A B C D E F G H I L M N O P R S T U V X Y

S

selectedTable - Variable in class view.History

A reference to the visible(chosen) table.

sep1 - Variable in class view.ParametersFrame

Seperator.

setBounds(int, int, int, int) - Method in class view.SWTTable

Sets the table bounds.

setBounds(Rectangle) - Method in class view.SWTTable

Sets the table bounds.

setColumn(String[]) - Method in class view.SWTTable

Initiates the table with the given strings as columns.

setColumnSize() - Method in class view.SWTTable

Sets each column size.

setCoordinates(double, double, double, double, char) - Method in class model.Line

Sets the line fields with the given parameters.

setGenomeProp(String) - Method in class model.Genome

Imports porp files into local variables.

setGenomes(String) - Method in class controller.DataHandler

setGenomes(String) - Method in interface controller.IDataHandler

Sets the controller genome array with genome information taken from the files in the directory

setGenomes() - Method in class view.DataView

Imports genome names by the controller, and sets combo boxes with the received set of names.

setIndexAt(int, int, String) - Method in class view.SWTTable

Stores text in a cell.

setLanguage(int) - Method in class controller.DataHandler

setLanguage(int) - Method in interface controller.IDataHandler

Sets Language according to and index.

setLanguage(String) - Method in class view.DataView

Sets the language index, used by controller.

setLineInVector(long, long, long, long, char) - Method in class model.ImportedTableFile

The genomes length(xScale/yScale) is set to be the range of canvas.

setLineVector(boolean) - Method in class model.ImportedTableFile

Sets the table lines into coordinates-Lines and then insert it into a the ImportedFileTable vector

setMappingDefaultVals() - Method in class view.ParametersFrame

Restores Magic contant mapping parameters.

setMapTable(boolean) - Method in class view.GRunTab

Sets the parameters table according to default values.

setMapTable() - Method in class view.History

Initiates the mapping parameters tables.

setMessageLang() - Method in class controller.DataHandler

setMessageLang() - Method in interface controller.IDataHandler

Sets the language from the view/database.

setNewRow(String[]) - Method in class view.SWTTable

Adds a single row to the table.

setParametersINI(String, SWTTable[]) - Method in class controller.DataHandler

setParametersINI(String, SWTTable[]) - Method in interface controller.IDataHandler

Stores parameters in a settings.ini file (taken from given array of tables).

setParametersINI(String, String, String, String) - Method in class view.ParametersFrame

Write user parameters into Magic.ini file.

setPreProccesingDefaultVals() - Method in class view.ParametersFrame

Restores Magic contant preprocessing parameters.

setPreTable(boolean) - Method in class view.GRunTab

Sets the parameters table according to default values.

setPreTable() - Method in class view.History

Initiates the preprocessing parameters tables.

setProgress - Variable in class view.GRunTab

A runnable that runs in parallel to a process to indicate it state at each part, it updates the progress bar accordingly.

setProgressLabel(String) - Method in class view.GRunTab

Sets the message during the a process to be "msg".

setRegularTableFileConfiguration(long, long, boolean) - Method in class model.ImportedTableFile

Sets the ImportedFileTable Default configurations.

setResultsPage(String, boolean) - Method in class view.GRunTab

Sets the tab with the adequate view (pre/map/result).

setSelected(CTabFolder) - Method in class view.GRunTab

Sets the tab to be selected in the main tab of magic.

setSize(int, int) - Method in class view.SWTTable

Sets table size.

setSize(Point) - Method in class view.SWTTable

Sets the table size.

setTable(SWTTable, String, String) - Method in class view.History

Initiates the table rows with relevant histroy regarding chosen genomes in the combo boxes, it searchs through the relevant histroy folder for directories with the relevant names.

setToolTip(String) - Method in class view.SWTTable

Sets the table tooltip text with the given text.

setUserParameters() - Method in class view.ParametersFrame

Sets parameters entered by the user to default, also stores data in the "Magic.ini" file.

setView(DataView) - Method in class controller.DataHandler

setView(DataView) - Method in interface controller.IDataHandler

Sets the controller reference to the logical view.

setVisible(boolean) - Method in class view.SWTTable

Sets the table to be visible/unvisible.

setWorkplace(boolean) - Method in class view.DataView

Sets the parameters as read from the settings file.

shell - Variable in class view.AddGenome

The add new genome shell.

shell - Variable in class view.DataView

The display shell(SWT properties).

shell - Static variable in class view.GRunTab

Data View shell.

shell - Variable in class view.Help

shell - Variable in class view.OptionDialog

OptionDialog shell, in order to view data in a seperate window.

shell - Variable in class view.RemoveGenome

OptionDialog shell, in order to view data in a seperate window.

show(CTabItem) - Method in class view.ParametersFrame

Sets parameters tabitem to be paraitem, and its control paratab.

ShowPButton - Variable in class view.GRunTab

Sets the parameters to be visible so the user can change them.

sign - Variable in class model.Line

Line sign.

skipSpaces(String, int) - Method in class model.ImportedTableFile

Return the updated index which is used to read a string after skipping spaces.

state - Variable in class view.GRunTab

A string that holds the state of process (0-100).

StatisGroup - Variable in class view.GRunTab

Group that holds the statistics when visible.

stitchDifference - Variable in class model.Magic

Parameter: stitch difference.

stitchDifference - Variable in class view.ParametersFrame

Default parameter.

stitchDifferencelabel - Variable in class view.ParametersFrame

Parameter label.

stitchDifferencetext - Variable in class view.ParametersFrame

Text field for the parameter.

stitchDistance - Variable in class model.Magic

Parameter: stitch distance.

stitchDistance - Variable in class view.ParametersFrame

Default parameter.

stitchDistancelabel - Variable in class view.ParametersFrame

Parameter label.

stitchDistancetext - Variable in class view.ParametersFrame

Text field for the parameter.

stitchMinLength - Variable in class model.Magic

Parameter: stitch minimum length.

stitchMinLength - Variable in class view.ParametersFrame

Default parameter.

stitchMinLengthlabel - Variable in class view.ParametersFrame

Parameter label.

stitchMinLengthtext - Variable in class view.ParametersFrame

Text field for the parameter.

SWTTable - Class in view

Title: Bioinformatics Project

SWTTable(Composite, boolean) - Constructor for class view.SWTTable

C'tor, builds an empty table, adds a listener in case it is editable.

SymbolicName - Variable in class model.Genome

Genome symbolic(short) name.