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A B C D E F G I J L M N O P R S T W

## A

Action - Interface in de.unibi.techfak.InSilicoDicer.Actions
  An simple interface defining a root type for all Actions implemented by ISD.
actionPerformed(ActionEvent) - Method in class de.unibi.techfak.InSilicoDicer.GUI.ISDHandler
actionPerformed(ActionEvent) - Method in class de.unibi.techfak.InSilicoDicer.GUI.MenuHandler
actionPerformed(ActionEvent) - Method in class de.unibi.techfak.InSilicoDicer.GUI.OptionHandler
addListDataListener(ListDataListener) - Method in class de.unibi.techfak.InSilicoDicer.GUI.SimilarListModel
addWarning(String) - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.PrecursorContainer
  Add a warning to internal warning list
align(PrecursorContainer) - Method in class de.unibi.techfak.InSilicoDicer.Actions.AlignPrecursors.ClustalWWS
align(PrecursorContainer) - Method in interface de.unibi.techfak.InSilicoDicer.Actions.AlignPrecursors.IMultipleAlignAction
  Creates Multiple Alignment
align(PrecursorContainer) - Method in class de.unibi.techfak.InSilicoDicer.Actions.AlignPrecursors.MA_ClustalW
align(int, int, int, String, String) - Method in interface de.unibi.techfak.InSilicoDicer.OperatingPackage.SearchMethods.SearchBySequence.ILocalAlign
  Executes a Local Alignment Action where searchSeq is the Nuleotide Sequence to align with all possible Precursor Sequences (dbSeq) in the miRNAdatabase
align(int, int, int, String, String) - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.SearchMethods.SearchBySequence.SWalign
alignScoredPrecursors(Vector, Vector) - Method in class de.unibi.techfak.InSilicoDicer.Actions.ScoreAlign
  Maps the scoring of the precursors to the alignment.
allSimilarConfirmButton - Variable in class de.unibi.techfak.InSilicoDicer.GUI.ISD
  Actions on top left
appendFasta(InputStream) - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.PrecursorContainer
  reads sequences in FASTA from Inputstream and append it to current PrecursorContainer
appendVienna(InputStream) - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.PrecursorContainer

## B

BAR - Static variable in class de.unibi.techfak.InSilicoDicer.GUI.Plot
  public const for plot style BAR
BMi - Class in de.unibi.techfak.InSilicoDicer.OperatingPackage.SearchMethods.SearchByName
BMi() - Constructor for class de.unibi.techfak.InSilicoDicer.OperatingPackage.SearchMethods.SearchByName.BMi

## C

calcAverageValues(Vector) - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.Operator
  Calculate array of average values(scores) from more than one precursor
calcCons(Vector) - Method in class de.unibi.techfak.InSilicoDicer.Actions.CalcConservation.CalcCons_Entropy
calcCons(Vector) - Method in class de.unibi.techfak.InSilicoDicer.Actions.CalcConservation.CalcCons_Entropy_seed
calcCons(Vector) - Method in interface de.unibi.techfak.InSilicoDicer.Actions.CalcConservation.ICalcConservationAction
  Calculates Cobservation profile by column by column
CalcCons_Entropy - Class in de.unibi.techfak.InSilicoDicer.Actions.CalcConservation
CalcCons_Entropy() - Constructor for class de.unibi.techfak.InSilicoDicer.Actions.CalcConservation.CalcCons_Entropy
CalcCons_Entropy_seed - Class in de.unibi.techfak.InSilicoDicer.Actions.CalcConservation
CalcCons_Entropy_seed() - Constructor for class de.unibi.techfak.InSilicoDicer.Actions.CalcConservation.CalcCons_Entropy_seed
checkJComponentEnabled() - Method in class de.unibi.techfak.InSilicoDicer.GUI.ISD
  Check, wether a action component could be activated
chooseDB - Variable in class de.unibi.techfak.InSilicoDicer.GUI.ISD
clean() - Method in class de.unibi.techfak.InSilicoDicer.Actions.Status
cleanWarnings() - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.PrecursorContainer
  Clean internal warning list.
clear - Variable in class de.unibi.techfak.InSilicoDicer.GUI.ISD
  Tree and around
clearInstance() - Static method in class de.unibi.techfak.InSilicoDicer.GUI.SplashFrame
  clear current instance of SplashScreen
clone() - Method in class de.unibi.techfak.InSilicoDicer.Actions.Status
ClustalWWS - Class in de.unibi.techfak.InSilicoDicer.Actions.AlignPrecursors
  Implementation of interface IFoldingAction, which uses RNAfold as webservice running on BiBiServ
ClustalWWS() - Constructor for class de.unibi.techfak.InSilicoDicer.Actions.AlignPrecursors.ClustalWWS
  Default Constructor - creates a new Status object and call constructor RNAFoldWS(Status status)
ClustalWWS(Status) - Constructor for class de.unibi.techfak.InSilicoDicer.Actions.AlignPrecursors.ClustalWWS
  Constructor
consChooser - Variable in class de.unibi.techfak.InSilicoDicer.GUI.ISD
countIntMm2IntBulges(String) - Method in class de.unibi.techfak.InSilicoDicer.Actions.ScorePrecursor.Score_Gaasterland
  Computes the ratio of internal mismatches to internal bulges.
countMismatches(String) - Method in class de.unibi.techfak.InSilicoDicer.Actions.ScorePrecursor.Score_Gaasterland
  Counts the number of all mismatches in the subsequence.
countTerminalMM(String) - Method in class de.unibi.techfak.InSilicoDicer.Actions.ScorePrecursor.Score_Gaasterland
  Counts the number of terminal mismatches in the subsequence.
createAndShowGUI() - Static method in class de.unibi.techfak.InSilicoDicer.GUI.ISD
  private static helper function which 'creates and showes GUI'
createDatabaseFromFile(String, String) - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.Operator
  Deprecated.
cutoffSpinner - Variable in class de.unibi.techfak.InSilicoDicer.GUI.ISD

## D

dbVector - Variable in class de.unibi.techfak.InSilicoDicer.GUI.ISD
de.unibi.techfak.InSilicoDicer.Actions - package de.unibi.techfak.InSilicoDicer.Actions
de.unibi.techfak.InSilicoDicer.Actions.AlignPrecursors - package de.unibi.techfak.InSilicoDicer.Actions.AlignPrecursors
de.unibi.techfak.InSilicoDicer.Actions.CalcConservation - package de.unibi.techfak.InSilicoDicer.Actions.CalcConservation
de.unibi.techfak.InSilicoDicer.Actions.FoldPrecursor - package de.unibi.techfak.InSilicoDicer.Actions.FoldPrecursor
de.unibi.techfak.InSilicoDicer.Actions.ScorePrecursor - package de.unibi.techfak.InSilicoDicer.Actions.ScorePrecursor
de.unibi.techfak.InSilicoDicer.GUI - package de.unibi.techfak.InSilicoDicer.GUI
de.unibi.techfak.InSilicoDicer.OperatingPackage - package de.unibi.techfak.InSilicoDicer.OperatingPackage
de.unibi.techfak.InSilicoDicer.OperatingPackage.SearchMethods.SearchByName - package de.unibi.techfak.InSilicoDicer.OperatingPackage.SearchMethods.SearchByName
de.unibi.techfak.InSilicoDicer.OperatingPackage.SearchMethods.SearchBySequence - package de.unibi.techfak.InSilicoDicer.OperatingPackage.SearchMethods.SearchBySequence
dispose() - Method in class de.unibi.techfak.InSilicoDicer.GUI.StatusFrame

## E

equals(Status) - Method in class de.unibi.techfak.InSilicoDicer.Actions.Status
  Equals a Status object with current status object
evaluate() - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.Evaluation
  Starts the evaluation: Calculation of mature miRNA position with intrinsic, intrinsicPlus and extrinsic method.
Evaluation - Class in de.unibi.techfak.InSilicoDicer.OperatingPackage
Evaluation() - Constructor for class de.unibi.techfak.InSilicoDicer.OperatingPackage.Evaluation
example - Static variable in class de.unibi.techfak.InSilicoDicer.GUI.ISD
  final example sequence for ISD
exampleButton - Variable in class de.unibi.techfak.InSilicoDicer.GUI.ISD
  Actions on top left
extrinsicProfile - Variable in class de.unibi.techfak.InSilicoDicer.GUI.ISD
  Profiles

## F

fillArrays(PrecursorContainer, int) - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.Evaluation
  Calculates Postion of mature miRNA by aligning similar Precursors Intrinsic & Extrinsic
fillSingleArrays(PrecursorContainer, int) - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.Evaluation
  Calculates Position of mature miRNA just by scoring the Precursor no alignment with others!
findStartInSinglePC(int, Vector) - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.Operator
finished() - Method in class de.unibi.techfak.InSilicoDicer.Actions.Status
  Return wether this status is in status finshed.
Fold_Vienna - Class in de.unibi.techfak.InSilicoDicer.Actions.FoldPrecursor
  Implementation of interface IFoldingAction, used RNAfold (locally) from Vienna package to support folding.
Fold_Vienna() - Constructor for class de.unibi.techfak.InSilicoDicer.Actions.FoldPrecursor.Fold_Vienna
  Constructor
Fold_Vienna(Status) - Constructor for class de.unibi.techfak.InSilicoDicer.Actions.FoldPrecursor.Fold_Vienna
  Constructor
foldChooser - Variable in class de.unibi.techfak.InSilicoDicer.GUI.ISD
foldPrecursor(PrecursorContainer) - Method in class de.unibi.techfak.InSilicoDicer.Actions.FoldPrecursor.Fold_Vienna
foldPrecursor(PrecursorContainer) - Method in interface de.unibi.techfak.InSilicoDicer.Actions.FoldPrecursor.IFoldingAction
  Creates a File with the Precursors Nucleotide Sequence; Folds the given precursor with vienna package; Adds the Folding to Precursor`s properties
foldPrecursor(PrecursorContainer) - Method in class de.unibi.techfak.InSilicoDicer.Actions.FoldPrecursor.RNAfoldWS
formula(PrecursorContainer) - Method in interface de.unibi.techfak.InSilicoDicer.Actions.ScorePrecursor.IScoreAction
  Scores the window (mature miRNA) by a defined Formula
formula(PrecursorContainer) - Method in class de.unibi.techfak.InSilicoDicer.Actions.ScorePrecursor.Score_Gaasterland

## G

getAllSim() - Method in class de.unibi.techfak.InSilicoDicer.GUI.ISD
getCalcconservationaction() - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.Operator
getCode() - Method in class de.unibi.techfak.InSilicoDicer.Actions.Status
getCutoff() - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.Operator
getDatabase() - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.Operator
  Get the actual Database to work with
getDescription() - Method in class de.unibi.techfak.InSilicoDicer.Actions.Status
getDescription() - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.Precursor
getElementAt(int) - Method in class de.unibi.techfak.InSilicoDicer.GUI.SimilarListModel
getExCb() - Method in class de.unibi.techfak.InSilicoDicer.GUI.OptionFrame
getExPspin() - Method in class de.unibi.techfak.InSilicoDicer.GUI.OptionFrame
getFile() - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.Operator
getFolding() - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.Precursor
getFoldingaction() - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.Operator
getFormatWarnString() - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.PrecursorContainer
  Return internal warning list as formated string and clean internal warning list afterwards.
getGenuineHash() - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.Operator
getId() - Method in class de.unibi.techfak.InSilicoDicer.Actions.Status
getId() - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.Precursor
getInCb() - Method in class de.unibi.techfak.InSilicoDicer.GUI.OptionFrame
getIndelScore() - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.Operator
getInPspin() - Method in class de.unibi.techfak.InSilicoDicer.GUI.OptionFrame
getInstance() - Static method in class de.unibi.techfak.InSilicoDicer.GUI.SplashFrame
  Returns an instance of SplashScreen, used for Singelton technique
getInstance() - Static method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.Operator
  Singleton
getInstance() - Static method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.PrettyPrinter
  Singleton
getInstance() - Static method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.Start_ISD
  Singleton
getLocalalign() - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.PrecursorContainer
getMatureSize() - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.Operator
getMatureSizeSpin() - Method in class de.unibi.techfak.InSilicoDicer.GUI.OptionFrame
getMethod() - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.Operator
getMirnaPOSinALIGN() - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.Operator
getMirnaPOSinPC() - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.Operator
getMScore() - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.Operator
getMultiplealignaction() - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.Operator
getPath() - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.Operator
getPatternmatching() - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.PrecursorContainer
getPrecursorByID(String) - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.PrecursorContainer
  Searches the miRNA Registry for the given ID
getPrecursorByName(String) - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.PrecursorContainer
  Searches all Precursor Descriptions of the miRNA Registry for the given String with the BM Algorithm
getPrecursorBySequence(String, int) - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.PrecursorContainer
  Searches all Precursor Sequences of miRNA Registry for Precursors with a Similarity to the given Sequence higher then the cutOff value
getPreCursorContainer() - Method in class de.unibi.techfak.InSilicoDicer.GUI.SimilarListModel
  Return PreCursorContainer of this SimilarListModel
getProgressBar() - Method in class de.unibi.techfak.InSilicoDicer.GUI.StatusFrame
  Returns internal reference of jprogressbar.
getProperties() - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.Operator
getRpScore() - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.Operator
getScoreaction() - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.Operator
getSelectedPCs() - Method in class de.unibi.techfak.InSilicoDicer.GUI.ISD
  Get the selected Precursors from JTree and put them into a PrecursorContainer
getSequence() - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.Precursor
getSimilarityTo() - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.Precursor
getSize() - Method in class de.unibi.techfak.InSilicoDicer.GUI.SimilarListModel
getSmoothWinSizeEx() - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.Operator
getSmoothWinSizeIn() - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.Operator
getStatus() - Method in interface de.unibi.techfak.InSilicoDicer.Actions.Action
  Returns the status of current Action
getStatus() - Method in class de.unibi.techfak.InSilicoDicer.Actions.AlignPrecursors.ClustalWWS
getStatus() - Method in class de.unibi.techfak.InSilicoDicer.Actions.AlignPrecursors.MA_ClustalW
getStatus() - Method in class de.unibi.techfak.InSilicoDicer.Actions.CalcConservation.CalcCons_Entropy
getStatus() - Method in class de.unibi.techfak.InSilicoDicer.Actions.CalcConservation.CalcCons_Entropy_seed
getStatus() - Method in class de.unibi.techfak.InSilicoDicer.Actions.FoldPrecursor.Fold_Vienna
getStatus() - Method in class de.unibi.techfak.InSilicoDicer.Actions.FoldPrecursor.RNAfoldWS
getStatus() - Method in class de.unibi.techfak.InSilicoDicer.Actions.ScorePrecursor.Score_Gaasterland
getStatus() - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.Operator
getTree() - Method in class de.unibi.techfak.InSilicoDicer.GUI.ISD
getWarnings() - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.PrecursorContainer
  Return a reference of internal warning list.

## I

ICalcConservationAction - Interface in de.unibi.techfak.InSilicoDicer.Actions.CalcConservation
IFoldingAction - Interface in de.unibi.techfak.InSilicoDicer.Actions.FoldPrecursor
ILocalAlign - Interface in de.unibi.techfak.InSilicoDicer.OperatingPackage.SearchMethods.SearchBySequence
IMultipleAlignAction - Interface in de.unibi.techfak.InSilicoDicer.Actions.AlignPrecursors
info - Variable in class de.unibi.techfak.InSilicoDicer.GUI.ISD
InfoFrame - Class in de.unibi.techfak.InSilicoDicer.GUI
InfoFrame(String, String) - Constructor for class de.unibi.techfak.InSilicoDicer.GUI.InfoFrame
  Creates the InfoFrame with a specified title and info String to show.
inputArea - Variable in class de.unibi.techfak.InSilicoDicer.GUI.ISD
inputConfirmButton - Variable in class de.unibi.techfak.InSilicoDicer.GUI.ISD
  Actions on top left
intrinsicPlot - Variable in class de.unibi.techfak.InSilicoDicer.GUI.ISD
  Profiles
intrinsicProfile - Variable in class de.unibi.techfak.InSilicoDicer.GUI.ISD
  Profiles
IPatternMatching - Interface in de.unibi.techfak.InSilicoDicer.OperatingPackage.SearchMethods.SearchByName
IScoreAction - Interface in de.unibi.techfak.InSilicoDicer.Actions.ScorePrecursor
ISD - Class in de.unibi.techfak.InSilicoDicer.GUI
  The class ISD builds a main Panel for the complete GUI WITHOUT JMenubar.
ISD() - Constructor for class de.unibi.techfak.InSilicoDicer.GUI.ISD
  Creates the MainPanel
ISD(String) - Constructor for class de.unibi.techfak.InSilicoDicer.GUI.ISD
  Creates the MainPanel;
ISD(JFrame) - Constructor for class de.unibi.techfak.InSilicoDicer.GUI.ISD
  Creates the MainPanel
ISD(JFrame, String) - Constructor for class de.unibi.techfak.InSilicoDicer.GUI.ISD
  Creates the MainPanel with Parent frame references
ISDHandler - Class in de.unibi.techfak.InSilicoDicer.GUI
ISDHandler(ISD) - Constructor for class de.unibi.techfak.InSilicoDicer.GUI.ISDHandler
  Constructor of ISDHandler
isU(String, int) - Method in class de.unibi.techfak.InSilicoDicer.Actions.ScorePrecursor.Score_Gaasterland
  Checks whether the substring starts with an 'U'.

## J

jcomponents - Variable in class de.unibi.techfak.InSilicoDicer.GUI.ISD
  List of all JComponents which should be deactivated, if any component is calculating

## L

LINE - Static variable in class de.unibi.techfak.InSilicoDicer.GUI.Plot
  public const for plot style LINE
loadPCs - Variable in class de.unibi.techfak.InSilicoDicer.GUI.ISD
  Actions on top left

## M

MA_ClustalW - Class in de.unibi.techfak.InSilicoDicer.Actions.AlignPrecursors
  Implementation of interface IMultipleAlignAction implements an alignments class using a locally installed clustalw tool.
MA_ClustalW() - Constructor for class de.unibi.techfak.InSilicoDicer.Actions.AlignPrecursors.MA_ClustalW
  Default Constructor - creates a new Status object and calls constructor MA_ClustalW(Status status)
MA_ClustalW(Status) - Constructor for class de.unibi.techfak.InSilicoDicer.Actions.AlignPrecursors.MA_ClustalW
  Constructor
maChooser - Variable in class de.unibi.techfak.InSilicoDicer.GUI.ISD
main(String[]) - Static method in class de.unibi.techfak.InSilicoDicer.GUI.ISD
main(String[]) - Static method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.Start_ISD
  Main method.
match(String, String) - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.SearchMethods.SearchByName.BMi
  wählt aus good-suffix-shift und bad-character-shift die maximale Verschiebung
match(String, String) - Method in interface de.unibi.techfak.InSilicoDicer.OperatingPackage.SearchMethods.SearchByName.IPatternMatching
  Executes exact Pattern Matching where the pattern is maybe a (part of) precursor description and the text is the desciption of a Precursor in a miRNA databse
maximum(int, int, int, int) - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.SearchMethods.SearchBySequence.SWalign
MenuHandler - Class in de.unibi.techfak.InSilicoDicer.GUI
MenuHandler() - Constructor for class de.unibi.techfak.InSilicoDicer.GUI.MenuHandler
MINIMUM_SEQUENCE_LENGTH - Static variable in class de.unibi.techfak.InSilicoDicer.OperatingPackage.PrecursorContainer
  Minimum sequence length, which is accepted.

## N

newContentPane - Variable in class de.unibi.techfak.InSilicoDicer.GUI.ISD
NUCLEICACID_CHARS - Static variable in class de.unibi.techfak.InSilicoDicer.OperatingPackage.PrecursorContainer
  small nucleo acid alphabet following IUPAC norm :

  code: description: A Adenosine C Cytidine G Guanine T Thymidine U Uracil N A G C T U (aNy)

## O

Operator - Class in de.unibi.techfak.InSilicoDicer.OperatingPackage
Operator() - Constructor for class de.unibi.techfak.InSilicoDicer.OperatingPackage.Operator
  DefaultConstructor, load the program properties from local directory.
Operator(URL) - Constructor for class de.unibi.techfak.InSilicoDicer.OperatingPackage.Operator
  Constructor, load the program properties from URL
OptionFrame - Class in de.unibi.techfak.InSilicoDicer.GUI
OptionFrame() - Constructor for class de.unibi.techfak.InSilicoDicer.GUI.OptionFrame
  Creates an Option Frame.
OptionHandler - Class in de.unibi.techfak.InSilicoDicer.GUI
OptionHandler(OptionFrame) - Constructor for class de.unibi.techfak.InSilicoDicer.GUI.OptionHandler

## P

paintComponent(Graphics) - Method in class de.unibi.techfak.InSilicoDicer.GUI.Plot
parent - Variable in class de.unibi.techfak.InSilicoDicer.GUI.ISD
  Reference of parentFrame
playground - Variable in class de.unibi.techfak.InSilicoDicer.GUI.ISD
Plot - Class in de.unibi.techfak.InSilicoDicer.GUI
Plot(ISD, Vector, int) - Constructor for class de.unibi.techfak.InSilicoDicer.GUI.Plot
  Creates a plot with the data to plot and a specified plot style (1 = line plot; 2 = bar plot)
plotFrame - Variable in class de.unibi.techfak.InSilicoDicer.GUI.ISD
plotPane - Variable in class de.unibi.techfak.InSilicoDicer.GUI.ISD
plots - Variable in class de.unibi.techfak.InSilicoDicer.GUI.ISD
Precursor - Class in de.unibi.techfak.InSilicoDicer.OperatingPackage
Precursor(String, String, String, String) - Constructor for class de.unibi.techfak.InSilicoDicer.OperatingPackage.Precursor
  Constructor : constructs a Precursor Object with id, description, sequence and folding.
Precursor(String, String, String) - Constructor for class de.unibi.techfak.InSilicoDicer.OperatingPackage.Precursor
  Constructor : constructs a new Precursor with id, description, sequence
PrecursorContainer - Class in de.unibi.techfak.InSilicoDicer.OperatingPackage
PrecursorContainer(Object[]) - Constructor for class de.unibi.techfak.InSilicoDicer.OperatingPackage.PrecursorContainer
  Constructor : constructs an PreCursorContainer from a Precursor Array
PrecursorContainer() - Constructor for class de.unibi.techfak.InSilicoDicer.OperatingPackage.PrecursorContainer
  Contructs an empty PrecursorContainer,
predictMatureMiRNAex(Vector) - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.Operator
  Predicts Position of mature miRNA on extrinsic data by... 1) finding start position of the window with MAXIMAL sum (relative to alignment) !
predictMatureMiRNAin(Vector) - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.Operator
  Predicts Position of mature miRNA on instrinsic data 1) calculating the avarage value of all precursors 2) finding the minimal value (relative to alignment) !
PrettyPrinter - Class in de.unibi.techfak.InSilicoDicer.OperatingPackage
PrettyPrinter() - Constructor for class de.unibi.techfak.InSilicoDicer.OperatingPackage.PrettyPrinter
printAlign(Vector, Vector) - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.PrettyPrinter
  Pretty-prints an alignment
printConservation(Vector, Vector, Vector) - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.PrettyPrinter
  Pretty-prints the conservation profile
printPrecursorContainer(PrecursorContainer) - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.PrettyPrinter
  Pretty-prints the content of a precursor container
printResults() - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.Evaluation
  Prints the results in a table.
printScores(Vector, Vector) - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.PrettyPrinter
  Pretty-prints the scores of each Precursor

## R

readFile(String) - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.Operator
  Reads a File
removeListDataListener(ListDataListener) - Method in class de.unibi.techfak.InSilicoDicer.GUI.SimilarListModel
RNAfoldWS - Class in de.unibi.techfak.InSilicoDicer.Actions.FoldPrecursor
  Implementation of interface IFoldingAction, which uses RNAfold as webservice running on BiBiServ
RNAfoldWS() - Constructor for class de.unibi.techfak.InSilicoDicer.Actions.FoldPrecursor.RNAfoldWS
  Default Constructor - creates a new Status object and call constructor RNAFoldWS(Status status)
RNAfoldWS(Status) - Constructor for class de.unibi.techfak.InSilicoDicer.Actions.FoldPrecursor.RNAfoldWS
  Constructor
root - Variable in class de.unibi.techfak.InSilicoDicer.GUI.ISD
run() - Method in class de.unibi.techfak.InSilicoDicer.GUI.StatusFrame
run_extrinsicAction() - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.Operator
  Actions & Predction with EXTRINSIC method
run_intrinsicAction() - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.Operator
  Action & Prediction with INTRINSIC method
run_intrinsicPlusAction() - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.Operator
  Action & Prediction with INTRINSIC extended method
run_ISD(String, String, int, PrecursorContainer, int) - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.Start_ISD
  Runs the prediction procedure

## S

Score_Gaasterland - Class in de.unibi.techfak.InSilicoDicer.Actions.ScorePrecursor
Score_Gaasterland() - Constructor for class de.unibi.techfak.InSilicoDicer.Actions.ScorePrecursor.Score_Gaasterland
ScoreAlign - Class in de.unibi.techfak.InSilicoDicer.Actions
ScoreAlign() - Constructor for class de.unibi.techfak.InSilicoDicer.Actions.ScoreAlign
scoreChooser - Variable in class de.unibi.techfak.InSilicoDicer.GUI.ISD
scroller - Variable in class de.unibi.techfak.InSilicoDicer.GUI.ISD
scrollTree - Variable in class de.unibi.techfak.InSilicoDicer.GUI.ISD
searchButton - Variable in class de.unibi.techfak.InSilicoDicer.GUI.ISD
  Actions on top left
selectAll - Variable in class de.unibi.techfak.InSilicoDicer.GUI.ISD
  Tree and around
selectedSimilarConfirmButton - Variable in class de.unibi.techfak.InSilicoDicer.GUI.ISD
  Actions on top left
serialVersionUID - Static variable in class de.unibi.techfak.InSilicoDicer.GUI.InfoFrame
serialVersionUID - Static variable in class de.unibi.techfak.InSilicoDicer.GUI.ISD
serialVersionUID - Static variable in class de.unibi.techfak.InSilicoDicer.GUI.OptionFrame
serialVersionUID - Static variable in class de.unibi.techfak.InSilicoDicer.GUI.Plot
serialVersionUID - Static variable in class de.unibi.techfak.InSilicoDicer.GUI.SplashFrame
serialVersionUID - Static variable in class de.unibi.techfak.InSilicoDicer.OperatingPackage.Operator
  set serial Version of current opbject
serialVersionUID - Static variable in class de.unibi.techfak.InSilicoDicer.OperatingPackage.Precursor
serialVersionUID - Static variable in class de.unibi.techfak.InSilicoDicer.OperatingPackage.PrecursorContainer
serialVersionUID - Static variable in class de.unibi.techfak.InSilicoDicer.OperatingPackage.SearchMethods.SearchBySequence.SWalign
  set serial Version of current opbject
setActionPCs(PrecursorContainer) - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.Operator
setAllSim(PrecursorContainer) - Method in class de.unibi.techfak.InSilicoDicer.GUI.ISD
setCalcconservationaction(ICalcConservationAction) - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.Operator
setCode(int) - Method in class de.unibi.techfak.InSilicoDicer.Actions.Status
setCutoff(int) - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.Operator
setDatabase(String) - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.Operator
  Set the choosen Database as Database to search in
setDescription(String) - Method in class de.unibi.techfak.InSilicoDicer.Actions.Status
setDescription(String) - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.Precursor
setEprofileAlignVec(Vector) - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.Operator
setEprofileConsVec(Vector) - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.Operator
setExCb(JCheckBox) - Method in class de.unibi.techfak.InSilicoDicer.GUI.OptionFrame
setExPspin(JSpinner) - Method in class de.unibi.techfak.InSilicoDicer.GUI.OptionFrame
setFile(File) - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.Operator
setFinished(boolean) - Method in class de.unibi.techfak.InSilicoDicer.Actions.Status
  Set finished flag of this status
setFolding(String) - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.Precursor
setFoldingaction(IFoldingAction) - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.Operator
setGenuineHash(Hashtable) - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.Operator
setId(String) - Method in class de.unibi.techfak.InSilicoDicer.Actions.Status
setId(String) - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.Precursor
setInCb(JCheckBox) - Method in class de.unibi.techfak.InSilicoDicer.GUI.OptionFrame
setInPspin(JSpinner) - Method in class de.unibi.techfak.InSilicoDicer.GUI.OptionFrame
setIplotScoreVec(Vector) - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.Operator
setIprofileAlignScoreVec(Vector) - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.Operator
setIprofileAlignVec(Vector) - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.Operator
setJComponentEnabled(boolean) - Method in class de.unibi.techfak.InSilicoDicer.GUI.ISD
  Enables or Disables all jcomponent components
setLocalalign(ILocalAlign) - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.PrecursorContainer
setMatureSize(int) - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.Operator
setMatureSizeSpin(JSpinner) - Method in class de.unibi.techfak.InSilicoDicer.GUI.OptionFrame
setMethod(String) - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.Operator
setMirnaPOSinALIGN(int) - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.Operator
setMirnaPOSinPC(int[]) - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.Operator
setMultiplealignaction(IMultipleAlignAction) - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.Operator
setPath(String) - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.Operator
setPatternmatching(IPatternMatching) - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.PrecursorContainer
setPrecCursorContainer(PrecursorContainer) - Method in class de.unibi.techfak.InSilicoDicer.GUI.SimilarListModel
  Set a new PreCursorContainer for this SimilarListModel
setPropertieserties(Properties) - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.Operator
setScoreaction(IScoreAction) - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.Operator
setSequence(String) - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.Precursor
setSimilarityTo(int) - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.Precursor
setSmoothWinSizeEx(int) - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.Operator
setSmoothWinSizeIn(int) - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.Operator
setStatus(Status) - Method in interface de.unibi.techfak.InSilicoDicer.Actions.Action
  Set the status of current Action
setStatus(Status) - Method in class de.unibi.techfak.InSilicoDicer.Actions.AlignPrecursors.ClustalWWS
setStatus(Status) - Method in class de.unibi.techfak.InSilicoDicer.Actions.AlignPrecursors.MA_ClustalW
setStatus(Status) - Method in class de.unibi.techfak.InSilicoDicer.Actions.CalcConservation.CalcCons_Entropy
setStatus(Status) - Method in class de.unibi.techfak.InSilicoDicer.Actions.CalcConservation.CalcCons_Entropy_seed
setStatus(Status) - Method in class de.unibi.techfak.InSilicoDicer.Actions.FoldPrecursor.Fold_Vienna
setStatus(Status) - Method in class de.unibi.techfak.InSilicoDicer.Actions.FoldPrecursor.RNAfoldWS
setStatus(Status) - Method in class de.unibi.techfak.InSilicoDicer.Actions.ScorePrecursor.Score_Gaasterland
setStatus(int, String) - Method in class de.unibi.techfak.InSilicoDicer.Actions.Status
  Set Status code and Status description of current Status
setStatus(Status) - Method in class de.unibi.techfak.InSilicoDicer.GUI.StatusFrame
  Set the Status of current StatusFrame
setStatus(Status) - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.Operator
setText(String) - Method in class de.unibi.techfak.InSilicoDicer.GUI.StatusFrame
  Set the StatusText (without changing the status) of current StatusFrame
setTree(JTree) - Method in class de.unibi.techfak.InSilicoDicer.GUI.ISD
show_extrinsicResults() - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.Operator
  Create output for EXTRINSIC method
show_intrinsicPlusResults() - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.Operator
  Create output of INTRINSIC extended method
show_intrinsicResults() - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.Operator
  Create output of INTRINSIC method
showErrorDialog(String) - Method in class de.unibi.techfak.InSilicoDicer.GUI.ISD
showInfoDialog(String) - Method in class de.unibi.techfak.InSilicoDicer.GUI.ISD
showWarnDialog(String) - Method in class de.unibi.techfak.InSilicoDicer.GUI.ISD
similarList - Variable in class de.unibi.techfak.InSilicoDicer.GUI.ISD
similarListModel - Variable in class de.unibi.techfak.InSilicoDicer.GUI.ISD
SimilarListModel - Class in de.unibi.techfak.InSilicoDicer.GUI
  Implementation of Interface ListModel for using as Similar JList component.
SimilarListModel() - Constructor for class de.unibi.techfak.InSilicoDicer.GUI.SimilarListModel
Smoother - Class in de.unibi.techfak.InSilicoDicer.Actions
Smoother(int) - Constructor for class de.unibi.techfak.InSilicoDicer.Actions.Smoother
  Contructs a Smoother with a defined smooth window size.
smoothValues(Vector) - Method in class de.unibi.techfak.InSilicoDicer.Actions.Smoother
  Smoothes all kind kind of values.
splashframe - Variable in class de.unibi.techfak.InSilicoDicer.GUI.ISD
SplashFrame - Class in de.unibi.techfak.InSilicoDicer.GUI
  Generates a SplashScreen before InSilicoDicer starts and shows a progressbar while the DataBase is loaded.
SplashFrame() - Constructor for class de.unibi.techfak.InSilicoDicer.GUI.SplashFrame
  Constructor of SplashScreen
SPLASHIMAGE - Static variable in class de.unibi.techfak.InSilicoDicer.GUI.SplashFrame
  location of the splashimage
split - Variable in class de.unibi.techfak.InSilicoDicer.GUI.ISD
Start_ISD - Class in de.unibi.techfak.InSilicoDicer.OperatingPackage
Start_ISD() - Constructor for class de.unibi.techfak.InSilicoDicer.OperatingPackage.Start_ISD
Status - Class in de.unibi.techfak.InSilicoDicer.Actions
  Status class, a central component where all Action should store their status code (+description).
Status() - Constructor for class de.unibi.techfak.InSilicoDicer.Actions.Status
  Default Constructor creates an empty status object
Status(int) - Constructor for class de.unibi.techfak.InSilicoDicer.Actions.Status
  Constructor, create a new Status object with given code
Status(int, String) - Constructor for class de.unibi.techfak.InSilicoDicer.Actions.Status
  Constructor,create a new Status object with given code and description
StatusFrame - Class in de.unibi.techfak.InSilicoDicer.GUI
  On Top Frame, which displays Status information, via TextOutput and ProgressBar
StatusFrame(String, Status) - Constructor for class de.unibi.techfak.InSilicoDicer.GUI.StatusFrame
  Constructor StatusFrame
StatusFrame(Container, String, Status) - Constructor for class de.unibi.techfak.InSilicoDicer.GUI.StatusFrame
  Constructor StatusFrame
StatusFrame(String, String) - Constructor for class de.unibi.techfak.InSilicoDicer.GUI.StatusFrame
  Constructor StatusFrame
StatusFrame(Container, String, String) - Constructor for class de.unibi.techfak.InSilicoDicer.GUI.StatusFrame
  Constructor StatuFrame
SWalign - Class in de.unibi.techfak.InSilicoDicer.OperatingPackage.SearchMethods.SearchBySequence
SWalign() - Constructor for class de.unibi.techfak.InSilicoDicer.OperatingPackage.SearchMethods.SearchBySequence.SWalign
swBuildMatrix(int, int, int, String, String) - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.SearchMethods.SearchBySequence.SWalign
swFindMaxScore(int[][], String, String) - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.SearchMethods.SearchBySequence.SWalign

## T

toFasta(boolean) - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.PrecursorContainer
  Returns a String containing all Precursor information in Fasta format with or without secundary structure information
toString() - Method in class de.unibi.techfak.InSilicoDicer.Actions.Status
toString() - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.Precursor
toString() - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.PrecursorContainer
tree - Variable in class de.unibi.techfak.InSilicoDicer.GUI.ISD
treeModel - Variable in class de.unibi.techfak.InSilicoDicer.GUI.ISD

## W

warn() - Method in class de.unibi.techfak.InSilicoDicer.OperatingPackage.PrecursorContainer
win - Variable in class de.unibi.techfak.InSilicoDicer.Actions.ScorePrecursor.Score_Gaasterland

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