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## 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)`

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