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

C

CancelButton - Variable in class view.GRunTab

For canceling the operation, and closing the tab.

canvas - Variable in class view.PaintChart

Chart canvas.

ChartGroup - Variable in class view.GRunTab

Group that holds the canvas when it is visible.

checkField(String, Shell) - Method in class controller.DataHandler

checkField(String, Shell) - Method in interface controller.IDataHandler

Returns true if the given string includes only numbers

checkField(String) - Method in class model.Genome

Returns the extracted number, in case it is not a number returns -1.

checkPath(String) - Method in class controller.DataHandler

checkPath(String) - Method in interface controller.IDataHandler

Returns true if the given path is legal and does exist.

ChosenDir - Variable in class view.History

The directory name of the Mapping/preprocessing history.

ChosenPart - Variable in class view.History

A string indicating the sub directories types.

Chromosome_num - Variable in class model.Genome

Genome chromosome number.

Circular - Variable in class view.AddGenome

Check box.

cleanISPerc - Variable in class model.Magic

Parameter: removing transposable elements.

cleanISPerc - Variable in class view.ParametersFrame

Default parameter.

cleanISPerclabel - Variable in class view.ParametersFrame

Parameter label.

cleanISPerctext - Variable in class view.ParametersFrame

Text field for the parameter.

cleanMinLen - Variable in class model.Magic

Parameter: removing short entries.

cleanMinLen - Variable in class view.ParametersFrame

Default parameter.

cleanMinLenlabel - Variable in class view.ParametersFrame

Parameter label.

cleanMinLentext - Variable in class view.ParametersFrame

Text field for the parameter.

cleanProPerc - Variable in class model.Magic

Parameter: removing prophages.

cleanProPerc - Variable in class view.ParametersFrame

Default parameter.

cleanProPerclabel - Variable in class view.ParametersFrame

Parameter label.

cleanProPerctext - Variable in class view.ParametersFrame

Text field for the parameter.

ClearTables() - Method in class view.GRunTab

Impties tables, so it can be refilled with new values.

ClearTables() - Method in class view.History

Cmapping - package Cmapping

combo - Variable in class view.OptionDialog

A combo box for language.

combo - Variable in class view.RemoveGenome

A combo box including genome names.

comboGene1 - Variable in class view.DataView

First genome combo box.

comboGene1 - Variable in class view.History

Genome combo for filtering the history tables.

comboGene2 - Variable in class view.DataView

Second genome combo box.

comboGene2 - Variable in class view.History

Genome combo for filtering the history tables.

comp - Variable in class view.PaintChart

Data view shell, in order to view with it the canvas.

computingLabel - Variable in class view.GRunTab

A label indicating a process is beeing done.

controller - package controller

controller_ - Variable in class view.AddGenome

The controller of magic.

controller_ - Variable in class view.DataView

The controller of magic.

controller_ - Variable in class view.GRunTab

Magic controller.

controller_ - Variable in class view.Help

Magic controller.

controller_ - Variable in class view.History

Magic controller.

controller_ - Variable in class view.OptionDialog

Magic controller.

controller_ - Variable in class view.ParametersFrame

Magic controller.

controller_ - Variable in class view.RemoveGenome

Magic controller.

copy(String, String) - Static method in class controller.FileCopy

Copies file given by the path fromFileName into a new file given by the path toFileName.

CopyFile(String, String) - Method in class controller.DataHandler

CopyFile(String, String) - Method in interface controller.IDataHandler

Copy file given by the path "from" to the file given by path "to"

copyValues() - Method in class view.AddGenome

Copies the the files entered by the user to the input directory.

Cpreprocessing - package Cpreprocessing

CreateDir(String, String, String, String) - Method in class controller.DataHandler

CreateDir(String, String, String, String) - Method in interface controller.IDataHandler

Creates a new history directory containing the mapping/preprocessing results.