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# Serialized Form

Package de.unibi.techfak.InSilicoDicer.GUI

Class de.unibi.techfak.InSilicoDicer.GUI.InfoFrame extends javax.swing.JFrame implements Serializable

serialVersionUID: 1L

Class de.unibi.techfak.InSilicoDicer.GUI.ISD extends javax.swing.JPanel implements Serializable

serialVersionUID: 1L

Serialized Fields

### handler

    ISDHandler handler

  private instance of implementing ActionListener for main GUI class

### jcomponents

    java.util.List<E> jcomponents

  List of all JComponents which should be deactivated, if any component is calculating

### splashframe

    javax.swing.JFrame splashframe

### loadPCs

    javax.swing.JButton loadPCs

  Actions on top left

### exampleButton

    javax.swing.JButton exampleButton

  Actions on top left

### inputConfirmButton

    javax.swing.JButton inputConfirmButton

  Actions on top left

### searchButton

    javax.swing.JButton searchButton

  Actions on top left

### allSimilarConfirmButton

    javax.swing.JButton allSimilarConfirmButton

  Actions on top left

### selectedSimilarConfirmButton

    javax.swing.JButton selectedSimilarConfirmButton

  Actions on top left

### inputArea

    javax.swing.JTextArea inputArea

### similarList

    javax.swing.JList similarList

### similarListModel

    SimilarListModel similarListModel

### allSim

    PrecursorContainer allSim

### extrinsicProfile

    javax.swing.JButton extrinsicProfile

  Profiles

### intrinsicProfile

    javax.swing.JButton intrinsicProfile

  Profiles

### intrinsicPlot

    javax.swing.JButton intrinsicPlot

  Profiles

### selectAll

    javax.swing.JButton selectAll

  Tree and around

### clear

    javax.swing.JButton clear

  Tree and around

### tree

    javax.swing.JTree tree

### parent

    javax.swing.JFrame parent

  Reference of parentFrame

### plots

    javax.swing.JTabbedPane plots

### plotFrame

    javax.swing.JInternalFrame plotFrame

### newContentPane

    javax.swing.JComponent newContentPane

### scroller

    javax.swing.JScrollPane scroller

### plotPane

    javax.swing.JPanel plotPane

### playground

    javax.swing.JSplitPane playground

### split

    javax.swing.JSplitPane split

### cutoffSpinner

    javax.swing.JSpinner cutoffSpinner

### dbVector

    java.util.Vector<E> dbVector

### chooseDB

    javax.swing.JComboBox chooseDB

### info

    javax.swing.JLabel info

### treeModel

    javax.swing.tree.DefaultTreeModel treeModel

### root

    javax.swing.tree.DefaultMutableTreeNode root

### scrollTree

    javax.swing.JScrollPane scrollTree

### maChooser

    javax.swing.JComboBox maChooser

### consChooser

    javax.swing.JComboBox consChooser

### foldChooser

    javax.swing.JComboBox foldChooser

### scoreChooser

    javax.swing.JComboBox scoreChooser

Class de.unibi.techfak.InSilicoDicer.GUI.OptionFrame extends javax.swing.JFrame implements Serializable

serialVersionUID: 1L

Serialized Fields

### inPspin

    javax.swing.JSpinner inPspin

### exPspin

    javax.swing.JSpinner exPspin

### matureSizeSpin

    javax.swing.JSpinner matureSizeSpin

### inCb

    javax.swing.JCheckBox inCb

### exCb

    javax.swing.JCheckBox exCb

Class de.unibi.techfak.InSilicoDicer.GUI.Plot extends javax.swing.JPanel implements Serializable

serialVersionUID: 1L

Serialized Fields

### log

    org.apache.log4j.Logger log

  private instance of Logger object

### oi

    Operator oi

  private reference of an operator

### isd

    ISD isd

  private reference of central ISD

### plotVec

    java.util.Vector<E> plotVec

  unkown

### plotStyle

    int plotStyle

  unkown

### data_ary

    double[] data_ary

  unknown

### inset

    int inset

  unknown

Class de.unibi.techfak.InSilicoDicer.GUI.SplashFrame extends javax.swing.JFrame implements Serializable

serialVersionUID: 1L

Serialized Fields

### jprogressbar

    javax.swing.JProgressBar jprogressbar

  JProgresBar

### splashimage

    javax.swing.JPanel splashimage

  JPanel for the splashimage;

Class de.unibi.techfak.InSilicoDicer.GUI.StatusFrame extends javax.swing.JFrame implements Serializable

serialVersionUID: 1L

Serialized Fields

### log

    org.apache.log4j.Logger log

  private instance of a Logger object

### running

    boolean running

  boolean flag for running information

### status

    Status status

  private reference of a Status object

### statustext

    javax.swing.JLabel statustext

  private reference of JLabel for representing Status object information or

### progressbar

    javax.swing.JProgressBar progressbar

  private reference of a JProgressbar, can be modefied via get method

Package de.unibi.techfak.InSilicoDicer.OperatingPackage

Class de.unibi.techfak.InSilicoDicer.OperatingPackage.Operator extends java.lang.Object implements Serializable

serialVersionUID: 1L

Serialized Fields

### log

    org.apache.log4j.Logger log

  private instance of an Logger

### properties

    java.util.Properties properties

  Properties which contains all properties set by configuration

### status

    Status status

  private instance of a Status object

### calcconservationaction

    ICalcConservationAction calcconservationaction

  private instance of currently used calccons class

### foldingaction

    IFoldingAction foldingaction

  private instance of currently used folding class

### multiplealignaction

    IMultipleAlignAction multiplealignaction

  private instacne of currently used ma class

### scoreaction

    IScoreAction scoreaction

  private instacne of currently used scoring class

### file

    java.io.File file

  private instance of file - used for loading pc's from local file

### path

    java.lang.String path

### method

    java.lang.String method

### matureSize

    int matureSize

### database

    PrecursorContainer database

### cutoff

    int cutoff

### smoothWinSizeEx

    int smoothWinSizeEx

### smoothWinSizeIn

    int smoothWinSizeIn

### mScore

    int mScore

### rpScore

    int rpScore

### indelScore

    int indelScore

### seedStart

    int seedStart

### seedEnd

    int seedEnd

### seedWeight

    double seedWeight

### mirnaPOSinALIGN

    int mirnaPOSinALIGN

### mirnaPOSinPC

    int[] mirnaPOSinPC

### genuineHash

    java.util.Hashtable<K,V> genuineHash

### actionPCs

    PrecursorContainer actionPCs

### iplotScoreVec

    java.util.Vector<E> iplotScoreVec

### iprofileAlignScoreVec

    java.util.Vector<E> iprofileAlignScoreVec

### iprofileAlignVec

    java.util.Vector<E> iprofileAlignVec

### eprofileConsVec

    java.util.Vector<E> eprofileConsVec

### eprofileAlignVec

    java.util.Vector<E> eprofileAlignVec

Class de.unibi.techfak.InSilicoDicer.OperatingPackage.Precursor extends java.lang.Object implements Serializable

serialVersionUID: 1L

Serialized Fields

### id

    java.lang.String id

  id of current Precursor

### description

    java.lang.String description

  description of current Precursor

### sequence

    java.lang.String sequence

  sequence of current Precursor

### folding

    java.lang.String folding

  secundary structure (dot bracket) of current Precursor

### similarityTo

    int similarityTo

  similarity of current structure

Class de.unibi.techfak.InSilicoDicer.OperatingPackage.PrecursorContainer extends java.util.Vector<Precursor> implements Serializable

serialVersionUID: 1L

Serialized Fields

### pattern

    java.util.regex.Pattern pattern

  A pattern for searching NuclecAcid chars

### warnings

    java.util.List<E> warnings

  A List containing warning occurred during parsing FASTA/Vienna format into a PreCursor

### log

    org.apache.log4j.Logger log

  private instance of a Logger

### oi

    Operator oi

  private instance of the central operator

### localalign

    ILocalAlign localalign

  private reference of an ILocalAlign implementation

### patternmatching

    IPatternMatching patternmatching

  private reference of am IPatternMatching implementation

Class de.unibi.techfak.InSilicoDicer.OperatingPackage.Start_ISD extends javax.swing.JApplet implements Serializable

Package de.unibi.techfak.InSilicoDicer.OperatingPackage.SearchMethods.SearchBySequence

Class de.unibi.techfak.InSilicoDicer.OperatingPackage.SearchMethods.SearchBySequence.SWalign extends java.lang.Object implements Serializable

serialVersionUID: 1L

Serialized Fields

### log

    org.apache.log4j.Logger log

### matrix

    int[][] matrix

### score

    int score

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