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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