C# Class PrimerDesigner.alignmentTests

Mostrar archivo Open project: igemsoftware/BU_Wellesley_Software_2011 Class Usage Examples

Public Methods

Method	Description
alignmentTests ( String primerSequence ) : System
calcDeltaG ( String s ) : Double	Calculates gibbs free energy for a processed string
generateHairpinArgs ( String possibilities ) : String[]	Generates the hairpin arguments to run through the command line. Must eliminate first and last possibilities
generateHairpinPossibilities ( ) : String[]	Generates hairpin possibilites based on the primer sequence. When processing with annealer.jar, first and last combos must be ommited because annealer.jar requires 2 string arguments and does not take " ";
hairpinRun ( ) : double	Runs the hairpin test via the command line.
heteroDimerRun ( String otherPrimer ) : double	Runs the heterodimer test.
selfDimerRun ( ) : double	Runs the Self-Dimer test via the command line.
worstCaseDeltaG ( ) : double	Returns most negative result alignment tests.

Private Methods

Method	Description
run ( String input ) : void	Runs given arguments (this code provides the backbone for multiple tests) Puts limit on number of results. Allignment must be more than half.

Method Details

alignmentTests() public method

public alignmentTests ( String primerSequence ) : System
primerSequence	String
return	System

calcDeltaG() public static method

Calculates gibbs free energy for a processed string

public static calcDeltaG ( String s ) : Double
s	String	String whose delta G is being calculated
return	Double

generateHairpinArgs() public method

Generates the hairpin arguments to run through the command line. Must eliminate first and last possibilities

public generateHairpinArgs ( String possibilities ) : String[]
possibilities	String	String array of possible hairpins
return	String[]

generateHairpinPossibilities() public method

Generates hairpin possibilites based on the primer sequence. When processing with annealer.jar, first and last combos must be ommited because annealer.jar requires 2 string arguments and does not take " ";

public generateHairpinPossibilities ( ) : String[]
return	String[]

hairpinRun() public method

Runs the hairpin test via the command line.

public hairpinRun ( ) : double
return	double

heteroDimerRun() public method

Runs the heterodimer test.

public heteroDimerRun ( String otherPrimer ) : double
otherPrimer	String
return	double

selfDimerRun() public method

Runs the Self-Dimer test via the command line.

public selfDimerRun ( ) : double
return	double

worstCaseDeltaG() public method

Returns most negative result alignment tests.

public worstCaseDeltaG ( ) : double
return	double