Overview

Package

Class

Tree

Deprecated

Index

Help

'STRAP:multiple sequence alignments '

PREV NEXT

FRAMES NO FRAMES

Serialized Form

Package charite.christo

Class charite.christo.ButColor extends ChButton implements Serializable

Serialized Fields

_colored

java.lang.Object _colored

_default

java.awt.Color _default

_reset

java.awt.Color _reset

_opt

long _opt

_slider

javax.swing.JSlider _slider

_cs

javax.swing.JColorChooser _cs

_panel

javax.swing.JComponent _panel

Class charite.christo.ChButton extends javax.swing.JButton implements Serializable

Serialized Fields

_contains

boolean _contains

_handleEvt

boolean _handleEvt

_tabSelected

boolean _tabSelected

_superPaint

boolean _superPaint

_typ

char _typ

_mX

int _mX

_mY

int _mY

_modi

int _modi

_height

int _height

_mc

int _mc

_fromTo

int[] _fromTo

_mnemonic

int _mnemonic

_opt

long _opt

MAPCP

java.util.Map<K,V> MAPCP

WEAK_REF

java.lang.Object WEAK_REF

_oIcon

java.lang.Object _oIcon

_actPerfWhen

long _actPerfWhen

LI

EvAdapter LI

_run

java.lang.Runnable _run

_radio1

javax.swing.AbstractButton _radio1

_cb1

javax.swing.AbstractButton _cb1

_propClass

java.lang.Class<T> _propClass

_propId

java.lang.String _propId

Class charite.christo.ChButton.MItem extends javax.swing.JMenuItem implements Serializable

Serialized Fields

MAPCP

java.util.Map<K,V> MAPCP

_init

boolean _init

Class charite.christo.ChCombo extends javax.swing.JComboBox implements Serializable

Serialized Fields

MAPCP

java.util.Map<K,V> MAPCP

_data

java.lang.Object _data

_options

long _options

_wasPainted

boolean _wasPainted

_handleEvent

boolean _handleEvent

_lastCount

int _lastCount

_mc_atPaint

int _mc_atPaint

_pan

javax.swing.JComponent _pan

_panHSnf

javax.swing.JComponent _panHSnf

_mc

int _mc

_clas

java.lang.Class<T> _clas

_id

java.lang.String _id

_containsClasses

boolean _containsClasses

_interface

java.lang.Class<T> _interface

labToString

ScrollLabel labToString

_mapSharedInstances

java.util.Map<K,V> _mapSharedInstances

Class charite.christo.ChFile extends java.io.File implements Serializable

Serialized Fields

_unknownDrive

boolean _unknownDrive

_toS

java.lang.String _toS

_name

java.lang.String _name

_hc

int _hc

Class charite.christo.ChFileChooser extends javax.swing.JFileChooser implements Serializable

Serialized Fields

_maps

java.util.Map<K,V>[] _maps

KEY

java.lang.Object KEY

_id

java.lang.String _id

_opt

long _opt

_context

FilePopup _context

_filters

Customize _filters

_vSelected

java.util.Set<E> _vSelected

_stringMatch

DialogStringMatch _stringMatch

_r4sb

java.lang.Runnable _r4sb

_lm

long _lm

Class charite.christo.ChFrame extends javax.swing.JFrame implements Serializable

Serialized Fields

_disposed

boolean _disposed

_shown

boolean _shown

_imgExcept

boolean _imgExcept

_opts

long _opts

Class charite.christo.ChJCheckBox extends javax.swing.JCheckBox implements Serializable

Serialized Fields

_but0

java.lang.Object _but0

_radio

boolean _radio

Class charite.christo.ChJList extends javax.swing.JList implements Serializable

Serialized Fields

_selMC

int _selMC

_opt

long _opt

_isInit

boolean _isInit

_miHelp

ChButton _miHelp

_miCtrl

ChButton _miCtrl

_popup

javax.swing.JPopupMenu _popup

MAPCP

java.util.Map<K,V> MAPCP

_list

java.util.List<E> _list

_iMouse

int _iMouse

Class charite.christo.ChJMenu extends javax.swing.JMenu implements Serializable

Serialized Fields

_b

ChButton _b

_isInit

boolean _isInit

_isSel

boolean _isSel

_awtMenu

java.awt.Menu _awtMenu

_awtMenuHC

long _awtMenuHC

_rplcMenuItems

java.lang.String[][] _rplcMenuItems

_oIcon

java.lang.Object _oIcon

Class charite.christo.ChJMenuBar extends javax.swing.JMenuBar implements Serializable

Class charite.christo.ChJScrollPane extends javax.swing.JScrollPane implements Serializable

Serialized Fields

_opt

long _opt

_c

java.lang.Object _c

_prefH

int _prefH

_countPaintHook

int _countPaintHook

_painted

int _painted

_d

java.awt.Dimension _d

_point

java.awt.Point _point

_jPopup

javax.swing.JPopupMenu _jPopup

Class charite.christo.ChJTable extends javax.swing.JTable implements Serializable

Serialized Fields

_headerTT

java.lang.String[] _headerTT

_initialized

boolean _initialized

_opt

long _opt

_dragRowSrc

java.lang.Object _dragRowSrc

_dragRowCols

int[] _dragRowCols

_mouseHeaderCol

int _mouseHeaderCol

_renderer

javax.swing.table.TableCellRenderer _renderer

Class charite.christo.ChJTextPane extends javax.swing.JTextPane implements Serializable

Serialized Fields

_tools

ChTextComponents _tools

Class charite.christo.ChJTree extends javax.swing.JTree implements Serializable

Serialized Fields

_painted

boolean _painted

_options

long _options

WEAK_REF

java.lang.Object WEAK_REF

vExpanded

java.util.Set<E> vExpanded

selectionPaths

javax.swing.tree.TreePath[] selectionPaths

mapPath

java.util.WeakHashMap<K,V> mapPath

_sb

BA _sb

_needsUpdate

boolean _needsUpdate

_threadUpdate

java.lang.Thread _threadUpdate

_sumChildsHC

long _sumChildsHC

Class charite.christo.ChListSelectionModel extends javax.swing.DefaultListSelectionModel implements Serializable

Serialized Fields

_refM

java.lang.Object _refM

set

java.util.Set<E> set

_anchorIndex

int _anchorIndex

_leadIndex

int _leadIndex

Class charite.christo.ChPanel extends javax.swing.JPanel implements Serializable

Serialized Fields

MAPCP

java.util.Map<K,V> MAPCP

WEAK_REF

java.lang.Object WEAK_REF

duration

long[] duration

Class charite.christo.ChRenderer extends javax.swing.border.AbstractBorder implements Serializable

Serialized Fields

LI

EvAdapter LI

_opt

int _opt

_origRend

java.lang.Object _origRend

_vSel

java.util.Collection<E> _vSel

_cbEd

javax.swing.AbstractButton _cbEd

_label

ChButton _label

_tf

ChTextField _tf

_rowEd

int _rowEd

_colEd

int _colEd

_value

java.lang.Object _value

_vCellEdLi

java.util.List<E> _vCellEdLi

_componentEd

java.awt.Component _componentEd

_component

java.awt.Component _component

_enable

IsEnabled _enable

_rendOpt

long[] _rendOpt

Class charite.christo.ChScrollBar extends javax.swing.JScrollBar implements Serializable

Serialized Fields

_hasSelection

boolean _hasSelection

_selII

int[] _selII

_selScale

int _selScale

_selBoxH

int _selBoxH

_warnTrack

int _warnTrack

_warnNoBut

int _warnNoBut

_selColor

java.awt.Color[] _selColor

_lock

long _lock

_rTrack

java.awt.Rectangle _rTrack

_rThumb

java.awt.Rectangle _rThumb

_method

java.lang.Object[] _method

_mUI

java.lang.Object _mUI

Class charite.christo.ChSlider extends javax.swing.JSlider implements Serializable

Serialized Fields

command

java.lang.String command

modi

int modi

labels

java.lang.String[] labels

lastIsEnabled

boolean lastIsEnabled

_clas

java.lang.Class<T> _clas

_id

java.lang.String _id

Class charite.christo.ChTableLayout extends ChPanel implements Serializable

Serialized Fields

_dragged

boolean _dragged

likeDivider

boolean likeDivider

likeDividerWhenMoved

boolean likeDividerWhenMoved

_resizing

boolean _resizing

_resizingCol

int _resizingCol

_tDivider

java.lang.Runnable _tDivider

_v

java.util.ArrayList<E> _v

_t

ChJTable _t

_opt

long _opt

H_BORDER

javax.swing.border.Border H_BORDER

BORDER

javax.swing.border.Border BORDER

msgUndock

java.lang.String[] msgUndock

selectedColumn

int selectedColumn

LABEL

ChButton LABEL

labelCol

int labelCol

columnUnderMouse

int columnUnderMouse

THREAD_LOCATION

java.lang.Runnable THREAD_LOCATION

tm

javax.swing.table.TableModel tm

paintedOrEvent

boolean paintedOrEvent

needs_setPrefAsIs

boolean needs_setPrefAsIs

RESIZABLE

boolean[] RESIZABLE

_d

java.awt.Dimension _d

Class charite.christo.ChTableModel extends javax.swing.table.AbstractTableModel implements Serializable

Serialized Fields

_options

long _options

_editable

boolean[] _editable

_columnNames

java.lang.String[] _columnNames

_rowData

java.lang.Object _rowData

_refTable

java.lang.Object _refTable

Class charite.christo.ChTabPane extends ChPanel implements Serializable

Serialized Fields

KEY_WHEN

java.lang.Object KEY_WHEN

KEY_TAB

java.lang.Object KEY_TAB

_collapseC

CollapseComponent _collapseC

_v

java.util.List<E> _v

_vFocus

java.util.List<E> _vFocus

_panTabs

javax.swing.JComponent _panTabs

_pTabs

javax.swing.JComponent _pTabs

_butPrev

javax.swing.JComponent _butPrev

_leftSide

boolean _leftSide

_panTabsPar

javax.swing.JComponent _panTabsPar

_jlHisto

javax.swing.JComponent _jlHisto

_bSelected

javax.swing.JComponent _bSelected

_pCenter

java.lang.Object _pCenter

_insets

java.awt.Insets _insets

Class charite.christo.ChTextArea extends javax.swing.JTextArea implements Serializable

Serialized Fields

_isPainting

boolean _isPainting

_isPainted

boolean _isPainted

_endV

boolean _endV

_v

java.util.List<E> _v

_isRunning

boolean _isRunning

_colorPos

int _colorPos

_color

java.awt.Color _color

_tools

ChTextComponents _tools

Class charite.christo.ChTextField extends javax.swing.JTextField implements Serializable

Serialized Fields

_defaultText

java.lang.String _defaultText

_painting

boolean _painting

_painted

boolean _painted

_contentType

java.lang.Object _contentType

_tools

ChTextComponents _tools

Class charite.christo.ChTextView extends ChPanel implements Serializable

Serialized Fields

_regionFromTo

int[] _regionFromTo

_modiCount

int _modiCount

_lineNumbers

int _lineNumbers

_maxLineWidth

int _maxLineWidth

_posClicked

int _posClicked

_regionFrom

int _regionFrom

_regionTo

int _regionTo

_refText

java.lang.Object _refText

_ba

BA _ba

_region

TextMatches _region

_tools

ChTextComponents _tools

_baMc

long _baMc

_file

java.io.File _file

_gpsMC

int _gpsMC

_endV

boolean _endV

Class charite.christo.DialogExecuteOnFile extends javax.swing.JPanel implements Serializable

Serialized Fields

_argv

java.lang.String[] _argv

_tf

ChTextField _tf

_combo

ChCombo _combo

_radioTf

java.lang.Object[] _radioTf

_cust

Customize _cust

_f

ChFrame _f

Class charite.christo.FreeMemoryBar extends ChButton implements Serializable

Serialized Fields

free

long free

max

long max

total

long total

_started

boolean _started

Class charite.christo.GraphSun extends javax.swing.JPanel implements Serializable

Serialized Fields

vNodes

UniqueList<T> vNodes

vEdges

UniqueList<T> vEdges

maxDistance

double maxDistance

minDistance

double minDistance

sliderScale

ChSlider sliderScale

butLines

javax.swing.JComponent butLines

butImage

javax.swing.JComponent butImage

buttonBar

javax.swing.JComponent buttonBar

Class charite.christo.HtmlDocEditorKit extends javax.swing.text.html.HTMLEditorKit implements Serializable

Serialized Fields

_packages

java.lang.String[] _packages

_origFactory

javax.swing.text.ViewFactory _origFactory

Class charite.christo.RenameFile extends javax.swing.JPanel implements Serializable

Serialized Fields

_ta

ChTextArea _ta

_taHeader

ChTextArea _taHeader

_labMsg

ChTextView _labMsg

Class charite.christo.RendererNumberAsOval extends javax.swing.JComponent implements Serializable

Serialized Fields

_scale

double _scale

_offset

double _offset

_value

double _value

_type

int _type

_error

java.lang.String _error

_refO

java.lang.Object _refO

Class charite.christo.ScrollLabel extends javax.swing.JPanel implements Serializable

Serialized Fields

_txt

java.lang.String _txt

_lastX

int _lastX

_scrollX

int _scrollX

_lastWhen

long _lastWhen

Package charite.christo.protein

Class charite.christo.protein.DAS extends ChRenderer implements Serializable

Class charite.christo.protein.Protein3d extends ChPanel implements Serializable

Serialized Fields

LI

EvAdapter LI

_vDisplayed

UniqueList<T> _vDisplayed

vNW

UniqueList<T> vNW

vNE

UniqueList<T> vNE

_sliderDistDna

javax.swing.JSlider _sliderDistDna

_durationPaint

int _durationPaint

_meanDuration

int _meanDuration

_size

int _size

_countLines

int _countLines

_ox

int _ox

_oy

int _oy

_prevx

int _prevx

_prevy

int _prevy

_pMC

int _pMC

_thumbY

int[] _thumbY

_whenKeyEvent

long _whenKeyEvent

_dxMean

double _dxMean

_dyMean

double _dyMean

_dzMean

double _dzMean

_mzT

double _mzT

_scale

float _scale

_xyzCursor

float[] _xyzCursor

_runLayout

java.lang.Runnable _runLayout

_tmat

Matrix3D _tmat

_m3D

Matrix3D _m3D

MOUSE

charite.christo.protein.Protein3d.Line MOUSE

MOUS_HET

charite.christo.protein.Protein3d.Line MOUS_HET

_autoRotating

boolean _autoRotating

_dragged

boolean _dragged

_isWheel

boolean _isWheel

_notYetScaled

boolean _notYetScaled

_mouseIn

boolean _mouseIn

_hideDistantDNS

boolean _hideDistantDNS

_comboBio

ChCombo _comboBio

_togBioColor

ChButton _togBioColor

_cbGui

ChButton _cbGui

_cbDetailBio

ChButton _cbDetailBio

_dataBio

java.lang.Object[][][] _dataBio

_tableBio

ChJTable _tableBio

PAN_SE

javax.swing.JComponent PAN_SE

_transp

javax.swing.JComponent[] _transp

_pp

java.lang.Object _pp

mouseMsgRect

java.awt.Rectangle mouseMsgRect

mouseMsg

java.lang.String[] mouseMsg

mouseMsgX

int[] mouseMsgX

mouseMsgW

int[] mouseMsgW

mouseMsgRun

java.lang.Runnable mouseMsgRun

_lastG

java.awt.Graphics _lastG

tipLast

java.lang.String tipLast

Class charite.christo.protein.ProteinLabel extends ChButton implements Serializable

Serialized Fields

_opt

long _opt

_doingDnd

boolean _doingDnd

Class charite.christo.protein.ShadingAA extends ChCombo implements Serializable

Package charite.christo.strap

Class charite.christo.strap.AbstractAlignmentProject extends AbstractDialogJPanel implements Serializable

Serialized Fields

_scrollPane

javax.swing.JScrollPane _scrollPane

_urls

java.net.URL[] _urls

_vAlignments

UniqueList<T> _vAlignments

Class charite.christo.strap.AbstractDialogJPanel extends ChPanel implements Serializable

Serialized Fields

_disposed

boolean _disposed

Class charite.christo.strap.AbstractDialogJTabbedPane extends javax.swing.JTabbedPane implements Serializable

Serialized Fields

_disposed

boolean _disposed

Class charite.christo.strap.AbstractDialogPredict extends AbstractDialogJTabbedPane implements Serializable

Serialized Fields

_comboClass

ChCombo _comboClass

_cbClone

javax.swing.AbstractButton _cbClone

_dClass

java.lang.Class<T> _dClass

_iClass

java.lang.Class<T> _iClass

_predictWhat

java.lang.String _predictWhat

_tp

javax.swing.JTabbedPane _tp

_ppl

ProteinList _ppl

_resultNum

int _resultNum

_predictor

PredictionFromAminoacidSequence _predictor

Class charite.christo.strap.AbstractDialogPredict.Result extends javax.swing.JPanel implements Serializable

Serialized Fields

_thread

java.lang.Thread _thread

_pp

Protein[] _pp

_finished

boolean _finished

_failed

boolean _failed

_predictor

PredictionFromAminoacidSequence _predictor

_lab

ChButton _lab

_tog3D

ChButton _tog3D

_togSB

ChButton _togSB

_vSel

UniqueList<T> _vSel

Class charite.christo.strap.ActivateDeactivate extends ChPanel implements Serializable

Serialized Fields

comboKeys

ChCombo comboKeys

choice

ChCombo choice

togFilter

ChButton togFilter

tfFilter

ChTextField tfFilter

hasResidueAnnotations

ContextObjects hasResidueAnnotations

Class charite.christo.strap.AddAnnotation extends javax.swing.JPanel implements Serializable

Serialized Fields

_cbVar

javax.swing.JComponent _cbVar

_cbSame

javax.swing.JComponent _cbSame

_butIns

javax.swing.JComponent _butIns

LABEL

ChButton LABEL

_jtf

ChTextField _jtf

_refAA

java.lang.Object[] _refAA

_jlValues

ChJList _jlValues

_vValues

javax.swing.DefaultListModel _vValues

_comboKeys

ChJList _comboKeys

_v

java.lang.String _v

Class charite.christo.strap.ComboKeys extends javax.swing.DefaultComboBoxModel implements Serializable

Serialized Fields

mainKeys

java.lang.Object[] mainKeys

Class charite.christo.strap.Dialog_bl2seq extends AbstractDialogJTabbedPane implements Serializable

Serialized Fields

_comboX

ProteinCombo _comboX

_comboY

ProteinCombo _comboY

Class charite.christo.strap.Dialog3DViewer extends AbstractDialogJPanel implements Serializable

Serialized Fields

comboClass

ChCombo comboClass

choiceProtein

ChCombo choiceProtein

Class charite.christo.strap.DialogAlign extends AbstractDialogJTabbedPane implements Serializable

Serialized Fields

_cbSecStru

javax.swing.AbstractButton _cbSecStru

_radio

javax.swing.AbstractButton[] _radio

togProfile

ChButton[] togProfile

_butInsertRB

ChButton _butInsertRB

_pC

javax.swing.JComponent[] _pC

_pMain

javax.swing.JComponent _pMain

_taResSel

ChTextArea _taResSel

_taProfile

ChTextArea[] _taProfile

_pList

ProteinList _pList

_comboClass

ChCombo _comboClass

_count

int _count

_pCnow

javax.swing.JComponent _pCnow

Class charite.christo.strap.DialogAlignOneToAll extends AbstractDialogJTabbedPane implements Serializable

Serialized Fields

_comboP

ProteinCombo _comboP

_listP

ProteinList _listP

_comboC

ChCombo _comboC

Class charite.christo.strap.DialogAlignOneToAllResult extends javax.swing.table.DefaultTableModel implements Serializable

Serialized Fields

_p

Protein _p

_pp

Protein[] _pp

_progress

javax.swing.JProgressBar _progress

_clazz

java.lang.Object _clazz

_disposed

boolean _disposed

LI

EvAdapter LI

_cbSortScore

ChButton _cbSortScore

_cbSelect

ChButton _cbSelect

_cbShadeStru

ChButton _cbShadeStru

vALignments

UniqueList<T> vALignments

_jt

ChJTable _jt

minMaxScore

float[] minMaxScore

_aligner

SequenceAligner _aligner

_font

int _font

_countSelect

int _countSelect

_sharedInst

java.lang.Object _sharedInst

dgs

DrawGappedSequence dgs

_panel

ChPanel _panel

Class charite.christo.strap.DialogAlignResult extends ChPanel implements Serializable

Serialized Fields

LI

EvAdapter LI

dgs

DrawGappedSequence dgs

_togSort

javax.swing.JComponent _togSort

_bApply

javax.swing.JComponent _bApply

_butDetails

javax.swing.JComponent _butDetails

_bUndo

javax.swing.JComponent _bUndo

_rowHeader

javax.swing.JComponent _rowHeader

_pAli

javax.swing.JComponent _pAli

thread

java.lang.Thread thread

_aligner

SequenceAligner _aligner

_tLayout

ChTableLayout _tLayout

_proteins

Protein[] _proteins

_iiSorting

int[] _iiSorting

_aligned

byte[][] _aligned

_rhAdjust

float _rhAdjust

_startIdx

int _startIdx

_localAliStartsAt

int[] _localAliStartsAt

_frequenciesOfAA

short[][] _frequenciesOfAA

_fontSize

int _fontSize

_fontSizePrev

int _fontSizePrev

_font

java.awt.Font _font

_isReady

boolean _isReady

_progress

java.lang.String _progress

Class charite.christo.strap.DialogBarChart extends AbstractDialogJPanel implements Serializable

Serialized Fields

_comboVOP

ChCombo _comboVOP

_comboPPD

ChCombo _comboPPD

_comboP2

ProteinCombo _comboP2

_tfFrom

ChTextField _tfFrom

_tfTo

ChTextField _tfTo

_togVOP

ChButton _togVOP

_togPPD

ChButton _togPPD

butTable

ChButton butTable

Class charite.christo.strap.DialogBlast extends AbstractDialogJTabbedPane implements Serializable

Serialized Fields

_pList

ProteinList _pList

_vDB

java.util.List<E>[] _vDB

_togDetail

ChButton _togDetail

_togAmino

ChButton _togAmino

_butDB

ChButton _butDB

_butGo

ChButton _butGo

_labDB

ChButton _labDB

_labFst

ChButton _labFst

_labLst

ChButton _labLst

_comboClass

ChCombo _comboClass

_comboNT

ChCombo _comboNT

_comboDB

ChCombo[] _comboDB

_pnlCount

javax.swing.JComponent _pnlCount

_lastRunning

SequenceBlaster _lastRunning

_tfFrom

java.lang.Object _tfFrom

_tfTo

java.lang.Object _tfTo

_tfSkip

java.lang.Object _tfSkip

_tfSkipNot

java.lang.Object _tfSkipNot

_radioDB

java.lang.Object[] _radioDB

_todo

java.lang.Runnable[] _todo

Class charite.christo.strap.DialogCompareProteins extends AbstractDialogJTabbedPane implements Serializable

Serialized Fields

_tfFrom

ChTextField _tfFrom

_tfTo

ChTextField _tfTo

_selOfProtRow

ProteinList _selOfProtRow

_selOfProtCol

ProteinList _selOfProtCol

_comboClass

ChCombo _comboClass

_pMain

javax.swing.JComponent _pMain

_listProtRow

javax.swing.JComponent _listProtRow

_listProtCol

javax.swing.JComponent _listProtCol

_pBoth

javax.swing.JComponent _pBoth

RADIO_GRAPH_TABLE

ChCombo RADIO_GRAPH_TABLE

Class charite.christo.strap.DialogCopyAnnotations extends AbstractDialogJPanel implements Serializable

Serialized Fields

comboProt

ProteinCombo comboProt

tfGroup

ChTextField tfGroup

Class charite.christo.strap.DialogDifferentResidues extends AbstractDialogJTabbedPane implements Serializable

Serialized Fields

_comboReplace

javax.swing.JComboBox _comboReplace

_choiceProt3D

ProteinCombo _choiceProt3D

_choiceProt

ProteinCombo _choiceProt

Class charite.christo.strap.DialogDotPlot extends AbstractDialogJPanel implements Serializable

Serialized Fields

_usage

Backtranslate.Codonusage _usage

_imageBall

java.awt.Image _imageBall

dotplotSeq

DialogDotPlot_Sequence[] dotplotSeq

panArrow

javax.swing.JComponent panArrow

_options

long _options

sequenceType

char[] sequenceType

LI

EvAdapter LI

togTrace

ChButton togTrace

butColor

ChButton butColor

butClear

ChButton butClear

butMark

ChButton butMark

togNT_X

ChButton togNT_X

togNT_Y

ChButton togNT_Y

_dotplot

javax.swing.JComponent _dotplot

nx

int nx

ny

int ny

_plotWidth

int _plotWidth

_plotHeight

int _plotHeight

valuesW

int valuesW

valuesH

int valuesH

alignmentPosX

int alignmentPosX

alignmentPosY

int alignmentPosY

labPosition

javax.swing.JLabel labPosition

comboProtX

ChCombo comboProtX

comboProtY

ChCombo comboProtY

comboUsage

ChCombo comboUsage

comboFilter

ChCombo comboFilter

sliderBrightness

javax.swing.JSlider sliderBrightness

sliderThreshold

javax.swing.JSlider sliderThreshold

sliderWidth

javax.swing.JSlider sliderWidth

rectCursor

java.awt.Rectangle rectCursor

color

java.awt.Color color

selected

int[] selected

nSelected

int nSelected

selectorX

BasicResidueSelection selectorX

selectorY

BasicResidueSelection selectorY

_bl2seq

int[][] _bl2seq

refValues

java.lang.Object refValues

_mcResSel

int _mcResSel

_drawMsg

java.lang.String _drawMsg

_log

BA _log

_ctrl

javax.swing.JComponent _ctrl

_hasCtrlPnl

java.lang.Object _hasCtrlPnl

Class charite.christo.strap.DialogDotPlot_Sequence extends javax.swing.JPanel implements Serializable

Serialized Fields

_dotplot

DialogDotPlot _dotplot

_xOrY

char _xOrY

_pnl

javax.swing.JComponent _pnl

_charH

int _charH

_charW

int _charW

last_sbPos

int last_sbPos

dgs

DrawGappedSequence dgs

proteinList

ProteinList proteinList

comboClass

ChCombo comboClass

comboFormat

ChCombo comboFormat

comboDNA

ChCombo comboDNA

_tfCols

ChTextField _tfCols

_tfFrom

ChTextField _tfFrom

_tfTo

ChTextField _tfTo

_cbExt

ChButton _cbExt

_cbSpc

ChButton _cbSpc

_count

int _count

Class charite.christo.strap.DialogExportProteins extends AbstractDialogJPanel implements Serializable

Serialized Fields

_pList

ProteinList _pList

_comboClass

ChCombo _comboClass

_comboFormat

ChCombo _comboFormat

_togRubber

ChButton _togRubber

Class charite.christo.strap.DialogExportWord extends AbstractDialogJTabbedPane implements Serializable

Serialized Fields

_tfFile

ChTextField _tfFile

_tfCharsInLine

ChTextField _tfCharsInLine

_comboTarget

ChCombo _comboTarget

_comboSecStru

ProteinCombo _comboSecStru

_bbCust

ChButton[] _bbCust

_bGo

ChButton _bGo

_cbFileExt

ChButton _cbFileExt

_cbPdbNum

ChButton _cbPdbNum

_cbUL

ChButton _cbUL

_cbProtIcons

ChButton _cbProtIcons

_cbJalviewSS

ChButton _cbJalviewSS

_cbSecStru1

ChButton _cbSecStru1

_cbSecStru

ChButton _cbSecStru

_cbSecStruBG

ChButton _cbSecStruBG

_panBrowsers

java.lang.Object _panBrowsers

_msgWysiwyg

java.lang.Object _msgWysiwyg

_count

int _count

Class charite.christo.strap.DialogFetchPdb extends AbstractDialogJTabbedPane implements Serializable

Serialized Fields

_comboPdbSite

ChCombo _comboPdbSite

_ta

ChTextArea _ta

_highlight

TextMatches _highlight

_ft

int[] _ft

Class charite.christo.strap.DialogFetchSRS extends AbstractDialogJTabbedPane implements Serializable

Serialized Fields

_ta

ChTextArea _ta

pLoad

javax.swing.JComponent pLoad

_words

java.lang.String[] _words

_highlight

TextMatches _highlight

Class charite.christo.strap.DialogGenbank extends AbstractDialogJTabbedPane implements Serializable

Serialized Fields

_count

int _count

_vProt

java.lang.Object[] _vProt

Class charite.christo.strap.DialogHighlightPattern extends AbstractDialogJPanel implements Serializable

Serialized Fields

_error

java.lang.String _error

_jt

ChJTable _jt

_v

UniqueList<T> _v

_panNavi

java.lang.Object _panNavi

_bbNext

ChButton[] _bbNext

_lab

ChButton _lab

_cbFwd

ChButton _cbFwd

_cbRev

ChButton _cbRev

_cbDetails

ChButton _cbDetails

_cbSelectedPP

ChButton _cbSelectedPP

_file

java.io.File _file

Class charite.christo.strap.DialogImportMFA extends AbstractDialogJTabbedPane implements Serializable

Serialized Fields

_ta

ChTextArea _ta

_togOverwrite

java.lang.Object[] _togOverwrite

_fs

ChFileChooser _fs

_frame

ChFrame _frame

_tfSeparator

ChTextField _tfSeparator

Class charite.christo.strap.DialogInferCDS extends AbstractDialogJPanel implements Serializable

Serialized Fields

comboProtein

ProteinCombo comboProtein

proteinList

ProteinList proteinList

butUndo

ChButton butUndo

butLog

ChButton butLog

_log

BA _log

Class charite.christo.strap.DialogNeighbors extends AbstractDialogJTabbedPane implements Serializable

Serialized Fields

_comboP

ProteinCombo _comboP

Class charite.christo.strap.DialogNeighborsResult extends AbstractDialogJPanel implements Serializable

Serialized Fields

KEY_CHAIN

java.lang.Object KEY_CHAIN

_interrupt

boolean[] _interrupt

_mapId2cb

java.util.Map<K,V> _mapId2cb

_iTab

int _iTab

_pdbId

java.lang.String _pdbId

_pp

Protein[] _pp

_tp

javax.swing.JTabbedPane _tp

_loaded

boolean _loaded

Class charite.christo.strap.DialogNewProtein extends AbstractDialogJPanel implements Serializable

Serialized Fields

_tf

javax.swing.JComponent _tf

_ta

javax.swing.JComponent _ta

_b

javax.swing.JComponent _b

Class charite.christo.strap.DialogNonRedundantSequenceSet extends AbstractDialogJTabbedPane implements Serializable

Serialized Fields

_cbCurrent

ChButton _cbCurrent

_comboClass

ChCombo _comboClass

_tfThreshold

ChTextField _tfThreshold

_proteinList

ProteinList _proteinList

Class charite.christo.strap.DialogPhylogeneticTree extends AbstractDialogJPanel implements Serializable

Serialized Fields

comboClass

ChCombo comboClass

Class charite.christo.strap.DialogPlot extends AbstractDialogJTabbedPane implements Serializable

Serialized Fields

_hasValues

HasModiCount _hasValues

_vor

ValueOfResidue _vor

_vap

ValueOfAlignPosition _vap

_listP

ProteinList _listP

_selectedAA

boolean[] _selectedAA

_selectedOffset

int _selectedOffset

_sliderL

ChSlider _sliderL

_sliderU

ChSlider _sliderU

_panel

javax.swing.JComponent _panel

_cbShow

ChButton _cbShow

CB

ChButton[] CB

_comboProt

ProteinCombo _comboProt

_color

java.awt.Color _color

_mc

int _mc

_tabbed

javax.swing.JTabbedPane _tabbed

_panSelection

javax.swing.JComponent _panSelection

_comboVoR

ChCombo _comboVoR

_comboVoAP

ChCombo _comboVoAP

_comboStyle

ChCombo _comboStyle

_selMC

int _selMC

Class charite.christo.strap.DialogPredictCoiledCoil extends AbstractDialogPredict implements Serializable

Class charite.christo.strap.DialogPredictSecondaryStructures extends AbstractDialogPredict implements Serializable

Class charite.christo.strap.DialogPredictTmHelices2 extends AbstractDialogPredict implements Serializable

Class charite.christo.strap.DialogPredictTmHelicesMulti extends DialogPredictTmHelices2 implements Serializable

Serialized Fields

proteinList

ProteinList proteinList

classList

ChJList classList

iResult

int iResult

_comboSettings

ChCombo _comboSettings

Class charite.christo.strap.DialogProteinList extends AbstractDialogJPanel implements Serializable

Serialized Fields

_fs

ChFileChooser _fs

_ta

ChTextArea _ta

Class charite.christo.strap.DialogPublishAlignment extends AbstractDialogJPanel implements Serializable

Serialized Fields

taPARA

ChTextArea taPARA

taENCODED

ChTextArea taENCODED

taForm

ChTextArea taForm

toggles

ChButton[] toggles

radioAnnotations

java.lang.Object[] radioAnnotations

Class charite.christo.strap.DialogResidueAnnotationChanges extends AbstractDialogJPanel implements Serializable

Serialized Fields

_tableData1

java.lang.String[][] _tableData1

_tableData2

java.util.List<E> _tableData2

_tm1

ChTableModel _tm1

_tm2

ChTableModel _tm2

_jTable1

ChJTable _jTable1

_jTable2

ChJTable _jTable2

_comboKeys

ChCombo _comboKeys

_comboNum

ChCombo _comboNum

_cbRegex

ChButton _cbRegex

_labInfo

ChButton _labInfo

cached

java.lang.Object[] cached

_num

int _num

_needsUpdate

boolean _needsUpdate

Class charite.christo.strap.DialogResidueAnnotationList extends javax.swing.JComponent implements Serializable

Serialized Fields

_comboP

ProteinCombo _comboP

_comboIdx

javax.swing.JComponent _comboIdx

_tfOffset

javax.swing.JComponent _tfOffset

_tfGroup

javax.swing.JComponent _tfGroup

_ta

ChTextArea _ta

Class charite.christo.strap.DialogRestoreFromBackup extends AbstractDialogJPanel implements Serializable

Serialized Fields

_listing

java.util.Vector<E> _listing

jList

javax.swing.JList jList

_fDir

java.io.File _fDir

Class charite.christo.strap.DialogSelectionOfResidues extends AbstractDialogJPanel implements Serializable

Serialized Fields

_class

java.lang.Object _class

_sharedI

ResidueSelection _sharedI

_bColor

ChButton _bColor

_cb1D

ChButton _cb1D

_cb3D

ChButton _cb3D

_cbSP

ChButton _cbSP

_comboStyle

ChCombo _comboStyle

_ppl

ProteinList _ppl

_v

UniqueList<T> _v

Class charite.christo.strap.DialogSelectionOfResiduesMain extends AbstractDialogJTabbedPane implements Serializable

Serialized Fields

comboClass

ChCombo comboClass

Class charite.christo.strap.DialogSimilarStructure extends AbstractDialogJTabbedPane implements Serializable

Serialized Fields

_pList

ProteinList _pList

_comboClass

ChCombo _comboClass

_count

int _count

Class charite.christo.strap.DialogSimilarStructureResult extends ChPanel implements Serializable

Serialized Fields

COMPUTING

java.lang.Object COMPUTING

_log

BA _log

_buttons

ChButton[] _buttons

_infoWait

ChButton _infoWait

_cbDetails

ChButton _cbDetails

_progress

javax.swing.JProgressBar _progress

_disposed

boolean _disposed

_opt

long _opt

_taByHand

ChTextArea _taByHand

_jt

ChJTable _jt

_tData

java.lang.Object[][] _tData

_main

java.lang.Object _main

Class charite.christo.strap.DialogSortProteins extends AbstractDialogJPanel implements Serializable

Serialized Fields

comboClass

ChCombo[] comboClass

Class charite.christo.strap.DialogSubcellularLocalization extends AbstractDialogJTabbedPane implements Serializable

Serialized Fields

classList

ChJList classList

proteinList

ProteinList proteinList

comboOrgansims

javax.swing.JComboBox comboOrgansims

LOG

ChTextView LOG

_countTab

int _countTab

lastPredictor

PredictSubcellularLocation lastPredictor

Class charite.christo.strap.DialogSuperimpose3D extends AbstractDialogJTabbedPane implements Serializable

Serialized Fields

_tfSelection

ChTextField[] _tfSelection

_choiceProteinR

ProteinCombo _choiceProteinR

_choiceProteinM

ProteinList _choiceProteinM

_choiceClass

ChCombo _choiceClass

_togOptions

javax.swing.JComponent _togOptions

Class charite.christo.strap.DialogSuperimpose3DResult extends javax.swing.JPanel implements Serializable

Serialized Fields

_msg

java.lang.String _msg

_s3d

Superimpose3D _s3d

_ta

ChTextArea _ta

_pp

Protein[] _pp

_dialog

DialogSuperimpose3D _dialog

_p3D

Protein3d _p3D

_m3d

Matrix3D _m3d

_butApply

java.lang.Object _butApply

_butUndo

java.lang.Object _butUndo

_butDist

java.lang.Object _butDist

_pSouth

java.lang.Object _pSouth

_butDetails

java.lang.Object _butDetails

Class charite.christo.strap.EditDna extends AbstractDialogJPanel implements Serializable

Serialized Fields

_pEditors

javax.swing.JComponent _pEditors

_pTables

javax.swing.JComponent _pTables

_tables

java.util.Map<K,V> _tables

Class charite.christo.strap.EditDnaParentPane extends java.lang.Object implements Serializable

Class charite.christo.strap.EditDnaTable extends javax.swing.table.DefaultTableModel implements Serializable

Serialized Fields

_p

Protein _p

_jt

ChJTable _jt

_tf

ChTextField _tf

_cbCompl

ChButton _cbCompl

_labProt

java.lang.Object _labProt

_ft

int[] _ft

_ftMc

int _ftMc

_mcEv

int _mcEv

Class charite.christo.strap.FilesFetchedFromServer extends AbstractDialogJPanel implements Serializable

Serialized Fields

_scroll

ChJScrollPane _scroll

_butDelError

ChButton _butDelError

_labStatus

ChTextView _labStatus

_vDownloaded

java.util.List<E> _vDownloaded

_vAlready

java.util.List<E> _vAlready

_vFailure

java.util.List<E> _vFailure

_jl

ChJList _jl

_jlAlready

ChJList _jlAlready

_jlFailure

ChJList _jlFailure

Class charite.christo.strap.HScrollBar extends ChScrollBar implements Serializable

Serialized Fields

_view

StrapView _view

_divider

boolean _divider

_clear

boolean _clear

_knob

boolean _knob

_img

java.lang.Object _img

_val

int _val

_dividerWidth

int _dividerWidth

_w

int _w

_h

int _h

LAST

long[] LAST

_dragged

char _dragged

_dragY

int _dragY

_maxDragX

int _maxDragX

_minDragX

int _minDragX

_dragFromY

int _dragFromY

Class charite.christo.strap.IntermediateSeq extends AbstractDialogJTabbedPane implements Serializable

Serialized Fields

_mapBlastResult

java.util.Map<K,V> _mapBlastResult

_vAli

java.util.List<E> _vAli

_vDB

java.util.List<E> _vDB

LI

EvAdapter LI

_progress

javax.swing.JProgressBar _progress

_comboDB

ChCombo _comboDB

_comboClass

ChCombo _comboClass

_butBlast

java.lang.Object _butBlast

_bLoad

java.lang.Object _bLoad

_log

BA _log

_logNoHits

BA _logNoHits

_listProt1

ProteinList _listProt1

_listProt2

ProteinList _listProt2

_ctrl

javax.swing.JComponent _ctrl

Class charite.christo.strap.IntermediateSeqPair extends javax.swing.JPanel implements Serializable

Serialized Fields

_p

Protein[] _p

_blosums

int[][] _blosums

_gapOpen

int _gapOpen

_gapExt

int _gapExt

_fontSize

int _fontSize

_font

java.awt.Font _font

_ctrl

javax.swing.JComponent _ctrl

dgs

DrawGappedSequence dgs

vAllAlignments

UniqueList<T> vAllAlignments

_plot

DialogDotPlot _plot

LOG

BA LOG

_jt

ChJTable _jt

_blastResult

BlastResult[] _blastResult

_tfExp

ChTextField _tfExp

_tfNum

ChTextField _tfNum

_labNum

ChTextField _labNum

_tfGapOpen

ChTextField _tfGapOpen

_tfGapExt

ChTextField _tfGapExt

_vSB

javax.swing.JScrollBar _vSB

_vHitView

UniqueList<T> _vHitView

_vHitViewShown

UniqueList<T> _vHitViewShown

Class charite.christo.strap.ProteinCombo extends ChCombo implements Serializable

Serialized Fields

_filter

long _filter

Class charite.christo.strap.ProteinList extends ChJList implements Serializable

Serialized Fields

_align

StrapAlign _align

_filter

long _filter

_selModel

ChListSelectionModel _selModel

_isInitialized

boolean _isInitialized

Class charite.christo.strap.ResidueAnnotationView extends javax.swing.table.DefaultTableModel implements Serializable

Serialized Fields

LI

EvAdapter LI

RENDERER

ChButton RENDERER

TOG_RENDERER

ChButton TOG_RENDERER

BUT_RENDERER

ChButton BUT_RENDERER

BUT_DEL

ChButton BUT_DEL

BUT_OPT

ChButton BUT_OPT

BUT

ChButton BUT

TOG

ChButton TOG

CB_VARIABLES

ChButton CB_VARIABLES

_jlVar

ChJList _jlVar

_rowEd

int _rowEd

_colEd

int _colEd

_rowTf

int _rowTf

_mc

int _mc

_rowCount

int _rowCount

_disposed

boolean _disposed

_pNorth

javax.swing.JComponent _pNorth

_panel

javax.swing.JComponent _panel

_jt

ChJTable _jt

_a

ResidueAnnotation _a

_color

java.awt.Color _color

listeners

java.util.List<E> listeners

_aa

AddAnnotation _aa

Class charite.christo.strap.SequenceFeatures extends javax.swing.table.DefaultTableModel implements Serializable

Serialized Fields

DRAW_MSG

BA DRAW_MSG

BUT_WEB

ChButton BUT_WEB

BUT_WEB_EDITOR

ChButton BUT_WEB_EDITOR

_butExpasy

ChButton _butExpasy

_butDefault

ChButton _butDefault

_ttRow

int _ttRow

_tt

java.lang.String _tt

labMsg

javax.swing.JComponent labMsg

_pnl

javax.swing.JComponent _pnl

_pNavi

javax.swing.JComponent _pNavi

_jt

ChJTable _jt

_frame

ChFrame _frame

_taWeb

ChTextArea _taWeb

_cbVisibility

ChButton _cbVisibility

_cbNotAll

ChButton _cbNotAll

_cbArrows

ChButton _cbArrows

_comboAll

ChCombo _comboAll

PRG_BARS

javax.swing.JProgressBar[] PRG_BARS

_renderer

ChRenderer _renderer

_row

int _row

mapNextPrev

java.util.Map<K,V> mapNextPrev

Class charite.christo.strap.StrapDAS extends ChRenderer implements Serializable

Serialized Fields

_diaSearch

DialogStringMatch _diaSearch

_progress

javax.swing.JProgressBar _progress

_panel

javax.swing.JComponent _panel

Class charite.christo.strap.StrapTree extends ChJTree implements Serializable

Serialized Fields

_painted

boolean _painted

_align

StrapAlign _align

_vMatching

java.util.Set<E> _vMatching

LI

EvAdapter LI

_root2

java.lang.Object[] _root2

Class charite.christo.strap.Texshade extends AbstractDialogJTabbedPane implements Serializable

Serialized Fields

_wSrc

ChFrame _wSrc

_instDetail

java.lang.Object _instDetail

_taBefore

ChTextArea _taBefore

_taIn

ChTextArea _taIn

_taSourceFiles

ChTextArea _taSourceFiles

_fPdf

java.io.File _fPdf

_fPdfCount

int _fPdfCount

_myExec

ChExec _myExec

_pChoiceRuler

ProteinCombo _pChoiceRuler

_subfamilyProtList

ProteinList _subfamilyProtList

_togDetails

ChButton _togDetails

_panInst

javax.swing.JComponent _panInst

_panPoster

javax.swing.JComponent _panPoster

_panViewers

javax.swing.JComponent _panViewers

butDvi

javax.swing.JComponent butDvi

butDviPs

javax.swing.JComponent butDviPs

butPS

javax.swing.JComponent butPS

butPdf

javax.swing.JComponent butPdf

butPosterViewPS

javax.swing.JComponent butPosterViewPS

butRunTex

javax.swing.JComponent butRunTex

butPoster

javax.swing.JComponent butPoster

cbCustomSize

javax.swing.JComponent cbCustomSize

cbLandscape

javax.swing.JComponent cbLandscape

cbNoExtension

javax.swing.JComponent cbNoExtension

cbPS

javax.swing.JComponent cbPS

cbSubstituteNames

javax.swing.JComponent cbSubstituteNames

cbSeparationLine

javax.swing.JComponent cbSeparationLine

cbUpperCase

javax.swing.JComponent cbUpperCase

cbHideLegend

javax.swing.JComponent cbHideLegend

cbFingerprint

javax.swing.JComponent cbFingerprint

cbHideConsensus

javax.swing.JComponent cbHideConsensus

cbDoFreqCorrect

javax.swing.JComponent cbDoFreqCorrect

cbHideSeqs

javax.swing.JComponent cbHideSeqs

choiceConsensus

ChCombo choiceConsensus

choiceConsensusLocation

ChCombo choiceConsensusLocation

choicePosterSize

ChCombo choicePosterSize

choiceShading

ChCombo choiceShading

choiceShowNames

ChCombo choiceShowNames

choiceEmph

ChCombo choiceEmph

_choiceNumbering

ChCombo _choiceNumbering

_choiceSeqLogo

ChCombo _choiceSeqLogo

choiceRuler

ChCombo choiceRuler

choiceSize

ChCombo choiceSize

_choiceSubfamilyLocation

ChCombo _choiceSubfamilyLocation

tfBargraphstretch

ChTextField tfBargraphstretch

tfVblockspace

ChTextField tfVblockspace

tfMarginL

ChTextField tfMarginL

tfMarginR

ChTextField tfMarginR

tfMarginT

ChTextField tfMarginT

tfMarginB

ChTextField tfMarginB

tfResiduesperline

ChTextField tfResiduesperline

tfPaperheight

ChTextField tfPaperheight

tfCustomWidth

ChTextField tfCustomWidth

tfCustomHeight

ChTextField tfCustomHeight

tfRulerstep

ChTextField tfRulerstep

tfSubfamilyName

ChTextField tfSubfamilyName

_resGraph

TexshadeGraph[] _resGraph

_consGraph

TexshadeGraph[] _consGraph

secGraph

charite.christo.strap.TexshadeSecStructure[] secGraph

runUpdateUI

java.lang.Runnable runUpdateUI

Class charite.christo.strap.TexshadeGraph extends javax.swing.Box implements Serializable

Serialized Fields

_vor

java.lang.Object[] _vor

_tfMin

java.lang.Object _tfMin

_tfMax

java.lang.Object _tfMax

_where

java.lang.String _where

_choiceP

ProteinCombo _choiceP

_choiceClass

ChCombo _choiceClass

_choiceColor

ChCombo _choiceColor

_toggle

ChButton _toggle

_butP

ChButton _butP

_interf

java.lang.Class<T> _interf

_ppl

ProteinList _ppl

Class charite.christo.strap.V3dListModel extends javax.swing.AbstractListModel implements Serializable

Serialized Fields

_type

int _type

Package charite.christo.strap.extensions

Class charite.christo.strap.extensions.DemoAssociateObjectsToProteins extends javax.swing.JPanel implements Serializable

Serialized Fields

_p

javax.swing.JComponent _p

vObjects

UniqueList<T> vObjects

align

StrapAlign align

pCombo

ProteinCombo pCombo

butAdd

ChButton butAdd

butRemove

ChButton butRemove

butCount

ChButton butCount

Package charite.christo.strap.science

Class charite.christo.strap.science.Flavine extends AbstractAlignmentProject implements Serializable

Serialized Fields

_ctrl

javax.swing.JComponent _ctrl

_mapChart

java.util.Map<K,V> _mapChart

_clickedC0

java.lang.String _clickedC0

_clickedC1

java.lang.String _clickedC1

Class charite.christo.strap.science.Prione extends AbstractAlignmentProject implements Serializable

Class charite.christo.strap.science.Proteasome extends AbstractAlignmentProject implements Serializable

Overview

Package

Class

Tree

Deprecated

Index

Help

'STRAP:multiple sequence alignments '

PREV NEXT

FRAMES NO FRAMES

'The most important classes are StrapAlign, Protein and StrapEvent.'