - Static method in class gui.GuiManager
 
setUp(String) - Method in class gui.myWindows.DialogMatrixInfo
 
setUp(boolean) - Method in class gui.myWindows.DialogSetConfig
 
setUpBayesDefaults() - Method in class data.Configuration
Set the current Configuration to use Bayesian Id. defaults
setUpTreeDefaults() - Method in class data.Configuration
Set the current Configuration to use Tree Id. defaults
setZeroSkipValue(float) - Method in class data.Configuration
 
SHOW_ITEM_LIMIT - Static variable in class gui.workSpace.PanelWSShowInfo
 
showAbout() - Method in class gui.MainBar
 
showFileChooseSave(String[], String) - Static method in class utils.FileUtils
Shows a JFileChooser and let the user choose one of the formats passed to the function.
showLibrary() - Static method in class gui.GuiManager
 
showLoadDialog() - Static method in class gui.workSpace.WorkspaceLoader
 
showLoadWorkspace() - Static method in class gui.GuiManager
 
showLog() - Method in class gui.workSpace.WorkspaceManager
 
showNewWorkspace() - Static method in class gui.GuiManager
 
showWelcome() - Static method in class gui.GuiManager
 
SignalScoreLimitLow - Variable in class data.Configuration
When determining if a test positive, negative or variable, there are two cut points.
SignalScoreLimitUpp - Variable in class data.Configuration
When determining if a test is positive, negative or variable, there are two cut points.
sortedIndexes(float[]) - Static method in class utils.ArrayUtils
Return the sorted list of the array indexes ordened by the value they point.
sortTaxaByProb() - Method in class data.Context
Returns the ordered array by descendent probabilities (higest probabilities at the lower array indexes)
sortTestByVal(int[]) - Method in class data.Context
Given a set of test indexes return the same set sorted by the goodness of the test
splitContex(int, Matrix, Configuration) - Method in class data.Context
Separates the current context in two others, discriminating one from each other using their estimation on the test result with especified identificator
startListen() - Method in class gui.matrixLibrary.PanelLibrary
 
stateChanged(ChangeEvent) - Method in class gui.workSpace.PanelWSMain
 
stateChanged(ChangeEvent) - Method in class gui.workSpace.WorkspaceManager
 
stopListen() - Method in class gui.matrixLibrary.PanelLibrary
 
sum - Variable in class core.Identifier
Mantains the sum of all probabilities

A B C D E F G H I J K L M N O P R S T U V W Z