Uses of Class
de.unibi.techfak.InSilicoDicer.OperatingPackage.PrecursorContainer

Packages that use PrecursorContainer

de.unibi.techfak.InSilicoDicer.Actions.AlignPrecursors
de.unibi.techfak.InSilicoDicer.Actions.FoldPrecursor
de.unibi.techfak.InSilicoDicer.Actions.ScorePrecursor
de.unibi.techfak.InSilicoDicer.GUI
de.unibi.techfak.InSilicoDicer.OperatingPackage

Uses of PrecursorContainer in de.unibi.techfak.InSilicoDicer.Actions.AlignPrecursors

Methods in de.unibi.techfak.InSilicoDicer.Actions.AlignPrecursors with parameters of type PrecursorContainer

java.util.Vector<java.lang.String>	ClustalWWS.align(PrecursorContainer pc)
java.util.Vector<java.lang.String>	IMultipleAlignAction.align(PrecursorContainer pc) Creates Multiple Alignment
java.util.Vector	MA_ClustalW.align(PrecursorContainer pc)

Uses of PrecursorContainer in de.unibi.techfak.InSilicoDicer.Actions.FoldPrecursor

Methods in de.unibi.techfak.InSilicoDicer.Actions.FoldPrecursor with parameters of type PrecursorContainer

void	IFoldingAction.foldPrecursor(PrecursorContainer pc) Creates a File with the Precursors Nucleotide Sequence; Folds the given precursor with vienna package; Adds the Folding to Precursor`s properties
void	Fold_Vienna.foldPrecursor(PrecursorContainer pc)
void	RNAfoldWS.foldPrecursor(PrecursorContainer pc)

Uses of PrecursorContainer in de.unibi.techfak.InSilicoDicer.Actions.ScorePrecursor

Methods in de.unibi.techfak.InSilicoDicer.Actions.ScorePrecursor with parameters of type PrecursorContainer

java.util.Vector	IScoreAction.formula(PrecursorContainer pc) Scores the window (mature miRNA) by a defined Formula
java.util.Vector	Score_Gaasterland.formula(PrecursorContainer pc)

Uses of PrecursorContainer in de.unibi.techfak.InSilicoDicer.GUI

Methods in de.unibi.techfak.InSilicoDicer.GUI that return PrecursorContainer

PrecursorContainer	ISD.getAllSim()
PrecursorContainer	ISD.getSelectedPCs() Get the selected Precursors from JTree and put them into a PrecursorContainer

Methods in de.unibi.techfak.InSilicoDicer.GUI with parameters of type PrecursorContainer

void	ISD.setAllSim(PrecursorContainer allSim)
void	SimilarListModel.setPrecCursorContainer(PrecursorContainer data) Set a new PreCursorContainer for this SimilarListModel

Uses of PrecursorContainer in de.unibi.techfak.InSilicoDicer.OperatingPackage

Methods in de.unibi.techfak.InSilicoDicer.OperatingPackage that return PrecursorContainer

PrecursorContainer	Operator.getDatabase() Get the actual Database to work with
PrecursorContainer	PrecursorContainer.getPrecursorByName(java.lang.String theName) Searches all Precursor Descriptions of the miRNA Registry for the given String with the BM Algorithm
PrecursorContainer	PrecursorContainer.getPrecursorBySequence(java.lang.String theSeq, int cutOFF) Searches all Precursor Sequences of miRNA Registry for Precursors with a Similarity to the given Sequence higher then the cutOff value

Methods in de.unibi.techfak.InSilicoDicer.OperatingPackage with parameters of type PrecursorContainer

void	Evaluation.fillArrays(PrecursorContainer lonelyPCs, int i) Calculates Postion of mature miRNA by aligning similar Precursors Intrinsic & Extrinsic
void	Evaluation.fillSingleArrays(PrecursorContainer lonelyPCs, int i) Calculates Position of mature miRNA just by scoring the Precursor no alignment with others!
java.lang.String	PrettyPrinter.printPrecursorContainer(PrecursorContainer pc) Pretty-prints the content of a precursor container
void	Start_ISD.run_ISD(java.lang.String pcPath, java.lang.String method, int matureSize, PrecursorContainer db, int cutOff) Runs the prediction procedure
void	Operator.setActionPCs(PrecursorContainer actionPCs)