| 메소드 | 설명 | |
|---|---|---|
| alignmentTests ( String primerSequence ) : System | ||
| calcDeltaG ( String s ) : Double |
Calculates gibbs free energy for a processed string
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| generateHairpinArgs ( String possibilities ) : String[] |
Generates the hairpin arguments to run through the command line. Must eliminate first and last possibilities
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| 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 " ";
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| hairpinRun ( ) : double |
Runs the hairpin test via the command line.
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| heteroDimerRun ( String otherPrimer ) : double |
Runs the heterodimer test.
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| selfDimerRun ( ) : double |
Runs the Self-Dimer test via the command line.
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| worstCaseDeltaG ( ) : double |
Returns most negative result alignment tests.
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| 메소드 | 설명 | |
|---|---|---|
| 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.
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| public alignmentTests ( String primerSequence ) : System | ||
| primerSequence | String | |
| 리턴 | System | |
| public static calcDeltaG ( String s ) : Double | ||
| s | String | String whose delta G is being calculated |
| 리턴 | Double | |
| public generateHairpinArgs ( String possibilities ) : String[] | ||
| possibilities | String | String array of possible hairpins |
| 리턴 | String[] | |
| public generateHairpinPossibilities ( ) : String[] | ||
| 리턴 | String[] | |
| public heteroDimerRun ( String otherPrimer ) : double | ||
| otherPrimer | String | |
| 리턴 | double | |