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