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

G

gapExtractLength - Variable in class model.Magic

Parameter: gap extraction length.

gapExtractLength - Variable in class view.ParametersFrame

Default parameter.

gapExtractLengthlabel - Variable in class view.ParametersFrame

Parameter label.

gapExtractLengthtext - Variable in class view.ParametersFrame

Text field for the parameter.

gapJoinLength - Variable in class model.Magic

Parameter: gap join length.

gapJoinLength - Variable in class view.ParametersFrame

Default parameter.

gapJoinLengthlabel - Variable in class view.ParametersFrame

Parameter label.

gapJoinLengthtext - Variable in class view.ParametersFrame

Text field for the parameter.

gCompDetails - Variable in class view.AddGenome

Group holding the required detail fields to add a new genome.

gen1 - Variable in class view.GRunTab

First genome short name.

gen2 - Variable in class view.GRunTab

Second genome short name.

GenFileText - Variable in class view.AddGenome

Text field for the genome file path.

Genome - Class in model

Title: Bioinformatics Project

Genome(String, String) - Constructor for class model.Genome

C'tor, imports data from prop file and saves genome files paths.

genome - Variable in class model.Genome

Genome genome file path.

genomeArray - Variable in class controller.DataHandler

A List containing genomes-objects (which contains genome information).

GenomeGroup - Variable in class view.GRunTab

Group containg the label, go button and cancel button, it also holds the progress bar when visible.

genomeNames - Variable in class view.GRunTab

A label clarifying the genomes names which it will run mapping/preprocessing phase on.

getAnchor() - Method in class model.Genome

returns the genome anchor file path.

getChromosome_num() - Method in class model.Genome

returns the genome chromosome gene num.

getcleanISPerc() - Method in class model.Magic

Retruns the removing transposable elements parameter.

getcleanMinLen() - Method in class model.Magic

Retruns the removing short entries parameter.

getcleanProPerc() - Method in class model.Magic

Retruns the removing prophages parameter.

getColumnName(int) - Method in class view.SWTTable

Returns a column name.

getDigNum(long) - Method in class view.PaintChart

Returns number of the digits in a given number.

getDirectory(SWTTable, int) - Method in class view.History

Constructs a string from the given table lines , this string used as an existing directory name.

getDisplay() - Method in class controller.DataHandler

getDisplay() - Method in interface controller.IDataHandler

Returns view display, for asynchronious execution of runnables that updates the shell.

getDisplay() - Method in class view.DataView

Returns DataView main display.

getdupPerc() - Method in class model.Magic

Retruns the finding duplicates parameter.

getEnt() - Method in class model.Genome

returns the genome ent file path.

geteval() - Method in class model.Magic

Retruns eval.

getFile(String[], String) - Method in class model.Genome

Locates the file with the extention ext in the directory list str.

getgapExtractLength() - Method in class model.Magic

Retruns the gap extract length.

getgapJoinLength() - Method in class model.Magic

Retruns the gap join length.

getGenome(String) - Method in class controller.DataHandler

Returns the genome object containing information about the genome that its short name is given.

getGenome() - Method in class model.Genome

returns the genome ".Genome" file path.

getGenomeLength(String) - Method in class controller.DataHandler

getGenomeLength(String) - Method in interface controller.IDataHandler

Lookup given genome by symbolic name and returns it length.

getGenomeName(String) - Method in class controller.DataHandler

getGenomeName(String) - Method in interface controller.IDataHandler

Finds genome by symbolic (short) name and returns it full name.

getGenomeName() - Method in class model.Genome

returns the genome full name.

getGenomeNames() - Method in class controller.DataHandler

getGenomeNames() - Method in interface controller.IDataHandler

Returns an array containing genomes full names.

getGenomeProp(String) - Method in class controller.DataHandler

getGenomeProp(String) - Method in interface controller.IDataHandler

Returns the genome "prop" file path.

getGenomeSymbolName(String) - Method in class controller.DataHandler

getGenomeSymbolName(String) - Method in interface controller.IDataHandler

Finds genome by real (Full) name and returns it symbolic name.

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

Returns a cell text.

getInputDirectory() - Method in class controller.DataHandler

getInputDirectory() - Method in interface controller.IDataHandler

Returns the input directory.

getInputDirectory() - Method in class model.Magic

Retruns the input directory.

getInputDirectory() - Method in class view.DataView

Retruns input directory as imported from the magic object.

getInputDirectory() - Method in class view.OptionDialog

Returns the input directory as updated by the user.

getItemCount() - Method in class view.SWTTable

Returns number of the rows in the table.

getLanguage() - Method in class model.Magic

Returns the language as imported from the settings file.

getLastDig(double, int) - Method in class view.PaintChart

Converts a number of regular digits number to 1 digit multiplyed with 10^number of the rest of the digits.

getLength() - Method in class model.Genome

returns the genome length(as imported from the prop).

getLineAt(int) - Method in class model.ImportedTableFile

Returns a vector item(coordinates-line)

getLineVector() - Method in class model.ImportedTableFile

Returns the ImportedTable data base

getMagicLang() - Method in class view.DataView

Returns language index from "magic" as initiated, used by controller.

getMapParameters(SWTTable, SWTTable, SWTTable) - Method in class controller.DataHandler

getMapParameters(SWTTable, SWTTable, SWTTable) - Method in interface controller.IDataHandler

Put the parameters taken from the mapping parameters table into an array of strings.

getMessageLang() - Method in class controller.DataHandler

getMessageLang() - Method in interface controller.IDataHandler

Returns the message bundle.

getNum(String) - Method in class controller.DataHandler

Removes the last char' of a string value of a number if it's not digit.

getNumber(String) - Method in class controller.DataHandler

Cuts the tail of a string which contains charactars other than digits, for extracting the only number.

getorthPerc() - Method in class model.Magic

Retruns the identifying orthologs parameter.

getOutDirectory() - Method in class view.DataView

Retruns output directory as imported from the magic object.

getOutputDirectory() - Method in class controller.DataHandler

getOutputDirectory() - Method in interface controller.IDataHandler

Returns the output directory.

getOutputDirectory() - Method in class model.Magic

Retruns the output directory.

getOutputDirectory() - Method in class view.OptionDialog

Returns the output directory as updated by the user.

getParametersFromINI(Magic) - Method in class view.ParametersFrame

Extract default parameters from Magic data structure.

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

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

Loads parameters from a settings.ini file into given array of tables.

getPlasmid_num() - Method in class model.Genome

returns the genome plasmid gene num.

getPreParameters(SWTTable, SWTTable, SWTTable) - Method in class controller.DataHandler

getPreParameters(SWTTable, SWTTable, SWTTable) - Method in interface controller.IDataHandler

Put the parameters taken from the pre-processing parameters table into an array of strings.

getProcessState(String) - Method in class controller.DataHandler

getProcessState(String) - Method in interface controller.IDataHandler

Returns a number between 0-100 from the trace file.

getProp() - Method in class model.Genome

returns the genome prop file path.

getProtein_gene_num() - Method in class model.Genome

returns the genome Protein gene num.

getRNA_gene_num() - Method in class model.Genome

returns the genome RNA gene num.

getRowsNumber(FileReader) - Method in class controller.DataHandler

Returns number of rows in a file.

getRowString(String, String) - Method in class view.History

Helper method,used in "setTable" method to extract the a line info from the given directory name.

getSelectedIndices() - Method in class view.SWTTable

Rturns an array contaning the selected indcies.

getSelectedItemIndex() - Method in class view.SWTTable

Returns the number of the selected row.

getSelectedLang() - Method in class controller.DataHandler

Returns the index of the chosen language.

getSelectedLang() - Method in interface controller.IDataHandler

Returns the language index.

getShell() - Method in class view.DataView

Returns DataView main shell.

getSign() - Method in class model.Line

returns the line sign is imported from the file.

getstitchDifference() - Method in class model.Magic

Retruns the stitch difference.

getstitchDistance() - Method in class model.Magic

Retruns the stitch distance.

getstitchMinLength() - Method in class model.Magic

Retruns the stitch minimum length.

getSymbolName() - Method in class model.Genome

returns the genome symbolic(short) name.

getTableLineNumber() - Method in class view.PaintChart

Returns number of the lines in the given vector.

getTE() - Method in class model.Genome

returns the genome te file path.

getVe() - Method in class model.Genome

returns the genome ve file path.

getVectorFromFile(String, long, long, boolean) - Method in class controller.DataHandler

getVectorFromFile(String, long, long, boolean) - Method in interface controller.IDataHandler

The Method take a file path as a parameter passes it to the model throught the data IDataManager interface.

getVectorFromFile(String, long, long, boolean) - Method in class model.DataManager

getVectorFromFile(String, long, long, boolean) - Method in interface model.IDataManager

Uses the ImportedTableFile to import the file with the given path and returns the Line-Vector.

getVIRUS() - Method in class model.Genome

returns the genome virus file path.

GLengText - Variable in class view.AddGenome

Text field for the length file path.

GnameText - Variable in class view.AddGenome

Text field for the genome full name.

goButton - Variable in class view.GRunTab

Runs the actual mapping/preprocssing phase.

gOptionDetails - Variable in class view.AddGenome

Group hodling an optional information fields about the genome.

group1 - Variable in class view.ParametersFrame

Parameters group: includes texts/labels.

group2 - Variable in class view.ParametersFrame

Parameters group: includes texts/labels.

group3 - Variable in class view.ParametersFrame

Parameters group: includes texts/labels.

group4 - Variable in class view.ParametersFrame

Parameters group: includes texts/labels.

group5 - Variable in class view.ParametersFrame

Parameters group: includes texts/labels.

group6 - Variable in class view.ParametersFrame

Parameters group: includes texts/labels.

GRunTab - Class in view

Title: Bioinformatics Project

GRunTab(CTabFolder, String, String, IDataHandler) - Constructor for class view.GRunTab

C'tor, creates the basic view of running pre-processing/mapping phase tab.

GSnameText - Variable in class view.AddGenome

Text field for the genome short name.

GTEfileText - Variable in class view.AddGenome

Text field for the te file path.

GVEfileText - Variable in class view.AddGenome

Text field for the ve file path.

GVirusfileText - Variable in class view.AddGenome

Text field for the virus file path.