A B C D E F G H I J K L M N O P Q R S T U V W X Y Z _

A

a(long) - Method in class charite.christo.BA

a(char) - Method in class charite.christo.BA

a(char, int) - Method in class charite.christo.BA

a(double) - Method in class charite.christo.BA

a(float) - Method in class charite.christo.BA

a(Object) - Method in class charite.christo.BA

a(boolean) - Method in class charite.christo.BA

a(Object, int, int) - Method in class charite.christo.BA

a(boolean, Object) - Method in class charite.christo.BA

a(long, int) - Method in class charite.christo.BA

a(double, int, int) - Method in class charite.christo.BA

a(Object) - Method in class charite.christo.ChLogger

a(Object) - Method in class charite.christo.ChTextArea

a(CharSequence) - Method in class charite.christo.ChTextView

a() - Static method in class charite.christo.strap.StrapUtils

a1(Object) - Method in class charite.christo.BA

aa2codon() - Method in class charite.christo.protein.Backtranslate.Codonusage

AA2NT - Static variable in class charite.christo.strap.DrawGappedSequence

AA_SHADING_CHANGED - Static variable in class charite.christo.protein.StrapEvent

aBigFloat(double, int) - Method in class charite.christo.BA

aboutDialog() - Static method in class charite.christo.strap.Strap

ABSTRACT - Static variable in class charite.christo.ChPubmed

AbstractAlignAndCompare - Class in charite.christo.strap

AbstractAlignAndCompare() - Constructor for class charite.christo.strap.AbstractAlignAndCompare

AbstractAligner - Class in charite.christo.strap

AbstractAligner() - Constructor for class charite.christo.strap.AbstractAligner

AbstractAlignerProxy - Class in charite.christo.strap

AbstractAlignerProxy() - Constructor for class charite.christo.strap.AbstractAlignerProxy

AbstractAlignmentProject - Class in charite.christo.strap

AbstractAlignmentProject() - Constructor for class charite.christo.strap.AbstractAlignmentProject

AbstractAlignmentProject.Alignment - Class in charite.christo.strap

AbstractBlaster - Class in charite.christo.blast

AbstractBlaster() - Constructor for class charite.christo.blast.AbstractBlaster

AbstractDialogJPanel - Class in charite.christo.strap

AbstractDialogJPanel() - Constructor for class charite.christo.strap.AbstractDialogJPanel

AbstractDialogJTabbedPane - Class in charite.christo.strap

AbstractDialogJTabbedPane() - Constructor for class charite.christo.strap.AbstractDialogJTabbedPane

AbstractDialogPredict - Class in charite.christo.strap

The user can predict secondary structure or TM helices in selected proteins.

AbstractDialogPredict() - Constructor for class charite.christo.strap.AbstractDialogPredict

AbstractInteractiveFileProcessor - Class in charite.christo

AbstractInteractiveFileProcessor() - Constructor for class charite.christo.AbstractInteractiveFileProcessor

AbstractPredictionFromAminoacidSequence - Class in charite.christo.protein

AbstractPredictionFromAminoacidSequence() - Constructor for class charite.christo.protein.AbstractPredictionFromAminoacidSequence

AbstractProteinViewerProxy - Class in charite.christo.protein

AbstractProteinViewerProxy() - Constructor for class charite.christo.protein.AbstractProteinViewerProxy

AbstractProxy - Class in charite.christo

AbstractProxy() - Constructor for class charite.christo.AbstractProxy

AbstractSubcellularLocation - Class in charite.christo.strap.extensions

AbstractSubcellularLocation() - Constructor for class charite.christo.strap.extensions.AbstractSubcellularLocation

AbstractValueOfResidue - Class in charite.christo.protein

AbstractValueOfResidue() - Constructor for class charite.christo.protein.AbstractValueOfResidue

AbstractVisibleIn123 - Class in charite.christo.protein

An abstract implementation of VisibleIn123.

AbstractVisibleIn123() - Constructor for class charite.christo.protein.AbstractVisibleIn123

accept(File) - Method in class charite.christo.ChFileFilter

AcceptAlignment2 - Class in charite.christo.strap

AcceptAlignment2(Protein[], int, byte[][]) - Constructor for class charite.christo.strap.AcceptAlignment2

ACTG - Static variable in class charite.christo.protein.ShadingAA

actg2int(byte[], int) - Static method in class charite.christo.DNA_Util

ACTGN - Static variable in class charite.christo.strap.ProteinList

ACTGUN - Static variable in class charite.christo.ChUtils

ACTION - Static variable in class charite.christo.Sil

ACTION_ADDED - Static variable in class charite.christo.ChTabPane

ACTION_backbone - Static variable in class charite.christo.strap.ProteinPopup

ACTION_BECOME_INVISIBLE - Static variable in class charite.christo.ChUtils

ACTION_BEFORE - Static variable in class charite.christo.DialogStringMatch

ACTION_CHANGE_EVENT - Static variable in class charite.christo.ChConstants

ACTION_CLICKED - Static variable in class charite.christo.ChConstants

ACTION_CLICKED_AFTER_SUPER - Static variable in class charite.christo.ChConstants

ACTION_CLICKED_DOUBLE - Static variable in class charite.christo.ChConstants

ACTION_CLICKED_DOUBLE_AFTER_SUPER - Static variable in class charite.christo.ChConstants

ACTION_close3d - Static variable in class charite.christo.strap.ProteinPopup

ACTION_COLOR_CHANGED - Static variable in class charite.christo.ChConstants

ACTION_CUSTOMIZE_CHANGED - Static variable in class charite.christo.ChConstants

ACTION_DATA_TRANSFER - Static variable in class charite.christo.ChStdout

ACTION_DATABASE_CLICKED - Static variable in class charite.christo.ChConstants

ACTION_DELETE_OR_BACKSPACE - Static variable in class charite.christo.ChConstants

ACTION_DOWNLOAD_PLUGIN - Static variable in class charite.christo.ChConstants

ACTION_edit - Static variable in class charite.christo.strap.ResidueSelectionPopup

ACTION_ENTER - Static variable in class charite.christo.ChConstants

ACTION_ERROR - Static variable in class charite.christo.ChExec

ACTION_FINISHED - Static variable in class charite.christo.DialogStringMatch

ACTION_FOCUS_GAINED - Static variable in class charite.christo.ChConstants

ACTION_FOCUS_LOST - Static variable in class charite.christo.ChConstants

ACTION_FULL_TEXT_ASSOCIATED - Static variable in class charite.christo.ChPubmed

ACTION_ignoreSEQRES - Static variable in class charite.christo.strap.StrapAlign

ACTION_INSERTED_TEXT_LONGER_ONE - Static variable in class charite.christo.ChTextComponents

ACTION_MENU_SELECTED - Static variable in class charite.christo.ChConstants

ACTION_MK_RESANO - Static variable in class charite.christo.strap.ResidueSelectionPopup

ACTION_newPan - Static variable in class charite.christo.strap.StrapAlign

ACTION_OPEN_DIALOG - Static variable in class charite.christo.HtmlDoc

ACTION_OPEN_TUTORIAL - Static variable in class charite.christo.HtmlDoc

ACTION_openPlugin - Static variable in class charite.christo.strap.StrapAlign

ACTION_REMOVED - Static variable in class charite.christo.ChTabPane

ACTION_SELECT - Static variable in class charite.christo.strap.StrapTree

ACTION_SELECTION_CHANGED - Static variable in class charite.christo.ChConstants

ACTION_SELECTION_CHANGED - Static variable in class charite.christo.ChTabPane

ACTION_showInList - Static variable in class charite.christo.strap.ProteinPopup

ACTION_TABLE_CHANGED - Static variable in class charite.christo.ChConstants

ACTION_TERMINATED - Static variable in class charite.christo.ChExec

ACTION_TEXT_CHANGED - Static variable in class charite.christo.ChConstants

ACTION_VIEW_SOURCE - Static variable in class charite.christo.HtmlDoc

ACTION_WINDOW_ACTIVATED - Static variable in class charite.christo.ChConstants

ACTION_WINDOW_CLOSING - Static variable in class charite.christo.ChConstants

ACTION_WINDOW_DEACTIVATED - Static variable in class charite.christo.ChConstants

actionCommand(AWTEvent) - Static method in class charite.christo.ChUtils

actionPerformed(ActionEvent) - Method in class charite.christo.AbstractInteractiveFileProcessor

actionPerformed(ActionEvent) - Method in class charite.christo.blast.AbstractBlaster

actionPerformed(ActionEvent) - Method in class charite.christo.ChExec

actionPerformed(ActionEvent) - Method in class charite.christo.ChJavadoc

actionPerformed(ActionEvent) - Method in class charite.christo.ChLogger

actionPerformed(ActionEvent) - Method in class charite.christo.ChMsgDia

actionPerformed(ActionEvent) - Method in class charite.christo.ChPubmed

actionPerformed(ActionEvent) - Method in class charite.christo.ChScriptPanel

actionPerformed(ActionEvent) - Method in class charite.christo.ChStdout

actionPerformed(ActionEvent) - Method in class charite.christo.Customize

actionPerformed(ActionEvent) - Method in class charite.christo.DialogExecuteOnFile

actionPerformed(ActionEvent) - Method in class charite.christo.DialogStringMatch

actionPerformed(ActionEvent) - Method in class charite.christo.EvAdapter

actionPerformed(ActionEvent) - Method in class charite.christo.GraphSun

actionPerformed(ActionEvent) - Method in class charite.christo.LAFChooser

actionPerformed(ActionEvent) - Method in class charite.christo.Microsoft

actionPerformed(ActionEvent) - Method in class charite.christo.PrgParasGUI

actionPerformed(ActionEvent) - Method in class charite.christo.protein.Protein

actionPerformed(ActionEvent) - Method in class charite.christo.protein.Pymol

actionPerformed(ActionEvent) - Method in class charite.christo.RenameFile

actionPerformed(ActionEvent) - Method in class charite.christo.strap.AbstractAlignmentProject

actionPerformed(ActionEvent) - Method in class charite.christo.strap.AbstractAlignmentProject.Alignment

actionPerformed(ActionEvent) - Method in class charite.christo.strap.AbstractDialogPredict

actionPerformed(ActionEvent) - Method in class charite.christo.strap.ActivateDeactivate

actionPerformed(ActionEvent) - Method in class charite.christo.strap.AddAnnotation

actionPerformed(ActionEvent) - Method in class charite.christo.strap.Aligner3D

actionPerformed(ActionEvent) - Method in class charite.christo.strap.Dialog3DViewer

actionPerformed(ActionEvent) - Method in class charite.christo.strap.DialogAlign

actionPerformed(ActionEvent) - Method in class charite.christo.strap.DialogAlignOneToAll

actionPerformed(ActionEvent) - Method in class charite.christo.strap.DialogBarChart

actionPerformed(ActionEvent) - Method in class charite.christo.strap.DialogBlast

actionPerformed(ActionEvent) - Method in class charite.christo.strap.DialogCompareProteins

actionPerformed(ActionEvent) - Method in class charite.christo.strap.DialogDifferentResidues

actionPerformed(ActionEvent) - Method in class charite.christo.strap.DialogDotPlot_Sequence

actionPerformed(ActionEvent) - Method in class charite.christo.strap.DialogExportProteins

actionPerformed(ActionEvent) - Method in class charite.christo.strap.DialogExportWord

actionPerformed(ActionEvent) - Method in class charite.christo.strap.DialogFetchPdb

actionPerformed(ActionEvent) - Method in class charite.christo.strap.DialogFetchSRS

actionPerformed(ActionEvent) - Method in class charite.christo.strap.DialogGenbank

actionPerformed(ActionEvent) - Method in class charite.christo.strap.DialogHighlightPattern

actionPerformed(ActionEvent) - Method in class charite.christo.strap.DialogImportMFA

actionPerformed(ActionEvent) - Method in class charite.christo.strap.DialogInferCDS

actionPerformed(ActionEvent) - Method in class charite.christo.strap.DialogManyInOneRow

actionPerformed(ActionEvent) - Method in class charite.christo.strap.DialogNeighbors

actionPerformed(ActionEvent) - Method in class charite.christo.strap.DialogNeighborsResult

actionPerformed(ActionEvent) - Method in class charite.christo.strap.DialogNewProtein

actionPerformed(ActionEvent) - Method in class charite.christo.strap.DialogNonRedundantSequenceSet

actionPerformed(ActionEvent) - Method in class charite.christo.strap.DialogPhylogeneticTree

actionPerformed(ActionEvent) - Method in class charite.christo.strap.DialogPlot

actionPerformed(ActionEvent) - Method in class charite.christo.strap.DialogPredictTexshade

actionPerformed(ActionEvent) - Method in class charite.christo.strap.DialogPredictTmHelicesMulti

actionPerformed(ActionEvent) - Method in class charite.christo.strap.DialogProteinList

actionPerformed(ActionEvent) - Method in class charite.christo.strap.DialogPublishAlignment

actionPerformed(ActionEvent) - Method in class charite.christo.strap.DialogRenameProteins

actionPerformed(ActionEvent) - Method in class charite.christo.strap.DialogRestoreFromBackup

actionPerformed(ActionEvent) - Method in class charite.christo.strap.DialogSelectionOfResidues

actionPerformed(ActionEvent) - Method in class charite.christo.strap.DialogSelectionOfResiduesMain

actionPerformed(ActionEvent) - Method in class charite.christo.strap.DialogSimilarStructure

actionPerformed(ActionEvent) - Method in class charite.christo.strap.DialogSimilarStructureResult

actionPerformed(ActionEvent) - Method in class charite.christo.strap.DialogSortProteins

actionPerformed(ActionEvent) - Method in class charite.christo.strap.DialogSubcellularLocalization

actionPerformed(ActionEvent) - Method in class charite.christo.strap.DialogSuperimpose3D

actionPerformed(ActionEvent) - Method in class charite.christo.strap.DialogSuperimpose3DResult

actionPerformed(ActionEvent) - Method in class charite.christo.strap.EditDna

actionPerformed(ActionEvent) - Method in class charite.christo.strap.EditDnaTable

actionPerformed(ActionEvent) - Method in class charite.christo.strap.extensions.AlignmentEntropy

actionPerformed(ActionEvent) - Method in class charite.christo.strap.extensions.DemoAssociateObjectsToProteins

actionPerformed(ActionEvent) - Method in class charite.christo.strap.extensions.Distance3DToHetero

actionPerformed(ActionEvent) - Method in class charite.christo.strap.extensions.Hydrophobicity

actionPerformed(ActionEvent) - Method in class charite.christo.strap.extensions.ResidueValues_from_textfile

actionPerformed(ActionEvent) - Method in class charite.christo.strap.HeteroPopup

actionPerformed(ActionEvent) - Method in class charite.christo.strap.IntermediateSeqPair

actionPerformed(ActionEvent) - Method in class charite.christo.strap.ProteinCombo

actionPerformed(ActionEvent) - Method in class charite.christo.strap.ProteinPopup

actionPerformed(ActionEvent) - Method in class charite.christo.strap.ProteinViewerPopup

actionPerformed(ActionEvent) - Method in class charite.christo.strap.ResidueSelectionPopup

actionPerformed(ActionEvent) - Method in class charite.christo.strap.science.Flavine

actionPerformed(ActionEvent) - Method in class charite.christo.strap.Strap

actionPerformed(ActionEvent) - Method in class charite.christo.strap.StrapPlugins

actionPerformed(ActionEvent) - Method in class charite.christo.strap.StrapView

actionPerformed(ActionEvent) - Method in class charite.christo.strap.Texshade

actionPerformed(ActionEvent) - Method in class charite.christo.strap.TexshadeGraph

ActivateDeactivate - Class in charite.christo.strap

HELP With this form the text entries in residue annotations can be activated or deactivated or deleted.

ActivateDeactivate(ContextObjects) - Constructor for class charite.christo.strap.ActivateDeactivate

ACTIVATION - Static variable in class charite.christo.AbstractProxy

ad(Object) - Method in class charite.christo.ChFrame

ad(T, T[], int, Class<T>) - Static method in class charite.christo.ChUtils

adAll(Object[], Collection) - Static method in class charite.christo.ChUtils

adAllUniq(Object[], Collection) - Static method in class charite.christo.ChUtils

ADAPTERS_JAR - Static variable in class charite.christo.AbstractProxy

add(E) - Method in class charite.christo.ChSet

add(String, String) - Static method in class charite.christo.TabItemTipIcon

add(int, int) - Method in class charite.christo.TextMatches

add(T) - Method in class charite.christo.UniqueList

add(int, T) - Method in class charite.christo.UniqueList

ADD_COMPONENT - Static variable in class charite.christo.ChDelay

ADD_MOLI_CHILDS - Static variable in class charite.christo.ChUtils

addActLi(ActionListener, Object) - Static method in class charite.christo.ChUtils

addAlignment(BlastAlignment) - Method in class charite.christo.blast.BlastHit

addAll(Collection<? extends E>) - Method in class charite.christo.ChSet

addAll(Collection<? extends T>) - Method in class charite.christo.UniqueList

addAll(int, Collection<? extends T>) - Method in class charite.christo.UniqueList

addAllA(T...) - Method in class charite.christo.UniqueList

addAlternativeUrl(String, String) - Static method in class charite.christo.ChUtils

AddAnnotation - Class in charite.christo.strap

HELP With this form annotations can be added to residue annotations.

AddAnnotation(ResidueAnnotation...) - Constructor for class charite.christo.strap.AddAnnotation

addBenchmark(char) - Static method in class charite.christo.ChUtils

addButton(JComponent, int) - Method in class charite.christo.GraphSun

addCDS(String, String[]) - Method in class charite.christo.protein.Protein

addCellEditorListener(CellEditorListener) - Method in class charite.christo.ChRenderer

addCellEditorListener(CellEditorListener) - Method in class charite.christo.strap.ResidueAnnotationView

addColoredBg(int, int, Color, JTextComponent) - Static method in class charite.christo.ChJHighlighter

addColumn(int, Object) - Method in class charite.christo.ChTableLayout

addCommandLineOption(String, boolean) - Method in class charite.christo.PrgParas

addComponentToContainer(Component, Container, Object, long) - Static method in class charite.christo.ChDelay

addCP(Object, Object, Object) - Static method in class charite.christo.ChUtils

addCP(Object, Object, Object, int) - Static method in class charite.christo.ChUtils

addDatabase(BlastDatabase) - Method in class charite.christo.blast.BlastResult

addDatabaseRef(String) - Method in class charite.christo.protein.Protein

addDebugGc(Object) - Static method in class charite.christo.ChUtils

addDialog(Customize...) - Static method in class charite.christo.Customize

addDialog(JComponent) - Static method in class charite.christo.strap.StrapAlign

addDialog(Object, boolean) - Static method in class charite.christo.strap.StrapAlign

Make an instance of a dialog and add it to the dialog pane.

addDialogSetClass(Object, Object) - Static method in class charite.christo.strap.StrapAlign

addDictionaries(String[]) - Static method in class charite.christo.ChJOrthoPROXY

addDnD(Object) - Method in class charite.christo.ChButton

addE(String, String) - Method in class charite.christo.strap.ResidueAnnotation

addE(long, String, String, boolean, int) - Method in class charite.christo.strap.ResidueAnnotation

addEdge(GraphEdge) - Method in class charite.christo.GraphSun

addEditor(Protein, boolean) - Method in class charite.christo.strap.EditDna

addEnS(String, String) - Method in class charite.christo.strap.ResidueAnnotation

addFilter(String) - Method in class charite.christo.ChFileChooser

addHeteroCompounds(long, HeteroCompound...) - Method in class charite.christo.protein.Protein

addHiddenEntries(boolean, String...) - Method in class charite.christo.Customize

addHighlight(TextMatches) - Method in class charite.christo.ChTextComponents

addHit(BlastHit) - Method in class charite.christo.blast.BlastResult

addHook(int, ChRunnable, String) - Method in class charite.christo.UniqueList

addHtmlTags(CharSequence) - Static method in class charite.christo.ChUtils

addHtmlTagsAsStrg(Object) - Static method in class charite.christo.ChUtils

addHyperlinkListener(JEditorPane) - Static method in class charite.christo.HtmlDoc

addIfNotNull(Object, Collection) - Static method in class charite.christo.ChUtils

addInvalidFeatureLine(CharSequence) - Method in class charite.christo.protein.Protein

addJavadocUrl(String, String) - Static method in class charite.christo.ChJavadoc

Classes with package have a Javadoc at url

addLi4CntxtMenu(Component) - Static method in class charite.christo.ChUtils

addLiDb(ActionListener) - Static method in class charite.christo.ChTextComponents

addLine(String) - Method in class charite.christo.Customize

addListDataListener(ListDataListener) - Method in class charite.christo.JListModel

addListDataListener(ListDataListener) - Method in class charite.christo.strap.ProteinComboModel

addListener(StrapListener) - Method in interface charite.christo.protein.ProteinAlignment

addListener(StrapListener) - Method in class charite.christo.strap.StrapAlign

addListeners(Object) - Static method in class charite.christo.strap.StrapAlign

addMarchingAnt(int, Object, Shape, Color, Color) - Static method in class charite.christo.ChUtils

addMenuItem(Object) - Method in class charite.christo.ChJScrollPane

addMenuItemSort(int...) - Method in class charite.christo.ChJScrollPane

addMoli(int, Component) - Static method in class charite.christo.ChUtils

addMsgOutOfMemoryError(String) - Static method in class charite.christo.ChStdout

addOption(long) - Method in class charite.christo.ChJScrollPane

addOptions(long) - Method in class charite.christo.ChJList

addOptions(long) - Method in class charite.christo.UniqueList

addOrRemove(char, Selection3D[], int, int, char, char) - Static method in class charite.christo.protein.Protein3dUtils

addOrRemoveButton(int, JComponent, int) - Method in class charite.christo.protein.Protein3d

addPaintHook(PaintHook, JComponent) - Static method in class charite.christo.ChUtils

addPdbId(String, Protein3d, Class) - Static method in class charite.christo.protein.Protein3dUtils

addPoints(byte[], int, boolean, int, byte[], int, boolean, int, double, int[][]) - Method in class charite.christo.strap.DialogDotPlot

addProfile(byte[][]) - Method in interface charite.christo.protein.SequenceAlignerTakesProfile

addProfile(byte[][]) - Method in class charite.christo.strap.AbstractAligner

addProfiles(SequenceAligner) - Method in class charite.christo.strap.DialogAlign

addProtein(int, Protein) - Method in class charite.christo.strap.StrapView

addProteins(Protein...) - Method in class charite.christo.protein.Protein3d

addProteins(int, Protein[]) - Method in class charite.christo.strap.StrapAlign

Load proteins

addProteinViewer(ProteinViewer) - Method in class charite.christo.protein.Protein

addRef(String, Object, Object) - Static method in class charite.christo.ChUtils

addResidueGap(int, int) - Method in class charite.christo.protein.Protein

addResidueSelection(ResidueSelection) - Method in class charite.christo.protein.Protein

Add a selection of residues

addSelectionInterval(int, int) - Method in class charite.christo.ChListSelectionModel

addSequenceRef(String) - Method in class charite.christo.protein.Protein

addService(Object, Object, Class) - Static method in class charite.christo.ChUtils

addServiceR(ChRunnable, Object, String) - Static method in class charite.christo.ChUtils

addShutdownHook1(Runnable) - Static method in class charite.christo.ChUtils

addSouth(JComponent) - Method in class charite.christo.ChTabPane

addStructure(File, Protein3d, Class) - Static method in class charite.christo.protein.Protein3dUtils

ADDTAB - Static variable in class charite.christo.ChDelay

addTab(JTabbedPane, JComponent, long) - Static method in class charite.christo.ChDelay

addTab(int, Component) - Method in class charite.christo.ChTabPane

addTab(Container, int) - Static method in class charite.christo.InteractiveDownload

addTableModelListener(TableModelListener) - Method in class charite.christo.strap.DialogHighlightPattern

addThreeLetterCode(String, char) - Static method in class charite.christo.protein.Protein

addTo(String, Object) - Method in class charite.christo.EvAdapter

addToEnvironement(Object) - Method in class charite.christo.ChExec

addToLookupTable(Object[], byte[][][]) - Static method in class charite.christo.OccurInText

addTooltip(TooltipProvider, JComponent) - Static method in class charite.christo.ChUtils

addToProteinDatabases(int, String[]) - Static method in class charite.christo.blast.BlastParser

addTreeModelListener(TreeModelListener) - Method in class charite.christo.ChTreeModel

addVariable(String, String) - Method in class charite.christo.PrgParas

addVariableE(String, String) - Method in class charite.christo.PrgParas

addWords(Object) - Static method in class charite.christo.ChJOrthoPROXY

Argument: An String or HasName or ChRunnable or an Array or Collection of them.

adjustmentValueChanged(AdjustmentEvent) - Method in class charite.christo.CollapseComponent

adMainTab(Object, JTabbedPane, Class) - Static method in class charite.christo.ChUtils

adSelListener(Component) - Static method in class charite.christo.ChUtils

adTab(int, String, Object, JTabbedPane) - Static method in class charite.christo.ChUtils

adToArray(int, int[], int) - Static method in class charite.christo.ChUtils

adToArray(T, T[], int, Class<T>) - Static method in class charite.christo.ChUtils

adToStrgs(String, String[], int) - Static method in class charite.christo.ChUtils

adUniq(Object, Collection) - Static method in class charite.christo.ChUtils

adUniq(T, int, List<T>) - Static method in class charite.christo.ChUtils

aFileNotZ(Object...) - Static method in class charite.christo.ChUtils

aFloat(double, int) - Method in class charite.christo.BA

afterAddProteins(Protein...) - Method in class charite.christo.protein.Protein3d

afterDL(String) - Static method in class charite.christo.Customize

afterMS(long, int, Object, long, Object) - Static method in class charite.christo.ChDelay

afterMS(long, int, Object, long, Object, long[]) - Static method in class charite.christo.ChDelay

aHex(long, int) - Method in class charite.christo.BA

aIfSze(int, Object, Object) - Method in class charite.christo.BA

ALIGN_CHANGE_ORDER - Static variable in class charite.christo.strap.SPUtils

Aligner3D - Class in charite.christo.strap

HELP Combining sequence alignment methods and 3D-superposition.

Aligner3D() - Constructor for class charite.christo.strap.Aligner3D

Aligner3D_Mapsci - Class in charite.christo.strap.extensions

Aligner3D_Mapsci() - Constructor for class charite.christo.strap.extensions.Aligner3D_Mapsci

Aligner3D_Matt - Class in charite.christo.strap.extensions

Aligner3D_Matt() - Constructor for class charite.christo.strap.extensions.Aligner3D_Matt

Aligner3D_Mustang - Class in charite.christo.strap.extensions

Authors: Arun S.

Aligner3D_Mustang() - Constructor for class charite.christo.strap.extensions.Aligner3D_Mustang

Aligner3D_Smolign - Class in charite.christo.strap.extensions

Author: Ivaylo Ilinkin and Ravi Janardan Publication: PUBMED:20122279

Aligner3D_Smolign() - Constructor for class charite.christo.strap.extensions.Aligner3D_Smolign

alignerInstance() - Static method in class charite.christo.strap.SPUtils

ALIGNMENT - Static variable in class charite.christo.protein.Bl2seq

ALIGNMENT_CHANGED - Static variable in class charite.christo.protein.StrapEvent

ALIGNMENT_SCROLLED - Static variable in class charite.christo.protein.StrapEvent

AlignmentEntropy - Class in charite.christo.strap.extensions

HELP A profile of the sequence variability of the multiple sequence alignment is displayed.

AlignmentEntropy() - Constructor for class charite.christo.strap.extensions.AlignmentEntropy

alignmentInstantiatedHook(AbstractAlignmentProject.Alignment) - Method in class charite.christo.strap.AbstractAlignmentProject

alignmentInstantiatedHook(AbstractAlignmentProject.Alignment) - Method in class charite.christo.strap.science.Flavine

alignmentPanel() - Static method in class charite.christo.strap.StrapAlign

AlignmentScore - Class in charite.christo.strap.extensions

AlignmentScore() - Constructor for class charite.christo.strap.extensions.AlignmentScore

AlignmentWriter - Interface in charite.christo.strap

AlignmentWriterHSSP - Class in charite.christo.strap.extensions

HELP Example

## PROTEINS : EMBL/SWISSPROT identifier and alignment statistics
NR.
AlignmentWriterHSSP() - 
Constructor for class charite.christo.strap.extensions.AlignmentWriterHSSP
 
alignProteins(SequenceAligner, List<Protein>, boolean[], long) - 
Static method in class charite.christo.strap.SPUtils
 
aliWithMidline(long, byte[], int, String, byte[], int, String, int, BA) - 
Static method in class charite.christo.protein.ChAlignUtils
 
ALL - 
Static variable in class charite.christo.HelpCommands
 
allClassesV(Class) - 
Static method in class charite.christo.strap.StrapPlugins
 
allCommands() - 
Static method in class charite.christo.protein.Protein3dUtils
 
allFiles() - 
Static method in class charite.christo.strap.SPUtils
 
allFnts() - 
Static method in class charite.christo.ChUtils
 
allScriptCommands() - 
Static method in class charite.christo.strap.StrapScriptInterpreter
 
aln(Object) - 
Method in class charite.christo.BA
 
aln(char) - 
Method in class charite.christo.BA
 
alSoftClr(int, Object[]) - 
Static method in class charite.christo.ChUtils
 
ALWAYS_CONTEXT_MENU - 
Static variable in class charite.christo.protein.ProteinLabel
 
ALWAYS_ON_TOP - 
Static variable in class charite.christo.ChFrame
 
AMINO_ACIDS - 
Static variable in class charite.christo.protein.Protein
 
ancestrs(Component) - 
Static method in class charite.christo.ChUtils
 
and(Object, char) - 
Method in class charite.christo.BA
 
and(char, Object) - 
Method in class charite.christo.BA
 
and(Object, Object) - 
Method in class charite.christo.BA
 
and(Object, Object, Object) - 
Method in class charite.christo.BA
 
ANIM_SET_CURS_SCROLL_TO_VISIBLE - 
Static variable in class charite.christo.strap.StrapAlign
 
ANNO - 
Static variable in class charite.christo.strap.V3dListModel
 
AnonymousFTP - Class in charite.christo
 
AnonymousFTP() - 
Constructor for class charite.christo.AnonymousFTP
 
AnonymousFTPPROXY - Class in charite.christo
HELP
The standard Java way to fetch files from the Internet fails for some FTP-addresses.
AnonymousFTPPROXY() - 
Constructor for class charite.christo.AnonymousFTPPROXY
 
anotherMethod() - 
Method in class charite.christo.test.SimulateSynDeadLock
 
ANSI - 
Static variable in class charite.christo.ChCodeViewer
 
ANSI_BLACK - 
Static variable in class charite.christo.ChConstants
 
ANSI_BLUE - 
Static variable in class charite.christo.ChConstants
 
ANSI_BOLD - 
Static variable in class charite.christo.ChConstants
 
ANSI_CYAN - 
Static variable in class charite.christo.ChConstants
 
ANSI_FG_BLACK - 
Static variable in class charite.christo.ChConstants
 
ANSI_FG_BLUE - 
Static variable in class charite.christo.ChConstants
 
ANSI_FG_CYAN - 
Static variable in class charite.christo.ChConstants
 
ANSI_FG_GREEN - 
Static variable in class charite.christo.ChConstants
 
ANSI_FG_MAGENTA - 
Static variable in class charite.christo.ChConstants
 
ANSI_FG_RED - 
Static variable in class charite.christo.ChConstants
 
ANSI_FG_WHITE - 
Static variable in class charite.christo.ChConstants
 
ANSI_FG_YELLOW - 
Static variable in class charite.christo.ChConstants
 
ANSI_GREEN - 
Static variable in class charite.christo.ChConstants
 
ANSI_MAGENTA - 
Static variable in class charite.christo.ChConstants
 
ANSI_RED - 
Static variable in class charite.christo.ChConstants
 
ANSI_RESET - 
Static variable in class charite.christo.ChConstants
 
ANSI_TERMINAL - 
Static variable in class charite.christo.ChConstants
 
ANSI_UL - 
Static variable in class charite.christo.ChConstants
 
ANSI_W_ON_B - 
Static variable in class charite.christo.ChConstants
 
ANSI_W_ON_R - 
Static variable in class charite.christo.ChConstants
 
ANSI_WHITE - 
Static variable in class charite.christo.ChConstants
 
ANSI_YELLOW - 
Static variable in class charite.christo.ChConstants
 
ansiColor(int) - 
Static method in class charite.christo.AnsiEscape
 
AnsiEscape - Class in charite.christo
 
AnsiEscape() - 
Constructor for class charite.christo.AnsiEscape
 
antiAliasing(Graphics) - 
Static method in class charite.christo.ChUtils
 
ANTS_PROTECT_ALIG - 
Static variable in class charite.christo.ChUtils
 
ANTS_SEARCH - 
Static variable in class charite.christo.ChUtils
 
ANY_VIEWER - 
Static variable in class charite.christo.strap.StrapScriptInterpreter
 
ANY_WIRE - 
Static variable in class charite.christo.strap.StrapScriptInterpreter
 
anyFrame() - 
Static method in class charite.christo.ChFrame
 
ANYWHERE - 
Static variable in interface charite.christo.protein.VisibleIn123
 
APPEND - 
Static variable in interface charite.christo.ChRunnable
 
appendName(String, int, BA) - 
Static method in class charite.christo.protein.ChAlignUtils
The gapped sequences may be 0-terminated!
appendNow(Object) - 
Method in class charite.christo.ChTextArea
 
applyAlignPositions(int[][], byte[][]) - 
Static method in class charite.christo.protein.ChAlignUtils
 
applyDict(String, Map<String, String>) - 
Static method in class charite.christo.ChUtils
 
applyPlugin(Object) - 
Static method in class charite.christo.strap.StrapPlugins
 
appndToFile(CharSequence, File) - 
Static method in class charite.christo.ChUtils
 
appndTooltips(Object, String, BA) - 
Static method in class charite.christo.ChUtils
 
aQuoteIfNecessary(Object) - 
Method in class charite.christo.BA
 
ARBITRARY_WORKING_DIRECTORY_ALLOWED - 
Static variable in class charite.christo.Insecure
 
Archive - Class in charite.christo
 
Archive(File, File) - 
Constructor for class charite.christo.Archive
 
Area - Class in charite.andrean
 
Area() - 
Constructor for class charite.andrean.Area
 
aRplc(char, char, Object) - 
Method in class charite.christo.BA
 
aRplc(Object, Object, TextMatches) - 
Method in class charite.christo.BA
 
aRplc(long, Object, Object, CharSequence) - 
Method in class charite.christo.BA
 
ARRAY_CP - 
Static variable in class charite.christo.ChConstants
 
ARRAY_DURATION - 
Static variable in class charite.christo.ChConstants
 
arraysEqul(Object[], Object[]) - 
Static method in class charite.christo.ChUtils
 
arraysEqul(Class, Object[], Object[]) - 
Static method in class charite.christo.ChUtils
 
ARROW_HEADS - 
Static variable in interface charite.christo.protein.VisibleIn123
 
ARROWS_MAXIMIZE - 
Static variable in class charite.christo.ChButton
 
arryToMenuBar(int, Object[][], JMenuBar) - 
Static method in class charite.christo.ChUtils
 
AS_TXT - 
Static variable in class charite.christo.ChJScrollPane
 
asArray() - 
Method in class charite.christo.ChSet
 
asArray(ChRunnable, String) - 
Method in class charite.christo.ChSet
 
asArray() - 
Method in class charite.christo.UniqueList
 
asBytearray(byte[]) - 
Method in class charite.christo.ChTokenizer
 
asChar() - 
Method in class charite.christo.ChTokenizer
 
asFloat() - 
Method in class charite.christo.ChTokenizer
 
asInt() - 
Method in class charite.christo.ChTokenizer
 
ASK_FOR_PERMISSION - 
Static variable in class charite.christo.protein.ChSoapEBI
 
askPermissionInstall(Object, Object) - 
Static method in class charite.christo.ChMsg
 
askUserHome(String) - 
Static method in class charite.christo.ChMsg
 
askViewersSharingView(ProteinViewer, Protein, String) - 
Static method in class charite.christo.protein.Protein3dUtils
 
asLong() - 
Method in class charite.christo.ChTokenizer
 
aSomeBytes(long, int) - 
Method in class charite.christo.BA
 
ASSERT_EDT - 
Static variable in class charite.christo.UniqueList
 
assrt() - 
Static method in class charite.christo.ChUtils
 
assrtEDT() - 
Static method in class charite.christo.ChUtils
 
assrtIsTxt(Object) - 
Static method in class charite.christo.ChUtils
 
asString() - 
Method in class charite.christo.ChTokenizer
 
asStringArray() - 
Method in class charite.christo.PrgParas
 
asStringIP() - 
Method in class charite.christo.ChTokenizer
 
ASTEX - 
Static variable in class charite.christo.protein.Protein3dUtils
 
asText() - 
Static method in class charite.christo.ChEnv
 
AT_CLICK - 
Static variable in class charite.christo.ChFrame
 
AT_CLICK_R - 
Static variable in class charite.christo.ChFrame
 
atLeastNumLettersInColumn(int, int, byte[][]) - 
Static method in class charite.christo.protein.ChAlignUtils
 
ATO - 
Static variable in class charite.christo.protein.PDB_Parser
 
atof(Object) - 
Static method in class charite.christo.ChUtils
 
atof(Object, int, int) - 
Static method in class charite.christo.ChUtils
 
atofLookup() - 
Static method in class charite.christo.ChUtils
 
atoi(Object, int) - 
Static method in class charite.christo.ChUtils
 
atoi(Object, int, int) - 
Static method in class charite.christo.ChUtils
 
atoi(Object) - 
Static method in class charite.christo.ChUtils
 
atoi_debug - 
Static variable in class charite.christo.ChUtils
 
atoiLookup() - 
Static method in class charite.christo.ChUtils
 
atoiOrDefault(Object, int) - 
Static method in class charite.christo.ChUtils
 
atoiOrDefault(Object, int, int) - 
Static method in class charite.christo.ChUtils
 
atol(Object) - 
Static method in class charite.christo.ChUtils
 
atol(Object, int, int) - 
Static method in class charite.christo.ChUtils
 
atolDecHex(Object, int) - 
Static method in class charite.christo.ChUtils
 
ATOM - 
Static variable in class charite.christo.protein.PDB_Parser
 
ATOM_CA - 
Static variable in class charite.christo.ChConstants
 
ATOM_COORDINATES_CHANGED - 
Static variable in class charite.christo.protein.StrapEvent
 
ATOM_LINES - 
Static variable in interface charite.christo.protein.ProteinWriter
 
atomNumber2residueIdx(int) - 
Method in class charite.christo.protein.Protein
Given a pdb Number (2nd column in pdb files)
       What is the residue index ?
ATOMS - 
Static variable in class charite.christo.strap.ResidueAnnotation
 
atomSelected(MoleculeRenderer, Atom) - 
Method in class charite.christo.protein.ChAstex
 
atomsOfAminos() - 
Static method in class charite.christo.protein.Protein3dUtils
 
AUTHORITIES - 
Static variable in class charite.christo.protein.DAS
 
AUTO - 
Static variable in class charite.christo.ChPubmed
 
autoProbeProxy() - 
Static method in class charite.christo.Web
 
AUX_FILE - 
Static variable in class charite.christo.strap.Texshade
 
available() - 
Method in class charite.christo.libs.UncompressInputStream
 

B

B - Static variable in class charite.christo.HtmlUtil

b(int) - Method in class charite.christo.strap.ResidueSelectionPopup

b(String) - Static method in class charite.christo.strap.Tutorials

B_INTO_SAME_LINE - Static variable in class charite.christo.protein.Protein

B_PROCESSED - Static variable in class charite.christo.protein.Protein

B_REGISTERD - Static variable in class charite.christo.protein.Protein

BA - Class in charite.christo

BA(byte[]) - Constructor for class charite.christo.BA

BA(byte[], int, int) - Constructor for class charite.christo.BA

BA(int) - Constructor for class charite.christo.BA

BA(CharSequence) - Constructor for class charite.christo.BA

ba4CurrThrd(Object) - Static method in class charite.christo.ChUtils

BACKGROUND_CHANGED - Static variable in class charite.christo.protein.StrapEvent

BACKSPACE_DEL_ITEM - Static variable in class charite.christo.ChJTable

Backtranslate - Class in charite.christo.protein

Backtranslate() - Constructor for class charite.christo.protein.Backtranslate

backtranslate(byte[], int, Backtranslate.Codonusage, boolean) - Static method in class charite.christo.protein.Backtranslate

Backtranslate.Codonusage - Class in charite.christo.protein

Backtranslate.Codonusage() - Constructor for class charite.christo.protein.Backtranslate.Codonusage

BACKUP_WRITTEN - Static variable in class charite.christo.protein.StrapEvent

baClr(Object[]) - Static method in class charite.christo.ChUtils

baClr(int, Object[]) - Static method in class charite.christo.ChUtils

ballonMsg(AWTEvent, String) - Static method in class charite.christo.ChUtils

BALLOON - Static variable in class charite.christo.strap.ResidueAnnotation

Base64 - Class in charite.christo.libs

BASE64_CHARS - Static variable in class charite.christo.ChConstants

BasicExecutable - Class in charite.christo

HELP

BasicExecutable(String) - Constructor for class charite.christo.BasicExecutable

BasicExecutable() - Constructor for class charite.christo.BasicExecutable

BasicResidueSelection - Class in charite.christo.protein

A skelleton of an Selection of Residues ResidueSelection.

BasicResidueSelection(ResidueSelection) - Constructor for class charite.christo.protein.BasicResidueSelection

BasicResidueSelection(int) - Constructor for class charite.christo.protein.BasicResidueSelection

baSoftClr(Object[]) - Static method in class charite.christo.ChUtils

baSoftClr(int, Object[]) - Static method in class charite.christo.ChUtils

baTip() - Static method in class charite.christo.ChUtils

begin() - Method in class charite.christo.BA

First text position +1

bExampleFiles(String) - Static method in class charite.christo.strap.Tutorials

bg() - Method in class charite.christo.AnsiEscape

bg(int) - Method in class charite.christo.ChButton

bg(Color) - Method in class charite.christo.ChTextView

BG_COLOR - Static variable in class charite.christo.ChDelay

BG_IMAGE - Static variable in class charite.christo.strap.ResidueAnnotation

BG_NOT_EDITABLE - Static variable in class charite.christo.ChConstants

BG_SELECTED - Static variable in class charite.christo.ChUtils

bgSelected() - Static method in class charite.christo.ChUtils

bin2hex(byte[]) - Static method in class charite.christo.Hex2bin

bin2hex(byte[], int, int) - Static method in class charite.christo.Hex2bin

BIOJAVA_3D - Static variable in class charite.christo.AbstractProxy

bit32To4chars(int, char[]) - Static method in class charite.christo.ChUtils

32 bit given as an int value are converted to a String of 4 characters.

BIT_SHIFT_LINE - Static variable in interface charite.christo.protein.VisibleIn123

Bl2seq - Class in charite.christo.protein

HELP Given is an amino acid sequence and one (or several) nucleotide sequences of unknown frame shift.

Bl2seq(long, byte[], byte[], String, BA) - Constructor for class charite.christo.protein.Bl2seq

BL2SEQ - Static variable in class charite.christo.strap.DialogDotPlot

Bl2seq.Hit - Class in charite.christo.protein

Bl2seq.Hit(Bl2seq, int, int, int, int, double) - Constructor for class charite.christo.protein.Bl2seq.Hit

BL2SEQ_MIDLINE - Static variable in class charite.christo.protein.Blosum

blankLabel() - Static method in class charite.christo.ChUtils

BlastAlignment - Class in charite.christo.blast

BlastAlignment() - Constructor for class charite.christo.blast.BlastAlignment

BlastDatabase - Class in charite.christo.blast

BlastDatabase(String, String) - Constructor for class charite.christo.blast.BlastDatabase

Blaster_local_NCBI - Class in charite.christo.blast

HELP NCBI-BLAST can be downloaded from ftp://ftp.ncbi.nih.gov/ or search GOOGLE{ ftp ncbi blast }.

Blaster_local_NCBI() - Constructor for class charite.christo.blast.Blaster_local_NCBI

Blaster_local_NCBI_gapped_PSI - Class in charite.christo.blast

HELP SEE_CLASS:Blaster_local_NCBI

Blaster_local_NCBI_gapped_PSI() - Constructor for class charite.christo.blast.Blaster_local_NCBI_gapped_PSI

Blaster_local_Wu - Class in charite.christo.blast

HELP WU-BLAST can be downloaded from http://blast.wustl.edu/licensing/.

Blaster_local_Wu() - Constructor for class charite.christo.blast.Blaster_local_Wu

Blaster_SOAP_ebi - Class in charite.christo.blast

Blaster_SOAP_ebi() - Constructor for class charite.christo.blast.Blaster_SOAP_ebi

BlastHit - Class in charite.christo.blast

BlastHit() - Constructor for class charite.christo.blast.BlastHit

BlastHitIntersection - Class in charite.christo.blast

BlastHitIntersection() - Constructor for class charite.christo.blast.BlastHitIntersection

BLASTMIDLINE - Static variable in class charite.christo.protein.Blosum

BLASTN - Static variable in class charite.christo.protein.Bl2seq

blastp - Static variable in class charite.christo.protein.Bl2seq

BlastParser - Class in charite.christo.blast

You probably do not need to use this class directly.

BlastParser() - Constructor for class charite.christo.blast.BlastParser

BlastResult - Class in charite.christo.blast

This class provids an object oriented structure of BLAST results.

BlastResult(BA) - Constructor for class charite.christo.blast.BlastResult

BLASTX - Static variable in class charite.christo.protein.Bl2seq

BLINK - Static variable in class charite.christo.AnsiEscape

Blosum - Class in charite.christo.protein

BLOSUM62 - Static variable in class charite.christo.protein.Blosum

BLOSUM62_MAX - Static variable in class charite.christo.protein.Blosum

BLOSUM62_MIN - Static variable in class charite.christo.protein.Blosum

blosumScore(float, float, byte[], byte[], byte[], int, int) - Static method in class charite.christo.protein.Blosum

BLUE_DEBUG - Static variable in class charite.christo.ChConstants

blueYellowRed(float) - Static method in class charite.christo.ChUtils

a value 0<=x<=1 is turned into a color blue ...

BOLD - Static variable in class charite.christo.AnsiEscape

boolEquls(boolean[], int, int, boolean[], int, int) - Static method in class charite.christo.ChUtils

boolObjct(boolean) - Static method in class charite.christo.ChUtils

boolOffstEquls(boolean[], int, boolean[], int) - Static method in class charite.christo.ChUtils

boolToLong(boolean[]) - Static method in class charite.christo.ChUtils

boolToSelection3D(boolean, boolean[], int, Protein, String) - Static method in class charite.christo.protein.Protein3dUtils

boolToText(boolean[], int, String, String) - Method in class charite.christo.BA

boolToText(long, int, String) - Method in class charite.christo.BA

boolToTxt(boolean[]) - Static method in class charite.christo.ChUtils

boundsToPos(boolean, Rectangle) - Method in class charite.christo.ChTextComponents

BUGFIX_OPENJDK_G2 - Static variable in class charite.christo.ChConstants

builtInClassesV(Class, List<Class>) - Static method in class charite.christo.strap.StrapPlugins

BUT_3D - Static variable in class charite.christo.strap.StrapView

BUT_ALIGN - Static variable in class charite.christo.strap.StrapView

BUT_ALIGN_CTRL - Static variable in class charite.christo.strap.StrapView

BUT_ALIGN_UNDO - Static variable in class charite.christo.strap.StrapView

BUT_EXEC - Static variable in class charite.christo.strap.ResidueSelectionPopup

BUT_EXPORT - Static variable in class charite.christo.strap.StrapView

BUT_FEATURE - Static variable in class charite.christo.strap.StrapView

BUT_hiddenP - Static variable in class charite.christo.strap.StrapAlign

BUT_IN_BROWSER - Static variable in class charite.christo.blast.AbstractBlaster

BUT_INFER3D_ALL - Static variable in class charite.christo.strap.StrapView

BUT_INS_VAR - Static variable in class charite.christo.strap.ResidueAnnotationView

BUT_LAB_Add - Static variable in class charite.christo.strap.DialogResidueAnnotationChanges

BUT_LAB_Apply - Static variable in class charite.christo.strap.DialogAlignResult

BUT_LAB_Apply - Static variable in class charite.christo.strap.DialogSuperimpose3D

BUT_LAB_Apply - Static variable in class charite.christo.strap.StrapHotswap

BUT_LAB_B - Static variable in class charite.christo.strap.DialogPublishAlignment

BUT_LAB_Edit - Static variable in class charite.christo.strap.StrapHotswap

BUT_LAB_EditSource - Static variable in class charite.christo.strap.Texshade

BUT_LAB_F - Static variable in class charite.christo.strap.DialogPublishAlignment

BUT_LAB_Kill - Static variable in class charite.christo.strap.DialogResidueAnnotationChanges

BUT_LAB_Load - Static variable in class charite.christo.strap.FilesFetchedFromServer

BUT_LAB_New - Static variable in class charite.christo.strap.StrapHotswap

BUT_LAB_P - Static variable in class charite.christo.strap.DialogPublishAlignment

BUT_LAB_Replace - Static variable in class charite.christo.strap.DialogResidueAnnotationChanges

BUT_LAB_U - Static variable in class charite.christo.strap.DialogPublishAlignment

BUT_LAB_VARIABLES - Static variable in class charite.christo.strap.ResidueAnnotationView

BUT_LAF - Static variable in class charite.christo.ChUtils

BUT_LAF - Static variable in class charite.christo.strap.StrapView

BUT_LIST_HET - Static variable in class charite.christo.strap.StrapView

BUT_LOG - Static variable in class charite.christo.ChUtils

BUT_NEW_PANEL - Static variable in class charite.christo.strap.StrapAlign

BUT_NEW_STRAP - Static variable in class charite.christo.strap.StrapAlign

BUT_NUCL - Static variable in class charite.christo.strap.StrapView

BUT_PREV_MSG - Static variable in class charite.christo.ChUtils

BUT_PROJECT_FOLDER - Static variable in class charite.christo.ChFileChooser

BUT_SAVE - Static variable in class charite.christo.strap.StrapAlign

BUT_SELECT_BY_NAME - Static variable in class charite.christo.strap.StrapAlign

BUT_SEQVISTA - Static variable in class charite.christo.strap.StrapView

BUT_STOP_ALL - Static variable in class charite.christo.strap.StrapAlign

BUT_TEST_PROXY - Static variable in class charite.christo.ChUtils

BUT_TXT - Static variable in class charite.christo.blast.AbstractBlaster

BUT_TXTe - Static variable in class charite.christo.blast.AbstractBlaster

BUT_UPDATEUI - Static variable in class charite.christo.strap.StrapAlign

BUT_WARN_MARCHING_ANTS - Static variable in class charite.christo.strap.StrapView

BUT_WIDTH - Static variable in class charite.christo.ChRenderer

BUT_XML - Static variable in class charite.christo.blast.AbstractBlaster

BUT_XMLb - Static variable in class charite.christo.blast.AbstractBlaster

BUT_ZIP - Static variable in class charite.christo.strap.StrapAlign

ButColor - Class in charite.christo

Opens a JColorChooser.

ButColor(long, Color, Object) - Constructor for class charite.christo.ButColor

butSave(File) - Method in class charite.christo.ChTextComponents

butSetDefault(Class, String) - Static method in class charite.christo.strap.StrapAlign

butShowComputedResults() - Static method in class charite.christo.ChMsg

BUTTN - Static variable in class charite.christo.ChUtils

buttn(int) - Static method in class charite.christo.ChUtils

buttn(AWTEvent) - Static method in class charite.christo.ChUtils

button - Variable in class charite.christo.blast.AbstractBlaster

button(int) - Method in class charite.christo.blast.AbstractBlaster

button(String) - Static method in class charite.christo.strap.StrapAlign

button(int) - Static method in class charite.christo.strap.StrapAlign

button(int) - Static method in class charite.christo.strap.StrapView

BUTTON_GO - Static variable in class charite.christo.ChButton

buttonShow() - Method in class charite.christo.ChLogger

bvect_mat_mult(double[], double[][], double[]) - Method in class charite.andrean.SpBigVector

byteArray() - Method in class charite.christo.ChTextComponents

byteArray() - Method in class charite.christo.ChTextView

bytes() - Method in class charite.christo.BA

The byte array used internally to store the text;

bytes2strg(byte[]) - Static method in class charite.christo.ChUtils

bytes2strg(byte[], int, int) - Static method in class charite.christo.ChUtils

bytsEquls(byte[], int, int, byte[], int) - Static method in class charite.christo.ChUtils

BZip2Constants - Class in charite.christo.libs.bzip2

BZip2Constants() - Constructor for class charite.christo.libs.bzip2.BZip2Constants

C

C(int) - Static method in class charite.christo.ChUtils

C(int, int) - Static method in class charite.christo.ChUtils

C_compiler - Static variable in class charite.christo.Customize

cachedResultsNotOlderThanSec(int) - Method in class charite.christo.blast.AbstractBlaster

cachedResultsNotOlderThanSec(int) - Method in interface charite.christo.blast.SequenceBlaster

Use cached results only when new

CacheResult - Class in charite.christo

HELP Some procedures are computationally expensive such as BLAST searches or 3D superpositions and results are stored on HD
Implementation: Several results are stored within one file.

cacheSK(char) - Method in class charite.christo.blast.AbstractBlaster

calcRoh(double[], double[]) - Static method in class charite.christo.strap.science.SpearmansRangCorrelation

callEvery(long, int, Runnable, String) - Static method in class charite.christo.ChThread

CALPHA - Static variable in class charite.christo.strap.ProteinList

CAN_BE_STOPPED - Static variable in class charite.christo.ChUtils

CanBeStopped - Interface in charite.christo

cancelCellEditing() - Method in class charite.christo.ChRenderer

cancelCellEditing() - Method in class charite.christo.strap.ResidueAnnotationView

canInstall() - Static method in class charite.christo.protein.Pymol

canModify(File) - Static method in class charite.christo.Insecure

canModifyNiceMsg(File) - Static method in class charite.christo.ChUtils

CAPABILITY_TYPE_feature - Static variable in class charite.christo.protein.DAS

capitalize(CharSequence) - Static method in class charite.christo.ChUtils

caretUpdate(CaretEvent) - Method in class charite.christo.ChScriptPanel

cb() - Method in class charite.christo.ChButton

cb1() - Method in class charite.christo.ChButton

CB_HITS - Static variable in class charite.christo.strap.DialogDotPlot

CB_LAB_Postscript - Static variable in class charite.christo.strap.Texshade

CB_LAB_Trace - Static variable in class charite.christo.strap.DialogDotPlot

cbCommutative(boolean) - Static method in class charite.christo.strap.AbstractAligner

cbDndTransformHetero() - Static method in class charite.christo.protein.HeteroCompound

cbox(boolean, String, String) - Static method in class charite.christo.ChUtils

cbox(String) - Static method in class charite.christo.ChUtils

CBZip2InputStream - Class in charite.christo.libs.bzip2

An input stream that decompresses from the BZip2 format (without the file header chars) to be read as any other stream.

CBZip2InputStream(InputStream) - Constructor for class charite.christo.libs.bzip2.CBZip2InputStream

Constructs a new CBZip2InputStream which decompresses bytes read from the specified stream.

cc(Object) - Static method in class charite.christo.Customize

CDS_GENE - Static variable in class charite.christo.protein.Protein

CDS_NOTE - Static variable in class charite.christo.protein.Protein

CDS_PRODUCT - Static variable in class charite.christo.protein.Protein

CDS_PROTEIN - Static variable in class charite.christo.protein.Protein

CDS_TRANSCRIPT_ID - Static variable in class charite.christo.protein.Protein

CDS_TRANSLATION - Static variable in class charite.christo.protein.Protein

CDS_XREFS - Static variable in class charite.christo.protein.Protein

cdsExpressionApplied() - Method in class charite.christo.protein.Protein

CENTER - Static variable in class charite.christo.ChFrame

CENTRIOLE - Static variable in interface charite.christo.protein.PredictSubcellularLocation

chain2color(int) - Static method in class charite.christo.protein.Protein3d

CHAIN_A - Static variable in interface charite.christo.protein.ProteinWriter

CHAIN_B - Static variable in interface charite.christo.protein.ProteinWriter

CHAIN_ID - Static variable in class charite.christo.protein.PDB_Parser

CHAIN_SPACE - Static variable in interface charite.christo.protein.ProteinWriter

CHAINS - Static variable in class charite.christo.strap.ProteinList

chainsInPDBfile(BA) - Static method in class charite.christo.PDB_separateChains

ChAlignUtils - Class in charite.christo.protein

ChAlignUtils() - Constructor for class charite.christo.protein.ChAlignUtils

changeAtoms(boolean, Selection3D[], String) - Static method in class charite.christo.protein.Protein3dUtils

changed() - Method in class charite.christo.strap.ProteinCombo

CHANGED_CHILDS_OF_PROTEIN - Static variable in class charite.christo.ChUtils

CHANGED_COMBOBOX - Static variable in class charite.christo.ChUtils

CHANGED_PLUGINS_ADDED_OR_REMOVED - Static variable in class charite.christo.ChUtils

CHANGED_PROTEIN_AT_CURSOR - Static variable in class charite.christo.ChUtils

CHANGED_PROTEIN_LABEL - Static variable in class charite.christo.ChUtils

CHANGED_PROTEIN_ORDER - Static variable in class charite.christo.ChUtils

CHANGED_SELECTED_OBJECTS - Static variable in class charite.christo.ChUtils

changedUpdate(DocumentEvent) - Method in class charite.christo.ChTextComponents

changeOrder(Object[], Object[]) - Method in class charite.christo.protein.Superimpose3D.Result

changeSelectedAA(boolean[], int, ResidueSelection) - Static method in class charite.christo.protein.BasicResidueSelection

ChAppleScript - Class in charite.christo

ChAppleScript() - Constructor for class charite.christo.ChAppleScript

ChAquaScrollBarUI - Class in charite.christo

ChAquaScrollBarUI() - Constructor for class charite.christo.ChAquaScrollBarUI

charA(Object) - Static method in class charite.christo.ChUtils

CHARACTER_SEQUENCE_CHANGED - Static variable in class charite.christo.protein.StrapEvent

charAt(int) - Method in class charite.christo.BA

charH(Object) - Static method in class charite.christo.ChUtils

charite.andrean - package charite.andrean

charite.christo - package charite.christo

charite.christo.blast - package charite.christo.blast

charite.christo.hotswap - package charite.christo.hotswap

charite.christo.libs - package charite.christo.libs

charite.christo.libs.bzip2 - package charite.christo.libs.bzip2

charite.christo.protein - package charite.christo.protein

charite.christo.strap - package charite.christo.strap

charite.christo.strap.extensions - package charite.christo.strap.extensions

charite.christo.strap.science - package charite.christo.strap.science

charite.christo.test - package charite.christo.test

charObjct(char) - Static method in class charite.christo.ChUtils

charsTo32bit(int, int, int, int) - Static method in class charite.christo.ChUtils

charsTo32bit(byte[], int) - Static method in class charite.christo.ChUtils

CHART_DATA - Static variable in class charite.christo.strap.AbstractAlignmentProject

chartMouseClicked(ChartMouseEvent) - Method in class charite.christo.strap.science.Flavine

chartMouseMoved(ChartMouseEvent) - Method in class charite.christo.strap.science.Flavine

charW(Object) - Static method in class charite.christo.ChUtils

ChAstex - Class in charite.christo.protein

ChAstex() - Constructor for class charite.christo.protein.ChAstex

ChAstexPROXY - Class in charite.christo.protein

HELP Home: http://openastexviewer.net http://www.astex-therapeutics.com/
License of OpenAstexViewer: WIKI:LGPL
Authors: Mike Hartshorn, Tom Oldfield

ChAstexPROXY() - Constructor for class charite.christo.protein.ChAstexPROXY

ChButton - Class in charite.christo

ChButton(AbstractButton) - Constructor for class charite.christo.ChButton

ChButton() - Constructor for class charite.christo.ChButton

ChButton(String) - Constructor for class charite.christo.ChButton

ChButton(String, long) - Constructor for class charite.christo.ChButton

ChButton(char, String) - Constructor for class charite.christo.ChButton

ChButton.MItem - Class in charite.christo

ChButton.MItem(String) - Constructor for class charite.christo.ChButton.MItem

ChCatdoc - Class in charite.christo

ChCatdoc() - Constructor for class charite.christo.ChCatdoc

ChClassLoader1 - Class in charite.christo

ChCodeViewer - Class in charite.christo

chColSize(int, int, int) - Method in class charite.christo.ChTableLayout

ChCombo - Class in charite.christo

extended choice box

ChCombo(String...) - Constructor for class charite.christo.ChCombo

ChCombo(long, Object) - Constructor for class charite.christo.ChCombo

ChComparator - Class in charite.christo

ChComparator(int) - Constructor for class charite.christo.ChComparator

ChCompilerJavac - Class in charite.christo

ChCompilerJavac() - Constructor for class charite.christo.ChCompilerJavac

ChCompilerJavacPROXY - Class in charite.christo

ChCompilerJavacPROXY() - Constructor for class charite.christo.ChCompilerJavacPROXY

ChConstants - Class in charite.christo

ChDelay - Class in charite.christo

This utility class manages threads.

ChDelay(long, int, Object, Object) - Constructor for class charite.christo.ChDelay

ChDelay(long, int, Object, long, Object, long[]) - Constructor for class charite.christo.ChDelay

checkForNewVersion(String) - Static method in class charite.christo.Web

checkForUpdates(Class[]) - Static method in class charite.christo.BasicExecutable

checkIntegrityOfZipFile(File, List<String>) - Static method in class charite.christo.ChZip

checkPermission(long, String[], String[], File) - Static method in class charite.christo.ChExecSecurity

CHEMICAL - Static variable in class charite.christo.protein.ShadingAA

ChEnv - Class in charite.christo

In Java1.4 the shell variables are read by calling the command "set".

chEvLi() - Static method in class charite.christo.ChUtils

ChExec - Class in charite.christo

execute external programs Several alternative command lines can be set.

ChExec(long) - Constructor for class charite.christo.ChExec

ChExecSecurity - Class in charite.christo

ChExecSecurity() - Constructor for class charite.christo.ChExecSecurity

ChFile - Class in charite.christo

ChFile(String, boolean) - Constructor for class charite.christo.ChFile

ChFile(File, String, boolean) - Constructor for class charite.christo.ChFile

ChFileChooser - Class in charite.christo

ChFileChooser(long, String) - Constructor for class charite.christo.ChFileChooser

ChFileFilter - Class in charite.christo

ChFileFilter(FileFilter[]) - Constructor for class charite.christo.ChFileFilter

ChFileFilter(String) - Constructor for class charite.christo.ChFileFilter

ChFrame - Class in charite.christo

ChFrame(String) - Constructor for class charite.christo.ChFrame

ChHttpClient - Class in charite.christo

ChHttpClient() - Constructor for class charite.christo.ChHttpClient

ChHttpClientPROXY - Class in charite.christo

HELP

ChHttpClientPROXY() - Constructor for class charite.christo.ChHttpClientPROXY

ChIcon - Class in charite.christo

HELP Image icons are a visual aid to recognize proteins and residue annotations.

ChIcon() - Constructor for class charite.christo.ChIcon

child(Component, Class<T>) - Static method in class charite.christo.ChUtils

child(Component, Class<T>, String) - Static method in class charite.christo.ChUtils

child(JComponent) - Method in class charite.christo.CollapseComponent

childs(Component) - Static method in class charite.christo.ChUtils

childsR(Component, Class<T>) - Static method in class charite.christo.ChUtils

ChInStream - Class in charite.christo

ChInStream(InputStream) - Constructor for class charite.christo.ChInStream

ChJarSignersHardLinker - Class in charite.christo

A utility class for working around the java webstart jar signing/security bug see http://bugs.sun.com/view_bug.do?bug_id=6967414 and http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=6805618

ChJarSignersHardLinker() - Constructor for class charite.christo.ChJarSignersHardLinker

ChJavadoc - Class in charite.christo

Utility classes for Javadoc.

ChJCheckBox - Class in charite.christo

the extended button class

ChJCheckBox(AbstractButton) - Constructor for class charite.christo.ChJCheckBox

ChJHighlighter - Class in charite.christo

ChJHighlighter(ChTextComponents) - Constructor for class charite.christo.ChJHighlighter

ChJList - Class in charite.christo

HELP This list supports WIKI:Drag_and_drop (Watch movie STRING:ChConstants#MOVIE_Export_Proteins STRING:ChConstants#MOVIE_Drag_to_another_STRAP STRING:ChConstants#MOVIE_Drag_protein_to_3D STRING:ChConstants#MOVIE_Sequence_Features_in_3D) Reordering WIKI:Context_menu (Watch movie STRING:ChConstants#MOVIE_Context_Menu) Keep window always visible: You may want to set the window "Floating on top".

ChJList(Object, long) - Constructor for class charite.christo.ChJList

ChJMenu - Class in charite.christo

ChJMenu(String) - Constructor for class charite.christo.ChJMenu

ChJMenu(ChButton) - Constructor for class charite.christo.ChJMenu

ChJMenuBar - Class in charite.christo

ChJMenuBar() - Constructor for class charite.christo.ChJMenuBar

ChJmol - Class in charite.christo.protein

Jmol Home: http://jmol.sourceforge.net/
License: WIKI:LGPL

ChJmol() - Constructor for class charite.christo.protein.ChJmol

ChJmolPROXY - Class in charite.christo.protein

HELP Home: http://jmol.sourceforge.net/
License: WIKI:LGPL
The protein structure viewer WIKI:Jmol is written in Java and understands Rasmol-instructions.

ChJmolPROXY() - Constructor for class charite.christo.protein.ChJmolPROXY

ChJnlp - Class in charite.christo

ChJnlp() - Constructor for class charite.christo.ChJnlp

ChJOrtho - Class in charite.christo

ChJOrtho() - Constructor for class charite.christo.ChJOrtho

ChJOrthoPROXY - Class in charite.christo

HELP Home:http://www.inetsoftware.de/other-products/jortho
License of JOrtho: GPL

ChJOrthoPROXY() - Constructor for class charite.christo.ChJOrthoPROXY

ChJScrollPane - Class in charite.christo

ChJScrollPane(long, Component) - Constructor for class charite.christo.ChJScrollPane

ChJTable - Class in charite.christo

ChJTable(TableModel, long) - Constructor for class charite.christo.ChJTable

CHJTABLE_BACKSPACE_DEACTIVATED - Static variable in class charite.christo.ChJTable

CHJTABLE_CLEAR - Static variable in class charite.christo.ChJTable

CHJTABLE_FOCUSED_BLACK - Static variable in class charite.christo.ChJTable

CHJTABLE_SHOW_BUT_MAXIM - Static variable in class charite.christo.ChJTable

ChJTextPane - Class in charite.christo

HELP

ChJTextPane(CharSequence) - Constructor for class charite.christo.ChJTextPane

ChJTree - Class in charite.christo

ChJTree(long, TreeModel) - Constructor for class charite.christo.ChJTree

ChListSelectionModel - Class in charite.christo

ChListSelectionModel(Object) - Constructor for class charite.christo.ChListSelectionModel

ChLogger - Class in charite.christo

ChLogger(int, int) - Constructor for class charite.christo.ChLogger

ChMap<K,V> - Class in charite.christo

ChMap() - Constructor for class charite.christo.ChMap

ChMap(long, Class, Class, int) - Constructor for class charite.christo.ChMap

ChMetalScrollBarUI - Class in charite.christo

ChMetalScrollBarUI() - Constructor for class charite.christo.ChMetalScrollBarUI

ChMsg - Class in charite.christo

Some modale message dialogs

ChMsgDia - Class in charite.christo

Some modale message dialogs

ChMsgDia(int, Object, String[], long) - Constructor for class charite.christo.ChMsgDia

choiceShading() - Static method in class charite.christo.strap.StrapView

CHOOSE_CONTEXT - Static variable in class charite.christo.strap.ResSelUtils

CHOOSE_EDIT - Static variable in class charite.christo.strap.ResSelUtils

CHOOSE_SINGLE - Static variable in class charite.christo.strap.ResSelUtils

chooseResSels(long, ResidueSelection[], AWTEvent, String, Runnable) - Static method in class charite.christo.strap.ResSelUtils

ChPanel - Class in charite.christo

ChPanel() - Constructor for class charite.christo.ChPanel

ChPdfUtils - Class in charite.christo

ChPdfUtils() - Constructor for class charite.christo.ChPdfUtils

ChPdfUtilsPROXY - Class in charite.christo

HELP Home: http://pdfbox.apache.org/
License of JPdf: Apache License v2.0

ChPdfUtilsPROXY() - Constructor for class charite.christo.ChPdfUtilsPROXY

ChPubmed - Class in charite.christo

HELP

ChPubmed() - Constructor for class charite.christo.ChPubmed

chrAt(int, Object) - Static method in class charite.christo.ChUtils

chrBnds(Font) - Static method in class charite.christo.ChUtils

chrClas(String) - Static method in class charite.christo.ChUtils

chrClas(int) - Static method in class charite.christo.ChUtils

chrClas1(char) - Static method in class charite.christo.ChUtils

ChRegex - Class in charite.christo

putln(ChRegex.replace(ChRegex.pattern("(34)"), " $1$1 ", "12345678"));

ChRenderer - Class in charite.christo

This list cell renderer is used for list components that contain java classes

ChRenderer() - Constructor for class charite.christo.ChRenderer

ChRunnable - Interface in charite.christo

ChScriptPanel - Class in charite.christo

ChScriptPanel(String, Object, URL, ChRunnable) - Constructor for class charite.christo.ChScriptPanel

ChScrollBar - Class in charite.christo

ChScrollBar(int) - Constructor for class charite.christo.ChScrollBar

ChSet<E> - Class in charite.christo

ChSet(long, Class) - Constructor for class charite.christo.ChSet

ChSlider - Class in charite.christo

convenient extension of JSlider

ChSlider(String, int, int, int) - Constructor for class charite.christo.ChSlider

ChSoapEBI - Class in charite.christo.protein

ChSprite - Class in charite.christo

ChSprite(long, Component, Point, Component, Point, Object, float) - Constructor for class charite.christo.ChSprite

ChStdout - Class in charite.christo

HELP

ChStdout() - Constructor for class charite.christo.ChStdout

chSze(int[], int) - Static method in class charite.christo.ChUtils

chSze(long[], int) - Static method in class charite.christo.ChUtils

chSze(String[], int) - Static method in class charite.christo.ChUtils

chSze(short[], int) - Static method in class charite.christo.ChUtils

chSze(byte[], int) - Static method in class charite.christo.ChUtils

chSze(byte[][], int) - Static method in class charite.christo.ChUtils

chSze(boolean[], int) - Static method in class charite.christo.ChUtils

chSze(float[], int) - Static method in class charite.christo.ChUtils

chSze(double[], int) - Static method in class charite.christo.ChUtils

chSze(Object[], int, Class<T>) - Static method in class charite.christo.ChUtils

ChTableLayout - Class in charite.christo

Container that arranges components horizontally.

ChTableLayout(long) - Constructor for class charite.christo.ChTableLayout

ChTableModel - Class in charite.christo

ChTableModel(long, String...) - Constructor for class charite.christo.ChTableModel

ChTabPane - Class in charite.christo

A reimplementation of tabbed pane since JTabbedPane does not work very well

ChTabPane(long) - Constructor for class charite.christo.ChTabPane

ChTar - Class in charite.christo

ChTar() - Constructor for class charite.christo.ChTar

ChTarPROXY - Class in charite.christo

HELP Home: http://www.gjt.org/servlets/JCVSlet/list/ice/com/ice/tar/
License of tar.zip: tar/doc/LICENSE says: "...You are free to use this work in any way you wish..."

ChTarPROXY() - Constructor for class charite.christo.ChTarPROXY

ChTextArea - Class in charite.christo

ChTextArea(CharSequence) - Constructor for class charite.christo.ChTextArea

ChTextArea(int, int) - Constructor for class charite.christo.ChTextArea

ChTextComponents - Class in charite.christo

Utilities for TextComponents

ChTextComponents(JComponent) - Constructor for class charite.christo.ChTextComponents

ChTextField - Class in charite.christo

ChTextField() - Constructor for class charite.christo.ChTextField

ChTextField(Object) - Constructor for class charite.christo.ChTextField

ChTextField(Object, long) - Constructor for class charite.christo.ChTextField

ChTextReplacement - Class in charite.christo

ChTextReplacement(String, String) - Constructor for class charite.christo.ChTextReplacement

ChTextView - Class in charite.christo

ChTextView(File) - Constructor for class charite.christo.ChTextView

ChTextView(CharSequence) - Constructor for class charite.christo.ChTextView

ChTextView(int) - Constructor for class charite.christo.ChTextView

ChThread - Class in charite.christo

Periodically calls Runnable objects.

ChTokenizer - Class in charite.christo

A fast Tokenizer

ChTokenizer() - Constructor for class charite.christo.ChTokenizer

ChTransferable - Class in charite.christo

HELP

Objects are dragged with the mouse and dropped on a target (see WIKI:Drag_and_drop).

ChTransferable(Object[], int) - Constructor for class charite.christo.ChTransferable

ChTreeModel - Class in charite.christo

ChTreeModel(long, Object) - Constructor for class charite.christo.ChTreeModel

ChUtils - Class in charite.christo

Static utility methods.

ChUtils.EvLi - Class in charite.christo

ChUtils.EvLi() - Constructor for class charite.christo.ChUtils.EvLi

ChWindowsScrollBarUI - Class in charite.christo

ChWindowsScrollBarUI() - Constructor for class charite.christo.ChWindowsScrollBarUI

ChZip - Class in charite.christo

to extract jar packages

ckHtml(Object) - Static method in class charite.christo.ChUtils

clas(Object) - Static method in class charite.christo.ChUtils

clasNam(Object) - Static method in class charite.christo.ChUtils

clasNamWithSlash(Object) - Static method in class charite.christo.ChUtils

CLASS_Aligner3D - Static variable in class charite.christo.ChConstants

CLASS_Aligner3D_Mapsci - Static variable in class charite.christo.ChConstants

CLASS_Aligner3D_Matt - Static variable in class charite.christo.ChConstants

CLASS_Aligner3D_Mustang - Static variable in class charite.christo.ChConstants

CLASS_Aligner3D_Smolign - Static variable in class charite.christo.ChConstants

CLASS_AlignmentEntropy - Static variable in class charite.christo.ChConstants

CLASS_AlignmentScore - Static variable in class charite.christo.ChConstants

CLASS_AlignmentWriterHSSP - Static variable in class charite.christo.ChConstants

CLASS_Blaster_local_NCBI - Static variable in class charite.christo.ChConstants

CLASS_Blaster_local_NCBI_gapped_PSI - Static variable in class charite.christo.ChConstants

CLASS_Blaster_local_Wu - Static variable in class charite.christo.ChConstants

CLASS_Blaster_SOAP_ebi - Static variable in class charite.christo.ChConstants

CLASS_ChAstexPROXY - Static variable in class charite.christo.ChConstants

CLASS_ChJmolPROXY - Static variable in class charite.christo.ChConstants

CLASS_CoiledCoil_PredictorRobinson - Static variable in class charite.christo.ChConstants

CLASS_ConsensusSequence - Static variable in class charite.christo.ChConstants

CLASS_CountResidues - Static variable in class charite.christo.ChConstants

CLASS_CrudeSequenceDisSimilarity - Static variable in class charite.christo.ChConstants

CLASS_DemoAssociateObjectsToProteins - Static variable in class charite.christo.ChConstants

CLASS_DesktopUtils - Static variable in class charite.christo.ChConstants

CLASS_Dialog3DViewer - Static variable in class charite.christo.ChConstants

CLASS_Dialog_bl2seq - Static variable in class charite.christo.ChConstants

CLASS_DialogAlign - Static variable in class charite.christo.ChConstants

CLASS_DialogAlignOneToAll - Static variable in class charite.christo.ChConstants

CLASS_DialogBarChart - Static variable in class charite.christo.ChConstants

CLASS_DialogBlast - Static variable in class charite.christo.ChConstants

CLASS_DialogCompareProteins - Static variable in class charite.christo.ChConstants

CLASS_DialogCopyAnnotations - Static variable in class charite.christo.ChConstants

CLASS_DialogDifferentResidues - Static variable in class charite.christo.ChConstants

CLASS_DialogDotPlot - Static variable in class charite.christo.ChConstants

CLASS_DialogExportAlignment - Static variable in class charite.christo.ChConstants

CLASS_DialogExportProteins - Static variable in class charite.christo.ChConstants

CLASS_DialogExportWord - Static variable in class charite.christo.ChConstants

CLASS_DialogFetchPdb - Static variable in class charite.christo.ChConstants

CLASS_DialogFetchSRS - Static variable in class charite.christo.ChConstants

CLASS_DialogGenbank - Static variable in class charite.christo.ChConstants

CLASS_DialogHighlightPattern - Static variable in class charite.christo.ChConstants

CLASS_DialogImportMFA - Static variable in class charite.christo.ChConstants

CLASS_DialogInferCDS - Static variable in class charite.christo.ChConstants

CLASS_DialogManyInOneRow - Static variable in class charite.christo.ChConstants

CLASS_DialogNewProtein - Static variable in class charite.christo.ChConstants

CLASS_DialogNonRedundantSequenceSet - Static variable in class charite.christo.ChConstants

CLASS_DialogPhylogeneticTree - Static variable in class charite.christo.ChConstants

CLASS_DialogPlot - Static variable in class charite.christo.ChConstants

CLASS_DialogPredictCoiledCoil - Static variable in class charite.christo.ChConstants

CLASS_DialogPredictSecondaryStructures - Static variable in class charite.christo.ChConstants

CLASS_DialogPredictTmHelices2 - Static variable in class charite.christo.ChConstants

CLASS_DialogPredictTmHelicesMulti - Static variable in class charite.christo.ChConstants

CLASS_DialogProteinList - Static variable in class charite.christo.ChConstants

CLASS_DialogPublishAlignment - Static variable in class charite.christo.ChConstants

CLASS_DialogRenameProteins - Static variable in class charite.christo.ChConstants

CLASS_DialogResidueAnnotationChanges - Static variable in class charite.christo.ChConstants

CLASS_DialogResidueAnnotationList - Static variable in class charite.christo.ChConstants

CLASS_DialogRestoreFromBackup - Static variable in class charite.christo.ChConstants

CLASS_DialogSelectionOfResidues - Static variable in class charite.christo.ChConstants

CLASS_DialogSelectionOfResiduesMain - Static variable in class charite.christo.ChConstants

CLASS_DialogSimilarStructure - Static variable in class charite.christo.ChConstants

CLASS_DialogSortProteins - Static variable in class charite.christo.ChConstants

CLASS_DialogSubcellularLocalization - Static variable in class charite.christo.ChConstants

CLASS_DialogSuperimpose3D - Static variable in class charite.christo.ChConstants

CLASS_Distance3DToCursor - Static variable in class charite.christo.ChConstants

CLASS_Distance3DToHetero - Static variable in class charite.christo.ChConstants

CLASS_DnaExonStart - Static variable in class charite.christo.ChConstants

CLASS_EditDna - Static variable in class charite.christo.ChConstants

CLASS_Example - Static variable in class charite.christo.Customize

CLASS_ExecPath - Static variable in class charite.christo.Customize

CLASS_FlavinePROXY - Static variable in class charite.christo.ChConstants

CLASS_Hydrophobicity - Static variable in class charite.christo.ChConstants

CLASS_Hyperrefs - Static variable in class charite.christo.ChConstants

CLASS_IndividualSequenceDisSimilarity - Static variable in class charite.christo.ChConstants

CLASS_InitCommands - Static variable in class charite.christo.Customize

CLASS_IntermediateSeq - Static variable in class charite.christo.ChConstants

CLASS_LateCommands - Static variable in class charite.christo.Customize

CLASS_MultipleAligner_SPEM - Static variable in class charite.christo.ChConstants

CLASS_MultipleAlignerAlign_m - Static variable in class charite.christo.ChConstants

CLASS_MultipleAlignerAmap - Static variable in class charite.christo.ChConstants

CLASS_MultipleAlignerClustalW - Static variable in class charite.christo.ChConstants

CLASS_MultipleAlignerDialign - Static variable in class charite.christo.ChConstants

CLASS_MultipleAlignerDialignT - Static variable in class charite.christo.ChConstants

CLASS_MultipleAlignerKalign - Static variable in class charite.christo.ChConstants

CLASS_MultipleAlignerMafft - Static variable in class charite.christo.ChConstants

CLASS_MultipleAlignerMuscle - Static variable in class charite.christo.ChConstants

CLASS_MultipleAlignerProbcons2 - Static variable in class charite.christo.ChConstants

CLASS_MultipleAlignerT_Coffee - Static variable in class charite.christo.ChConstants

CLASS_NAMES - Static variable in class charite.christo.ChRenderer

CLASS_PairAlignerJAlignerPROXY - Static variable in class charite.christo.ChConstants

CLASS_PairAlignerNeoBioPROXY - Static variable in class charite.christo.ChConstants

CLASS_PhylogeneticTree_Archaeopteryx - Static variable in class charite.christo.ChConstants

CLASS_PhylogeneticTree_TreeTop - Static variable in class charite.christo.ChConstants

CLASS_Prione - Static variable in class charite.christo.ChConstants

CLASS_Proteasome - Static variable in class charite.christo.ChConstants

CLASS_Protein3d - Static variable in class charite.christo.ChConstants

CLASS_ProteinsSorter_with3D_without3D - Static variable in class charite.christo.ChConstants

CLASS_Pymol - Static variable in class charite.christo.ChConstants

CLASS_RENDERER - Static variable in class charite.christo.ChJTable

CLASS_ResidueAnnotationView - Static variable in class charite.christo.ChConstants

CLASS_ResidueHydrophobicity_TOPPRED - Static variable in class charite.christo.ChConstants

CLASS_ResidueSolventAccessibility - Static variable in class charite.christo.ChConstants

CLASS_ResidueValues_from_textfile - Static variable in class charite.christo.ChConstants

CLASS_SecondaryStructure_Jnet - Static variable in class charite.christo.ChConstants

CLASS_SecondaryStructure_NNPREDICT - Static variable in class charite.christo.ChConstants

CLASS_SecondaryStructure_Sopma - Static variable in class charite.christo.ChConstants

CLASS_SequenceDisSimilarityAsAligned - Static variable in class charite.christo.ChConstants

CLASS_SimilarPdb_blastEBI - Static variable in class charite.christo.ChConstants

CLASS_StrapHotswap - Static variable in class charite.christo.ChConstants

CLASS_Superimpose_CEPROXY - Static variable in class charite.christo.ChConstants

CLASS_Superimpose_GangstaPlus - Static variable in class charite.christo.ChConstants

CLASS_Superimpose_GoedePROXY - Static variable in class charite.christo.ChConstants

CLASS_Superimpose_LajollaProteinPROXY - Static variable in class charite.christo.ChConstants

CLASS_Superimpose_LajollaRNA - Static variable in class charite.christo.ChConstants

CLASS_Superimpose_native_CE - Static variable in class charite.christo.ChConstants

CLASS_Superimpose_TM_align - Static variable in class charite.christo.ChConstants

CLASS_Texshade - Static variable in class charite.christo.ChConstants

CLASS_TransmembraneHelix_DAS - Static variable in class charite.christo.ChConstants

CLASS_TransmembraneHelix_HMMTOP - Static variable in class charite.christo.ChConstants

CLASS_TransmembraneHelix_MEMSAT - Static variable in class charite.christo.ChConstants

CLASS_TransmembraneHelix_ORIENTM - Static variable in class charite.christo.ChConstants

CLASS_TransmembraneHelix_Phobius - Static variable in class charite.christo.ChConstants

CLASS_TransmembraneHelix_PRED_TMR - Static variable in class charite.christo.ChConstants

CLASS_TransmembraneHelix_SOSUI - Static variable in class charite.christo.ChConstants

CLASS_TransmembraneHelix_SPLIT3 - Static variable in class charite.christo.ChConstants

CLASS_TransmembraneHelix_SPLIT4 - Static variable in class charite.christo.ChConstants

CLASS_TransmembraneHelix_THUMBUP - Static variable in class charite.christo.ChConstants

CLASS_TransmembraneHelix_TMAP - Static variable in class charite.christo.ChConstants

CLASS_TransmembraneHelix_TMAP_MULTI - Static variable in class charite.christo.ChConstants

CLASS_TransmembraneHelix_TMHMM2 - Static variable in class charite.christo.ChConstants

CLASS_TransmembraneHelix_TMPRED - Static variable in class charite.christo.ChConstants

CLASS_TransmembraneHelix_TOPPRED - Static variable in class charite.christo.ChConstants

CLASS_TransmembraneHelix_WaveTM - Static variable in class charite.christo.ChConstants

classChoice(Class) - Static method in class charite.christo.strap.StrapAlign

CLASSES - Static variable in interface charite.christo.protein.SimilarPdbFinder

CLASSLOADER - Static variable in class charite.christo.ChUtils

CLASSLOADING_ALLOWED - Static variable in class charite.christo.Insecure

CLASSPATH - Static variable in class charite.christo.Customize

classpth(boolean, File) - Static method in class charite.christo.ChUtils

classRenderer(Class) - Method in class charite.christo.ChCombo

clazz(Object) - Static method in class charite.christo.ChUtils

clear() - Method in class charite.christo.ChMap

clear() - Method in class charite.christo.ChSet

clear() - Method in class charite.christo.TextMatches

clear() - Method in class charite.christo.UniqueList

clearImage() - Method in class charite.christo.strap.HScrollBar

clearSelection() - Method in class charite.christo.ChListSelectionModel

clipBnds(Graphics) - Static method in class charite.christo.ChUtils

clipBnds(Graphics, int, int) - Static method in class charite.christo.ChUtils

cln() - Method in class charite.christo.ChButton

cln() - Method in class charite.christo.ChCombo

cln() - Method in class charite.christo.ChSlider

cloneProtein(P) - Method in class charite.christo.protein.Protein

clos(int, Object) - Static method in class charite.christo.ChUtils

CLOSE - Static variable in class charite.christo.ChFileChooser

close() - Method in class charite.christo.libs.bzip2.CBZip2InputStream

CLOSE_ALLOWED - Static variable in class charite.christo.ChConstants

CLOSE_ASK - Static variable in class charite.christo.ChConstants

CLOSE_CHILDS - Static variable in class charite.christo.ChConstants

CLOSE_CtrlW - Static variable in class charite.christo.ChConstants

CLOSE_CtrlW_ESC - Static variable in class charite.christo.ChConstants

CLOSE_DISPOSE - Static variable in class charite.christo.ChConstants

CLOSE_DISPOSE_TABS - Static variable in class charite.christo.ChConstants

CLOSE_ESC - Static variable in class charite.christo.ChConstants

CLOSE_MASK - Static variable in class charite.christo.ChConstants

CLOSE_NO_REMOVE - Static variable in class charite.christo.ChConstants

CLOSE_RM_CHILDS - Static variable in class charite.christo.ChConstants

closeOnKey(int, Component, Object) - Static method in class charite.christo.ChUtils

closeOpts(Object) - Static method in class charite.christo.ChUtils

closestProtein(Protein[], long) - Method in class charite.christo.protein.HeteroCompound

closeStrm(Object) - Static method in class charite.christo.ChUtils

closeW(int, Object) - Static method in class charite.christo.ChUtils

closeWithCtxtMenu(Object) - Static method in class charite.christo.ChUtils

clr() - Method in class charite.christo.BA

clrEvt(AWTEvent) - Static method in class charite.christo.ChUtils

CLUSTALW - Static variable in class charite.christo.protein.MultipleSequenceParser

CLUSTALW - Static variable in interface charite.christo.strap.AlignmentWriter

cmd() - Static method in class charite.christo.Microsoft

CMD_ALL_MENUS - Static variable in class charite.christo.strap.StrapAlign

CMD_ALL_POPUP - Static variable in class charite.christo.strap.StrapAlign

CMD_CLEAR - Static variable in class charite.christo.ChConstants

CMD_DEL_ICONS - Static variable in class charite.christo.strap.StrapAlign

CMD_FOND_NAME - Static variable in class charite.christo.ChRenderer

CMD_HL_DIFF - Static variable in class charite.christo.strap.ProteinPopup

CMD_MENU_SELECTION_CHANGED - Static variable in class charite.christo.ChConstants

CMD_MIDDLE_MOUSE_BUTTON - Static variable in class charite.christo.ChConstants

CMD_PDB_ICONS - Static variable in class charite.christo.strap.StrapAlign

CMD_SPECIES_ICONS - Static variable in class charite.christo.strap.StrapAlign

CMD_TABLE_ICONS - Static variable in class charite.christo.strap.StrapAlign

CMD_WSDBFETCH_ERROR - Static variable in class charite.christo.protein.FetchSeqs

CMD_WSDBFETCH_SEND_QUERY - Static variable in class charite.christo.protein.FetchSeqs

CMD_WSDBFETCH_SUCCESS - Static variable in class charite.christo.protein.FetchSeqs

cmdExists(String...) - Static method in class charite.christo.ChUtils

CNSEW - Static variable in class charite.christo.ChUtils

cntains(Object, Object[]) - Static method in class charite.christo.ChUtils

cntainsAll(Object[], Object[]) - Static method in class charite.christo.ChUtils

cntainsAll(Object, Object[]) - Static method in class charite.christo.ChUtils

cntainsAssignblFrm(Class, Object[]) - Static method in class charite.christo.ChUtils

cntainsAtLeastOne(Object[], Object) - Static method in class charite.christo.ChUtils

cntainsOnly(int, Object) - Static method in class charite.christo.ChUtils

cntainsOnly(int, Object, int, int) - Static method in class charite.christo.ChUtils

cntainsOnly(boolean[], Object, int, int) - Static method in class charite.christo.ChUtils

cntainsRef(Object, Object[]) - Static method in class charite.christo.ChUtils

CNTXT_OBJCTS - Static variable in class charite.christo.ChUtils

coding2allPositions() - Method in class charite.christo.protein.Protein

An array mapping nucleotide indices.

codonUsage(String) - Static method in class charite.christo.protein.Backtranslate

CoiledCoil_Predictor - Interface in charite.christo.protein

Classes that provide a prediction of coiled coils.

CoiledCoil_PredictorRobinson - Class in charite.christo.strap.extensions

CoiledCoil_PredictorRobinson() - Constructor for class charite.christo.strap.extensions.CoiledCoil_PredictorRobinson

col2x(int) - Method in class charite.christo.strap.StrapView

COLLAPSE - Static variable in class charite.christo.ChTabPane

CollapseComponent - Class in charite.christo

HELP Tool-bars and menu-bars waste space on the screen.

CollapseComponent(JComponent, String) - Constructor for class charite.christo.CollapseComponent

collapseNSEW(String) - Method in class charite.christo.CollapseComponent

collectIDs(String, BA, String) - Static method in class charite.christo.ChUtils

collectIDs(String, byte[], int, int, String) - Static method in class charite.christo.ChUtils

collectWordsAfter(String, CharSequence) - Static method in class charite.christo.Hyperrefs

COLOR - Static variable in class charite.christo.strap.ResidueAnnotation

color() - Method in class charite.christo.TextMatches

COLOR_REF - Static variable in class charite.christo.ChConstants

COLOR_REF_GRAY - Static variable in class charite.christo.ChConstants

colorAllAminos(Color, ProteinViewer) - Static method in class charite.christo.strap.V3dUtils

Colored - Interface in charite.christo

Implemented by colored objects.

coloredBall(Color, Component) - Static method in class charite.christo.ChIcon

colorMark(ResidueSelection, BA) - Static method in class charite.christo.strap.ExportAlignment

colorOrIcon() - Method in class charite.christo.TextMatches

colors2rgb(Color[]) - Static method in class charite.christo.ChUtils

colr(Object) - Static method in class charite.christo.ChUtils

cols(int, boolean, boolean) - Method in class charite.christo.ChTextField

column2indexZ(int) - Method in class charite.christo.protein.Protein

Get index of residue at the horizontal alignment position col.

column2letterIdx(byte[]) - Static method in class charite.christo.protein.ChAlignUtils

column2letterIdx(byte[], int) - Static method in class charite.christo.protein.ChAlignUtils

column2nextIndexZ(int) - Method in class charite.christo.protein.Protein

Get index of residue at the horizontal alignment position h or the next index if h points to a gap.

column2thisOrPreviousIndex(int) - Method in class charite.christo.protein.Protein

Get index of residue at the horizontal alignment position col.

COLUMN_ADDED - Static variable in class charite.christo.ChTableLayout

COLUMN_EXTRA_WIDTH - Static variable in class charite.christo.ChJTable

COLUMN_MARGIN_CHANGED - Static variable in class charite.christo.ChJTable

COLUMN_MOVED - Static variable in class charite.christo.ChJTable

COLUMN_REMOVED - Static variable in class charite.christo.ChTableLayout

COLUMN_SEQUENCE - Static variable in interface charite.christo.protein.Superimpose3D

COLUMN_TITLE - Static variable in interface charite.christo.ChRunnable

COLUMN_WIDTH_4_DIGITS - Static variable in class charite.christo.ChJTable

columnMarginChanged(ChangeEvent) - Method in class charite.christo.ChJTable

columnMoved(TableColumnModelEvent) - Method in class charite.christo.ChJTable

columns2indices() - Method in class charite.christo.protein.Protein

Get indeces of residues at horizontal alignment positions col.

columns2nextIndices() - Method in class charite.christo.protein.Protein

An array to map horizontal residue positions to residue indices.

columnWidth(int) - Method in class charite.christo.ChTableLayout

comboClass() - Method in class charite.christo.strap.AbstractAlignAndCompare

ComboKeys - Class in charite.christo.strap

Choice menu for keys of residue selections.

ComboKeys(boolean) - Constructor for class charite.christo.strap.ComboKeys

COMMAND_HIDE_EVERYTHING - Static variable in interface charite.christo.protein.ProteinViewer

COMMANDbackground - Static variable in interface charite.christo.protein.ProteinViewer

COMMANDbiomolecule - Static variable in interface charite.christo.protein.ProteinViewer

COMMANDcartoon - Static variable in interface charite.christo.protein.ProteinViewer

COMMANDcenter - Static variable in interface charite.christo.protein.ProteinViewer

COMMANDcenter_amino - Static variable in interface charite.christo.protein.ProteinViewer

COMMANDchange_object_color - Static variable in interface charite.christo.protein.ProteinViewer

COMMANDcolor - Static variable in interface charite.christo.protein.ProteinViewer

COMMANDdots - Static variable in interface charite.christo.protein.ProteinViewer

COMMANDhighlight_selected_amino_acids - Static variable in interface charite.christo.protein.ProteinViewer

COMMANDhighlight_selected_atoms - Static variable in interface charite.christo.protein.ProteinViewer

CommandInterpreter - Interface in charite.christo

Command interpreters can interpret commands given as a command line.

COMMANDlabel - Static variable in interface charite.christo.protein.ProteinViewer

COMMANDlabel_color - Static variable in interface charite.christo.protein.ProteinViewer

commandLineParametersForProxy() - Static method in class charite.christo.ChUtils

COMMANDlines - Static variable in interface charite.christo.protein.ProteinViewer

COMMANDmesh - Static variable in interface charite.christo.protein.ProteinViewer

COMMANDobject_delete - Static variable in interface charite.christo.protein.ProteinViewer

COMMANDribbons - Static variable in interface charite.christo.protein.ProteinViewer

COMMANDrotate - Static variable in interface charite.christo.protein.ProteinViewer

COMMANDsa_surface - Static variable in interface charite.christo.protein.ProteinViewer

COMMANDselect - Static variable in interface charite.christo.protein.ProteinViewer

COMMANDselection_name - Static variable in interface charite.christo.protein.ProteinViewer

COMMANDset_rotation_translation - Static variable in interface charite.christo.protein.ProteinViewer

COMMANDshowScriptPanel - Static variable in interface charite.christo.protein.ProteinViewer

COMMANDspheres - Static variable in interface charite.christo.protein.ProteinViewer

COMMANDsticks - Static variable in interface charite.christo.protein.ProteinViewer

COMMANDsurface - Static variable in interface charite.christo.protein.ProteinViewer

COMMANDsurface_color - Static variable in interface charite.christo.protein.ProteinViewer

COMMANDzoom - Static variable in interface charite.christo.protein.ProteinViewer

commonPdbId(Protein[]) - Static method in class charite.christo.protein.Protein

COMMONS_COLLECTIONS - Static variable in class charite.christo.AbstractProxy

COMP - Static variable in class charite.christo.protein.PDB_Parser

COMP_P_ALPHA - Static variable in class charite.christo.protein.ProteinUtils

COMP_P_XYZ - Static variable in class charite.christo.protein.ProteinUtils

COMP_SEL_VIS - Static variable in class charite.christo.protein.ProteinUtils

comparator(int) - Static method in class charite.christo.ChUtils

comparator(int) - Static method in class charite.christo.protein.ProteinUtils

compare(Object, Object) - Method in class charite.christo.blast.SortBlastDatabases

compare(Object, Object) - Method in class charite.christo.ChComparator

compare(Object, Object) - Method in class charite.christo.ChJTable

compare(Object, Object) - Method in class charite.christo.ChTabPane

compare(Object, Object) - Method in class charite.christo.protein.DAS

compare(Object, Object) - Method in class charite.christo.protein.ProteinUtils

compare(Object, Object) - Method in class charite.christo.strap.ExportAlignment

compare(Object, Object) - Method in class charite.christo.strap.ResSelUtils

compare(Object, Object) - Method in class charite.christo.strap.SequenceFeatures

compare(Object, Object) - Method in class charite.christo.strap.SPUtils

COMPARE_ALPHABET - Static variable in class charite.christo.ChUtils

COMPARE_ALPHABET_IC - Static variable in class charite.christo.ChUtils

COMPARE_ID - Static variable in class charite.christo.ChUtils

COMPARE_NAME - Static variable in class charite.christo.ChUtils

COMPARE_RENDERER_TEXT - Static variable in class charite.christo.ChUtils

COMPARE_REVERT - Static variable in class charite.christo.ChUtils

COMPARE_SIZE - Static variable in class charite.christo.ChUtils

COMPARE_WHEN_CREATED - Static variable in class charite.christo.ChUtils

COMPARE_WHEN_MODIFIED - Static variable in class charite.christo.ChUtils

compareAlphabetically(Object, Object, boolean) - Static method in class charite.christo.ChUtils

compareTo(Object) - Method in class charite.christo.BA

compareTo(Object) - Method in class charite.christo.protein.Selection3D

COMPENSATE_GAPS - Static variable in class charite.christo.strap.DialogRenameProteins

compile(File[], File) - Method in class charite.christo.ChCompilerJavacPROXY

COMPL_ALLOW_SPC_IN_FILE - Static variable in class charite.christo.ChTextComponents

COMPL_HYPERREFS - Static variable in class charite.christo.ChTextComponents

COMPL_IC - Static variable in class charite.christo.ChTextComponents

COMPL_INFER_CASE - Static variable in class charite.christo.ChTextComponents

COMPL_TAB - Static variable in class charite.christo.ChTextComponents

COMPLEMENT - Static variable in class charite.christo.DNA_Util

complement(byte) - Static method in class charite.christo.DNA_Util

complement(byte[], int) - Static method in class charite.christo.DNA_Util

COMPLEMENT - Static variable in class charite.christo.protein.Protein

COMPLETE_PDB - Static variable in interface charite.christo.protein.ProteinWriter

COMPLETION_DIRECTORY_PATH - Static variable in class charite.christo.ChConstants

COMPLETION_FILES_IN_WORKING_DIR - Static variable in class charite.christo.ChConstants

componentHidden(ComponentEvent) - Method in class charite.christo.EvAdapter

componentMoved(ComponentEvent) - Method in class charite.christo.EvAdapter

componentResized(ComponentEvent) - Method in class charite.christo.EvAdapter

componentShown(ComponentEvent) - Method in class charite.christo.EvAdapter

COMPRESS_SUFFIX - Static variable in class charite.christo.ChUtils

COMPUTATION_STARTED - Static variable in class charite.christo.protein.StrapEvent

computationDone(String, Object) - Static method in class charite.christo.ChMsg

compute() - Method in class charite.christo.blast.AbstractBlaster

compute() - Method in interface charite.christo.blast.SequenceBlaster

Computation is typically very time consuming

compute() - Method in class charite.christo.protein.AbstractPredictionFromAminoacidSequence

compute(String) - Method in class charite.christo.protein.AbstractPredictionFromAminoacidSequence

compute() - Method in class charite.christo.protein.Bl2seq

compute() - Method in class charite.christo.protein.MultiFromPairAligner

compute() - Method in interface charite.christo.protein.PredictionFromAminoacidSequence

Computation is started and may take long time.

compute() - Method in interface charite.christo.protein.SequenceAligner

The time consuming computation.

compute() - Method in interface charite.christo.protein.Superimpose3D

compute() - Method in interface charite.christo.protein.ValueOfProtein

When it is time consuming then do the calculation in the compute method.

compute() - Method in class charite.christo.strap.AbstractAlignAndCompare

compute() - Method in class charite.christo.strap.AbstractAligner

compute() - Method in class charite.christo.strap.AbstractAlignerProxy

compute() - Method in class charite.christo.strap.Aligner3D

compute(Object, Protein[]) - Method in class charite.christo.strap.DialogSimilarStructureResult

compute() - Method in class charite.christo.strap.extensions.CoiledCoil_PredictorRobinson

compute() - Method in class charite.christo.strap.extensions.CountResidues

compute() - Method in class charite.christo.strap.extensions.SecondaryStructure_Jnet

compute(String) - Method in class charite.christo.strap.extensions.SecondaryStructure_NNPREDICT

compute(String) - Method in class charite.christo.strap.extensions.SecondaryStructure_Sopma

compute() - Method in class charite.christo.strap.extensions.Superimpose_Goede

compute() - Method in class charite.christo.strap.extensions.Toppred

compute(String) - Method in class charite.christo.strap.extensions.TransmembraneHelix_DAS

compute(String) - Method in class charite.christo.strap.extensions.TransmembraneHelix_HMMTOP

compute(String) - Method in class charite.christo.strap.extensions.TransmembraneHelix_MEMSAT

compute(String) - Method in class charite.christo.strap.extensions.TransmembraneHelix_ORIENTM

compute(String) - Method in class charite.christo.strap.extensions.TransmembraneHelix_Phobius

compute(String) - Method in class charite.christo.strap.extensions.TransmembraneHelix_PRED_TMR

compute(String) - Method in class charite.christo.strap.extensions.TransmembraneHelix_SOSUI

compute(String) - Method in class charite.christo.strap.extensions.TransmembraneHelix_SPLIT3

compute(String) - Method in class charite.christo.strap.extensions.TransmembraneHelix_SPLIT4

compute(String) - Method in class charite.christo.strap.extensions.TransmembraneHelix_THUMBUP

compute(String) - Method in class charite.christo.strap.extensions.TransmembraneHelix_TMAP

compute() - Method in class charite.christo.strap.extensions.TransmembraneHelix_TMAP_MULTI

compute(String) - Method in class charite.christo.strap.extensions.TransmembraneHelix_TMHMM2

compute(String) - Method in class charite.christo.strap.extensions.TransmembraneHelix_TMPRED

compute() - Method in class charite.christo.strap.extensions.TransmembraneHelix_TOPPRED

compute(String) - Method in class charite.christo.strap.extensions.TransmembraneHelix_WaveTM

compute() - Method in interface charite.christo.strap.ProteinProteinValue

When it is time consuming then do the calculation in the compute method.

compute() - Method in class charite.christo.strap.Texshade

COMPUTE_IF_NO_UNIPROT_ID - Static variable in class charite.christo.protein.FindUniprotID

computeColumns(int[], int[], int, int[]) - Static method in class charite.christo.protein.Gaps2Columns

computeIt() - Method in class charite.christo.blast.AbstractBlaster

computeIt() - Method in class charite.christo.blast.Blaster_local_Wu

computeIt() - Method in class charite.christo.blast.Blaster_SOAP_ebi

computeKey(File[], File) - Static method in class charite.christo.ChClassLoader1

computeLabelSize(Font, Rectangle, String, Rectangle) - Method in class charite.christo.protein.Protein

computeOutput() - Method in class charite.christo.strap.extensions.AbstractSubcellularLocation

computeOutput() - Method in class charite.christo.strap.extensions.SubcellularLocationHum_mPloc

computeOutput() - Method in class charite.christo.strap.extensions.SubcellularLocationPLOC

computePhFile(byte[][], String) - Method in class charite.christo.strap.extensions.MultipleAlignerClustalW

option -OUTPUTTREE=nj

computeResult(byte[][], Protein[]) - Method in class charite.christo.strap.AbstractAligner

computeResult(byte[][], Protein[]) - Method in class charite.christo.strap.extensions.Aligner3D_Mapsci

computeResult(byte[][], Protein[]) - Method in class charite.christo.strap.extensions.Aligner3D_Matt

computeResult(byte[][], Protein[]) - Method in class charite.christo.strap.extensions.Aligner3D_Mustang

computeResult(byte[][], Protein[]) - Method in class charite.christo.strap.extensions.Aligner3D_Smolign

computeResult(byte[][], Protein[]) - Method in class charite.christo.strap.extensions.MultipleAligner_SPEM

computeResult(byte[][], Protein[]) - Method in class charite.christo.strap.extensions.MultipleAlignerAlign_m

computeResult(byte[][], Protein[]) - Method in class charite.christo.strap.extensions.MultipleAlignerAmap

computeResult(byte[][], Protein[]) - Method in class charite.christo.strap.extensions.MultipleAlignerClustalW

computeResult(byte[][], Protein[]) - Method in class charite.christo.strap.extensions.MultipleAlignerDialign

computeResult(byte[][], Protein[]) - Method in class charite.christo.strap.extensions.MultipleAlignerDialignT

computeResult(byte[][], Protein[]) - Method in class charite.christo.strap.extensions.MultipleAlignerKalign

computeResult(byte[][], Protein[]) - Method in class charite.christo.strap.extensions.MultipleAlignerMafft

computeResult(byte[][], Protein[]) - Method in class charite.christo.strap.extensions.MultipleAlignerMuscle

computeResult(byte[][], Protein[]) - Method in class charite.christo.strap.extensions.MultipleAlignerProbcons2

computeResult(byte[][], Protein[]) - Method in class charite.christo.strap.extensions.MultipleAlignerT_Coffee

computeResult(byte[][], Protein[]) - Method in class charite.christo.strap.extensions.PairAlignerJAligner

computeResult(byte[][], Protein[]) - Method in class charite.christo.strap.extensions.PairAlignerNeoBio

computeResult(byte[][], Protein[]) - Method in class charite.christo.strap.extensions.Superimpose_CE

computeResult(byte[][], Protein[]) - Method in class charite.christo.strap.extensions.Superimpose_GangstaPlus

computeResult(byte[][], Protein[]) - Method in class charite.christo.strap.extensions.Superimpose_LajollaProtein

computeResult(byte[][], Protein[]) - Method in class charite.christo.strap.extensions.Superimpose_native_CE

computeResult(byte[][], Protein[]) - Method in class charite.christo.strap.extensions.Superimpose_TM_align

computeWide2narrow(Protein[]) - Method in class charite.christo.protein.Gaps2Columns

Calculates the horizontal position (column) of all residues in the alignment.

COMPUTING - Static variable in class charite.christo.protein.FindUniprotID

concat(byte[], int, int, byte[], int, int, byte[]) - Static method in class charite.christo.ChUtils

concat(byte[], int, int, byte[], int, int, byte[], int, int, byte[]) - Static method in class charite.christo.ChUtils

CONE - Static variable in class charite.christo.protein.PDB_Parser

ConsensusSequence - Class in charite.christo.strap.extensions

HELP All identical residues of aligned protein sequences are determined.

ConsensusSequence() - Constructor for class charite.christo.strap.extensions.ConsensusSequence

contains(String) - Method in class charite.christo.Archive

contains(Object) - Static method in class charite.christo.ChDelay

contains(Object) - Method in class charite.christo.ChSet

contains(Object) - Method in class charite.christo.UniqueList

containsAll(Collection<?>) - Method in class charite.christo.ChSet

containsAll(Collection<?>) - Method in class charite.christo.UniqueList

containsClasses() - Method in class charite.christo.ChCombo

containsHeteroCompound(HeteroCompound) - Method in class charite.christo.protein.Protein

containsHtmlTags(CharSequence) - Static method in class charite.christo.ChUtils

containsInvalidFeatureLine(CharSequence) - Method in class charite.christo.protein.Protein

containsKey(Object) - Method in class charite.christo.ChMap

containsOnly(int) - Method in class charite.christo.ChTokenizer

containsOnlyACTGNX() - Method in class charite.christo.protein.Protein

containsValue(Object) - Method in class charite.christo.ChMap

CONTENTS_CHANGED - Static variable in class charite.christo.ChDelay

contentsChanged(JComponent, long) - Static method in class charite.christo.ChDelay

contextObjects(Object, Object[]) - Static method in class charite.christo.ChUtils

ContextObjects - Class in charite.christo.strap

ContextObjects(boolean, Object, String) - Constructor for class charite.christo.strap.ContextObjects

contextObjectsAt(AWTEvent) - Static method in class charite.christo.ChUtils

contextObjectsAt(Point, Object) - Static method in class charite.christo.ChUtils

convertToResidueAnnotation(boolean, ResidueSelection...) - Static method in class charite.christo.strap.ResSelUtils

COPY - Static variable in class charite.christo.strap.DialogRenameProteins

COPY_ADD_TO_PROTEIN - Static variable in class charite.christo.strap.ResSelUtils

COPY_ASK_NAME - Static variable in class charite.christo.strap.ResSelUtils

copy_mat(double[][], double[][]) - Method in class charite.andrean.SpBigMatrix

COPY_REPORT - Static variable in class charite.christo.strap.ResSelUtils

COPY_SINGLE - Static variable in class charite.christo.strap.ResSelUtils

copyIsOs(InputStream, OutputStream) - Static method in class charite.christo.ChUtils

CORNETTE - Static variable in class charite.christo.strap.extensions.Hydrophobicity

couldNotLaunch() - Method in class charite.christo.ChExec

count() - Method in class charite.christo.TextMatches

count01234(int) - Static method in class charite.christo.ChUtils

countAnsiEscapes() - Method in class charite.christo.BA

countAtoms() - Method in class charite.christo.protein.HeteroCompound

countAtoms() - Method in class charite.christo.protein.Protein

number of atoms in the model.

countCalpha() - Method in class charite.christo.protein.Protein

Are calpha-coordinates known ?

countColumns() - Method in class charite.christo.protein.Gaps2Columns

countColumns() - Method in class charite.christo.strap.StrapView

countFasta(BA, int) - Static method in class charite.christo.protein.MultipleSequenceParser

countHits() - Method in class charite.christo.blast.BlastParser

countLettrs(byte[]) - Static method in class charite.christo.ChUtils

countLettrs(byte[], int, int) - Static method in class charite.christo.ChUtils

countMismatch(int, int, int[]) - Method in class charite.christo.protein.ReferenceSequence

countNotNull(Object[]) - Static method in class charite.christo.ChUtils

countNovelHits() - Method in class charite.christo.blast.BlastParser

countNucleotides() - Method in class charite.christo.protein.Protein

countNull(Object[]) - Static method in class charite.christo.ChUtils

countResidues() - Method in class charite.christo.protein.Protein

number of residues, returns getResidueType().length

CountResidues - Class in charite.christo.strap.extensions

HELP This class counts the amino acids in a protein.

CountResidues() - Constructor for class charite.christo.strap.extensions.CountResidues

countResiduesInChain(byte) - Method in class charite.christo.protein.Protein

countResults() - Method in class charite.christo.protein.AbstractPredictionFromAminoacidSequence

countRows() - Method in interface charite.christo.protein.ProteinAlignment

countRows() - Method in class charite.christo.strap.StrapAlign

How many alignment rows ?

countRows() - Method in class charite.christo.strap.StrapView

countTokens() - Method in class charite.christo.ChTokenizer

countTrue(boolean[]) - Static method in class charite.christo.ChUtils

countTrue(boolean[], int, int) - Static method in class charite.christo.ChUtils

countType(char, ResidueSelection[]) - Static method in class charite.christo.strap.ResSelUtils

cp(Object, Object) - Method in class charite.christo.ChButton

cp(Object, Object) - Method in class charite.christo.ChJMenu

cp(Object, Object) - Method in class charite.christo.ChPanel

cp(Object, Object) - Method in class charite.christo.ChTextComponents

CplusPlus_compiler - Static variable in class charite.christo.Customize

cpy(File, File) - Static method in class charite.christo.ChUtils

cpy(InputStream, File) - Static method in class charite.christo.ChUtils

cpyIfDiffers(File, File) - Static method in class charite.christo.ChUtils

cpyWords(Object) - Static method in class charite.christo.ChJOrtho

crc32Table() - Static method in class charite.christo.libs.bzip2.BZip2Constants

create(Element) - Method in class charite.christo.HtmlDocEditorKit

createPairfitTarget(Protein, Matrix3D, BA) - Static method in class charite.christo.protein.ProteinWriter1

cropSequences(int, ResidueSelection[]) - Static method in class charite.christo.strap.ResSelUtils

CROSSING_OUT - Static variable in class charite.christo.ChButton

CrudeSequenceDisSimilarity - Class in charite.christo.protein

Counting dissimilar residues in two aligned sequences.

CrudeSequenceDisSimilarity() - Constructor for class charite.christo.protein.CrudeSequenceDisSimilarity

CrudeSequenceSimilarity - Class in charite.christo.protein

Counting identical residues in two aligned sequences.

CsaWeb - Class in charite.christo.strap

CsaWeb() - Constructor for class charite.christo.strap.CsaWeb

CSS_BROWSER - Static variable in interface charite.christo.strap.AlignmentWriter

cssAlignBrowser - Static variable in class charite.christo.Customize

cssColors(Protein[], BA) - Static method in class charite.christo.strap.SequenceFeatures

cssH1H2H3(double) - Static method in class charite.christo.ChUtils

ct(Object) - Method in class charite.christo.ChTextField

ctrlPnl() - Static method in class charite.christo.ChUtils

currentKey(Object) - Static method in class charite.christo.strap.AddAnnotation

cursor() - Method in class charite.christo.strap.ProteinPopup

CURSOR_CHANGED_PROTEIN - Static variable in class charite.christo.protein.StrapEvent

CURSOR_CLICKED - Static variable in class charite.christo.protein.StrapEvent

CURSOR_COLUMN - Static variable in class charite.christo.strap.StrapView

CURSOR_MOVED_WITHIN_PROTEIN - Static variable in class charite.christo.protein.StrapEvent

CURSOR_MOVED_WITHIN_PROTEIN_DELAYED - Static variable in class charite.christo.protein.StrapEvent

cursr(int) - Static method in class charite.christo.ChUtils

Customize - Class in charite.christo

HELP The customize-dialogs are used to set program options.

Customize(String, String[], String, int) - Constructor for class charite.christo.Customize

customize(int) - Static method in class charite.christo.Customize

customizeKeys() - Static method in class charite.christo.strap.AddAnnotation

CYGWIN_CORE - Static variable in class charite.christo.Microsoft

CYGWIN_DLL - Static variable in class charite.christo.ChExec

CYGWIN_LATEX - Static variable in class charite.christo.Microsoft

CYGWINSH - Static variable in class charite.christo.ChExec

CYTOSKELETON - Static variable in interface charite.christo.protein.PredictSubcellularLocation

CYTOSOL - Static variable in interface charite.christo.protein.PredictSubcellularLocation

D

D_melanogaster_P40301 - Static variable in class charite.christo.strap.DialogRenameProteins

darkerColors(Color[]) - Static method in class charite.christo.ChUtils

DAS - Class in charite.christo.protein

DAS() - Constructor for class charite.christo.protein.DAS

DAS.Capability - Class in charite.christo.protein

DAS.Capability() - Constructor for class charite.christo.protein.DAS.Capability

DAS.Coordinates - Class in charite.christo.protein

DAS.Coordinates() - Constructor for class charite.christo.protein.DAS.Coordinates

DAS.Entry - Class in charite.christo.protein

DAS.Entry() - Constructor for class charite.christo.protein.DAS.Entry

dashedStroke(int) - Static method in class charite.christo.ChUtils

databases - Static variable in class charite.christo.Customize

DATABASES - Static variable in class charite.christo.protein.FetchSeqs

DATABASES_FULL_LIST - Static variable in interface charite.christo.blast.SequenceBlaster

Names of available databases depend on the type of query (AA or NT)

DATABASES_NUCLEOTIDES - Static variable in interface charite.christo.blast.SequenceBlaster

Names of available databases depend on the type of query (AA or NT)

dateOfCompilation() - Static method in class charite.christo.ChUtils

day(long) - Static method in class charite.christo.ChUtils

DAYS_VALID - Static variable in class charite.christo.protein.DAS

DB_EMBL - Static variable in class charite.christo.protein.FetchSeqs

DB_NCBI_AA - Static variable in class charite.christo.protein.FetchSeqs

DB_SOURCE - Static variable in class charite.christo.protein.DAS

DB_UNIPARC - Static variable in class charite.christo.protein.FetchSeqs

DB_UNIPROT - Static variable in class charite.christo.protein.FetchSeqs

dbColonID2file(String) - Static method in class charite.christo.protein.FetchSeqs

DEBUG - Static variable in class charite.christo.ChExec

debug(Object) - Static method in class charite.christo.ChUtils

debugExit(Object...) - Static method in class charite.christo.ChUtils

debugGC() - Static method in class charite.christo.ChUtils

debugJComponent(Object) - Static method in class charite.christo.ChUtils

debugListThreads(BA) - Static method in class charite.christo.ChThread

debugMC(Protein[]) - Static method in class charite.christo.protein.Protein

debugTime(CharSequence, long) - Static method in class charite.christo.ChUtils

decode(byte[], int, int) - Static method in class charite.christo.libs.Base64

Very low-level access to decoding ASCII characters in the form of a byte array.

decodeEscChrs(BA, char) - Static method in class charite.christo.ChUtils

For reading manpages

DEF - Static variable in class charite.christo.strap.AbstractAlignmentProject

DEFAULT_BACKGROUND - Static variable in class charite.christo.ChConstants

DEFAULT_BACKGROUND_D - Static variable in class charite.christo.ChConstants

DEFAULT_BINARY - Static variable in class charite.christo.BasicExecutable

DEFAULT_RENDERER - Static variable in class charite.christo.ChJTable

defaultAligner2Class() - Static method in class charite.christo.protein.ChAlignUtils

defaultInstance() - Static method in class charite.christo.strap.ContextObjects

defaultTK() - Static method in class charite.christo.ChUtils

DEFINE_THIS_COLOR - Static variable in class charite.christo.protein.Pymol

defineGUI(long, String) - Method in class charite.christo.PrgParas

defineParameters(long, String) - Method in class charite.christo.BasicExecutable

defineParameters(long, String) - Method in class charite.christo.blast.AbstractBlaster

defineParameters(long, String) - Method in interface charite.christo.HasPrgParas

defineParameters(long, String) - Method in class charite.christo.strap.AbstractAligner

defineParameters(long, String) - Method in class charite.christo.strap.extensions.AbstractSubcellularLocation

DEFINITION - Static variable in class charite.christo.HelpCommands

deflaterAccordingToExtension(InputStream, String) - Static method in class charite.christo.ChUtils

delAfter(String, Object, boolean) - Static method in class charite.christo.ChUtils

delBlanksL() - Method in class charite.christo.BA

delBlanksR() - Method in class charite.christo.BA

delet(Object, Object[], Class<T>) - Static method in class charite.christo.ChUtils

delet(Object, Object[], Class<T>, boolean) - Static method in class charite.christo.ChUtils

deleteCacheResult(Class, String) - Static method in class charite.christo.CacheResult

DELETED_OBJECTS - Static variable in class charite.christo.strap.V3dListModel

deleteTree(File) - Static method in class charite.christo.ChUtils

delFile(File) - Static method in class charite.christo.ChUtils

delFile(boolean, File) - Static method in class charite.christo.ChUtils

delFileOnExit(File) - Static method in class charite.christo.ChUtils

delFileOnExit(String) - Static method in class charite.christo.ChUtils

delFromChar(String, char) - Static method in class charite.christo.ChUtils

delGaps(Protein[], int, int, byte[][]) - Static method in class charite.christo.strap.AcceptAlignment2

delimiterL() - Method in class charite.christo.TextMatches

delimiterR() - Method in class charite.christo.TextMatches

delPfx(char, Object) - Static method in class charite.christo.ChUtils

delPfx(String, String) - Static method in class charite.christo.ChUtils

delSfx(char, Object) - Static method in class charite.christo.ChUtils

delSfx(String, Object) - Static method in class charite.christo.ChUtils

delSuffix(String) - Method in class charite.christo.BA

delToLstChr(String, char) - Static method in class charite.christo.ChUtils

DemoAssociateObjectsToProteins - Class in charite.christo.strap.extensions

HELP This demo shows how own objects can be attached, retrieved and removed from proteins.

DemoAssociateObjectsToProteins() - Constructor for class charite.christo.strap.extensions.DemoAssociateObjectsToProteins

deref(Object, Class<T>) - Static method in class charite.christo.ChUtils

deref(Object) - Static method in class charite.christo.ChUtils

derefArray(Object, Class<T>) - Static method in class charite.christo.ChUtils

derefArray(boolean, Object, Class<T>, List) - Static method in class charite.christo.ChUtils

derefJC(Object) - Static method in class charite.christo.ChUtils

derefViewer(Object) - Static method in class charite.christo.protein.Protein3dUtils

describeExec(long, String[], String[], File) - Static method in class charite.christo.ChExecSecurity

DesktopUtils - Class in charite.christo

DesktopUtils() - Constructor for class charite.christo.DesktopUtils

detach3DStructure() - Method in class charite.christo.protein.Protein

determinante(double[][]) - Method in class charite.andrean.SpBigMatrix

dHomePage(Object) - Static method in class charite.christo.ChUtils

Dialog3DViewer - Class in charite.christo.strap

HELP PACKAGE:charite.christo.strap.extensions.

Actions which are performed when objects are dropped on certain targets.

	D r o p p e d O b j e c t s				Drop target	Proteins	Residue selections	Hetero groups Images
Proteins		Copy selection to protein	Add heteros to protein	Set icon image
Residue selections				Set background image
3D-View	Add 3D-structure to view	Highlight atoms/amino acids in 3D	Add hetero structure to view
Alignment panel	Load or un-hide protein	Copy selection to protein	Add heteros to protein
Tree-node "Hidden"	Hide proteins			Desktop or file browser	Copy protein file		Write PDB-file

CLASS_REF:ChJmolPROXYJMOL CLASS_REF:PymolPYMOL CLASS_REF:ChAstexPROXYOpenAstex Installed by STRAP allways Linux Linux, Windows, Mac always Operation system all X-Windows all all Performance medium high high with accelerated video cards high Memory consumption high low medium medium # models per view many 1 many many Shows superimposed proteins yes no yes yes
Protein PDB structure viewers are used for detailed 3D-visualization.

Dialog3DViewer() - Constructor for class charite.christo.strap.Dialog3DViewer

Dialog_bl2seq - Class in charite.christo.strap

HELP BL2SEQ produces all local alignments of two given sequences (UBIC:bl2seq).

Dialog_bl2seq() - Constructor for class charite.christo.strap.Dialog_bl2seq

DialogAlign - Class in charite.christo.strap

HELP The Dialog is used to align a number of selected proteins (see WIKI:Sequence_alignment).

DialogAlign() - Constructor for class charite.christo.strap.DialogAlign

DialogAlignOneToAll - Class in charite.christo.strap

HELP With this dialog a reference protein can be aligned to many other proteins producing a pair-alignments for each protein.

DialogAlignOneToAll() - Constructor for class charite.christo.strap.DialogAlignOneToAll

DialogAlignOneToAllResult - Class in charite.christo.strap

HELP

DialogAlignOneToAllResult(Protein[], Protein, ChCombo) - Constructor for class charite.christo.strap.DialogAlignOneToAllResult

DialogAlignResult - Class in charite.christo.strap

DialogBarChart - Class in charite.christo.strap

HELP The bar chart visualizes values assigned to single proteins.

DialogBarChart() - Constructor for class charite.christo.strap.DialogBarChart

DialogBlast - Class in charite.christo.strap

HELP STRAP allows to search public and private sequence databases to identify sequences that are similar to a query sequences.

DialogBlast() - Constructor for class charite.christo.strap.DialogBlast

DialogCompareProteins - Class in charite.christo.strap

HELP This dialog allows the pairwise comparison of a set of proteins.

DialogCompareProteins() - Constructor for class charite.christo.strap.DialogCompareProteins

DialogCopyAnnotations - Class in charite.christo.strap

HELP Residue annotations of one protein can be copied to the equivalent positions in another aligned protein.

DialogCopyAnnotations() - Constructor for class charite.christo.strap.DialogCopyAnnotations

DialogDifferentResidues - Class in charite.christo.strap

HELP Based on the current sequence alignment two aligned proteins are compared residue by residue and all different residues are collected in a table.

DialogDifferentResidues() - Constructor for class charite.christo.strap.DialogDifferentResidues

DialogDotPlot - Class in charite.christo.strap

HELP A dot-plot is a correlogram of two sequence WIKI:Dot_plot_(bioinformatics).

DialogDotPlot() - Constructor for class charite.christo.strap.DialogDotPlot

DialogDotPlot(long, Protein, Protein) - Constructor for class charite.christo.strap.DialogDotPlot

DialogDotPlot_Sequence - Class in charite.christo.strap

DialogDotPlot_Sequence(DialogDotPlot, char) - Constructor for class charite.christo.strap.DialogDotPlot_Sequence

DialogExecuteOnFile - Class in charite.christo

HELP With this dialog obtainable from the "plugin"-menu shell programs can be run on files or character sequences.

DialogExecuteOnFile(Customize) - Constructor for class charite.christo.DialogExecuteOnFile

DialogExportAlignment - Class in charite.christo.strap

HELP The sequence alignment can be exported in various formats: HTML WIKI:Fasta_format HSSP-format is not frequently used: http://www.predictprotein.org/Dexa/out_hssp.html MSF-format: http://bmerc-www.bu.edu/examples/output/seqlist.msf.html ClustalW-format: http://www.molecularevolution.org/mbl/resources/fileformats/ SEE_DIALOG:Texshade SEE_DIALOG:DialogImportMFA SEE_DIALOG:DialogExportProteins

DialogExportAlignment() - Constructor for class charite.christo.strap.DialogExportAlignment

DialogExportProteins - Class in charite.christo.strap

HELP

DialogExportProteins() - Constructor for class charite.christo.strap.DialogExportProteins

DialogExportWord - Class in charite.christo.strap

DialogExportWord() - Constructor for class charite.christo.strap.DialogExportWord

DialogFetchPdb - Class in charite.christo.strap

HELP This dialog aims at loading many PDB-files from file servers.

DialogFetchPdb() - Constructor for class charite.christo.strap.DialogFetchPdb

DialogFetchSRS - Class in charite.christo.strap

HELP With this dialog a number of sequence files can be loaded from public servers.

DialogFetchSRS() - Constructor for class charite.christo.strap.DialogFetchSRS

DialogFindInText - Class in charite.christo

views html and plain text

DialogFindInText() - Constructor for class charite.christo.DialogFindInText

DialogGenbank - Class in charite.christo.strap

HELP

   1    AAACATGGCG CTGGCTAGCG TGTTGCAGCG ...
DialogGenbank() - 
Constructor for class charite.christo.strap.DialogGenbank
 
DialogHighlightPattern - Class in charite.christo.strap
HELP

   This dialog is used to underline all occurrences of sequence
   patterns.
DialogHighlightPattern() - 
Constructor for class charite.christo.strap.DialogHighlightPattern
 
DialogImportMFA - Class in charite.christo.strap
HELP
Multiple sequence files (WIKI:FASTA_format, MSF, BIOWIKI:NexusFormat, WIKI:Stockholm_format ) can be directly dragged into the
alignment panel.
DialogImportMFA() - 
Constructor for class charite.christo.strap.DialogImportMFA
 
DialogInferCDS - Class in charite.christo.strap
HELP

   With this Dialog one or more nucleotide sequences can be translated to
   amino acids according to the WIKI:Genetic_code.
DialogInferCDS() - 
Constructor for class charite.christo.strap.DialogInferCDS
 
DialogManyInOneRow - Class in charite.christo.strap
HELP

For manipulating several proteins
simultaneously, more than one protein may be stacked in one single
line by pressing either button:

 JCOMPONENT:DialogManyInOneRow#getButton("A")! or
 
 JCOMPONENT:DialogManyInOneRow#getButton("X")! 


Only one representative is shown and the others are hidden.
DialogManyInOneRow() - 
Constructor for class charite.christo.strap.DialogManyInOneRow
 
DialogNeighbors - Class in charite.christo.strap
HELP

PACKAGE:charite.christo.strap.
DialogNeighbors() - 
Constructor for class charite.christo.strap.DialogNeighbors
 
DialogNeighborsResult - Class in charite.christo.strap
 
DialogNeighborsResult(Protein[], String) - 
Constructor for class charite.christo.strap.DialogNeighborsResult
 
DialogNewProtein - Class in charite.christo.strap
HELP

The user enters the name of a protein and an amino acid sequence.
DialogNewProtein() - 
Constructor for class charite.christo.strap.DialogNewProtein
 
DialogNonRedundantSequenceSet - Class in charite.christo.strap
HELP
   A set of proteins is generated from the selected proteins

   where the sequence identity ratio is not higher than the given threshold.



   Proteins are excluded from the set for which another very similar protein exists.

   This procedure is rather primitive and more sophisticated programs for this task exist (E.g.
DialogNonRedundantSequenceSet() - 
Constructor for class charite.christo.strap.DialogNonRedundantSequenceSet
 
DialogPhylogeneticTree - Class in charite.christo.strap
HELP

   This dialog is used to draw phylogenetic dendrograms of aligned
   protein sequences.
DialogPhylogeneticTree() - 
Constructor for class charite.christo.strap.DialogPhylogeneticTree
 
DialogPlot - Class in charite.christo.strap
HELP

With this dialog numeric data is plotted along the sequence/alignment.
DialogPlot() - 
Constructor for class charite.christo.strap.DialogPlot
 
DialogPredictCoiledCoil - Class in charite.christo.strap
HELP

WIKI:Coiled_coil regions are predicted from amino acid sequences.
DialogPredictCoiledCoil() - 
Constructor for class charite.christo.strap.DialogPredictCoiledCoil
 
DialogPredictSecondaryStructures - Class in charite.christo.strap
HELP

WIKI:Secondary_structure  are predicted from the amino acid sequences.
DialogPredictSecondaryStructures() - 
Constructor for class charite.christo.strap.DialogPredictSecondaryStructures
 
DialogPredictTexshade - Class in charite.christo.strap
HELP
   Makes texshade commands for the structure prediction
   Text lines starting with a percent sign are ignored since "%" preceeds comments in WIKI:LaTeX.
DialogPredictTexshade(char[][], Protein[], String) - 
Constructor for class charite.christo.strap.DialogPredictTexshade
 
DialogPredictTmHelices2 - Class in charite.christo.strap
HELP

At least one third of all proteins are transmembrane proteins but the 3D-structures of only a few are solved.
DialogPredictTmHelices2() - 
Constructor for class charite.christo.strap.DialogPredictTmHelices2
 
DialogPredictTmHelicesMulti - Class in charite.christo.strap
 
DialogPredictTmHelicesMulti() - 
Constructor for class charite.christo.strap.DialogPredictTmHelicesMulti
 
DialogProteinList - Class in charite.christo.strap
HELP

A list of protein files is entered into the text area.
DialogProteinList() - 
Constructor for class charite.christo.strap.DialogProteinList
 
DialogPublishAlignment - Class in charite.christo.strap
HELP



    

Comparing different 3D-viewers