charite.christo.protein
Class Protein3d

java.lang.Object
  java.awt.Component
      java.awt.Container
          javax.swing.JComponent
              javax.swing.JPanel
                  charite.christo.ChPanel
                      charite.christo.protein.Protein3d

All Implemented Interfaces:

ChRunnable, Disposable, PaintHook, ProcessEv, TooltipProvider, java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, javax.accessibility.Accessible, javax.swing.Scrollable

public class Protein3d
extends ChPanel
implements Disposable, ChRunnable, TooltipProvider, ProcessEv, PaintHook

HELP PACKAGE:charite.christo.strap. The simple 3D-viewer visualizes the C-alpha trace of one or several proteins as a polygon. The advantage over the full featured view options also available in Strap is, that it opens without delay and uses only very little memory. Helices may be drawn in red and sheets in yellow.
Mouse Actions:

• CTRL+drag or mouse-wheel: rotate in screen pane
• CTRL+mouse wheel or CTRL-plus: zoom. (This is consistent with office programs).
• clicking an C-alpha atom: moves alignment cursor to the clicked residue

Picking amino acids: Amino acids can be picked by clicking the C-alpha atom. A tool-panel will appear which acts on the picked protein.

List of proteins: The toggle "List of proteins" can be activated to show a list of all proteins in this view. Each protein in the list comes with a color-chooser.

Color-chooser: The color chooser is shown if CB:"List proteins" is activated. Four color-schemes are available. JCOMPONENT:Protein3d#docuColorChooser()

• Each chain in a different color (striped box)
• Secondary structure: helices red, sheets yellow (yellow-red box)
• Entire protein in one color (monochrome boxes)
• Protein entirely hidden (black box)

With the CTRL key the color of all proteins can be changed at once.

Adding proteins to the 3D-view: Proteins are added by WIKI:Drag_and_drop (See STRING:ChConstants#MOVIE_Drag_protein_to_3D ).

See Also:

Serialized Form

Nested Class Summary

static class

Protein3d.PView

Nested classes/interfaces inherited from class javax.swing.JComponent

javax.swing.JComponent.AccessibleJComponent

Nested classes/interfaces inherited from class java.awt.Component

java.awt.Component.BaselineResizeBehavior

Field Summary

static java.lang.String	ID_DISPOSED
static java.lang.String	ID_PROTEIN_VIEWER
static java.lang.String	KEY_BIO_MOLECULES
static java.lang.String	KEY_INITIALLY_SHOW
static java.lang.String	KEY_INTERPRET_AFTER_LOADING
static java.lang.String	KEY_MSG_NO_PROTEIN
static java.lang.String	SPIN

Fields inherited from class charite.christo.ChPanel

KEY_REPRESENT_COMPONENT

Fields inherited from class javax.swing.JComponent

TOOL_TIP_TEXT_KEY, UNDEFINED_CONDITION, WHEN_ANCESTOR_OF_FOCUSED_COMPONENT, WHEN_FOCUSED, WHEN_IN_FOCUSED_WINDOW

Fields inherited from class java.awt.Component

BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT

Fields inherited from interface charite.christo.Disposable

NONE

Fields inherited from interface charite.christo.ChRunnable

APPEND, COLUMN_TITLE, DOWNLOAD_FINISHED, GET_PANEL, ICON, INTERPRET_LINE, IS_DRAG4XY, ITEM_TEXT, MODIFY_RENDERER_COMPONENT, PROGRESS, REPAINT_CURSOR, SAY_DOWNLOADING, SET_ICON_IMAGE, SET_TREE_VALUE, SHOW_IN_FRAME, TAB_TEXT, TIP_TEXT

Fields inherited from interface java.awt.image.ImageObserver

ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH

Constructor Summary

Protein3d()

Method Summary

void	addOrRemoveButton(int pos, javax.swing.JComponent b, int where)
void	addProteins(Protein... pp0)
void	afterAddProteins(Protein... pp)
static java.awt.Color	chain2color(int i)
void	dispose()
static javax.swing.JComponent	docuColorChooser()
boolean	eachProteinInDifferentColor(boolean asChain, boolean testOnly)
void	enableDisable()
Protein	getProteinAtMouse()
Protein[]	getProteins()
int	getResidueIndexAtMouse()
Matrix3D	getRotationAndTranslationOfView()
java.lang.String	getToolTipText(java.awt.event.MouseEvent ev)
Protein3d.PView	getView(Protein prot)
void	highlightAminoAcid(float[] xyz)
void	highlightAminoAcid(Protein p, int idx)
boolean	isNucleotideChainVisible(HeteroCompound ha)
boolean	isPreview()
boolean	isProteinShown(Protein p)
void	paintChildren(java.awt.Graphics g)
void	paintComponent(java.awt.Graphics g)
boolean	paintHook(javax.swing.JComponent component, java.awt.Graphics g, boolean after)
void	processEv(java.awt.AWTEvent ev)
java.lang.String	provideTip(java.lang.Object objOrEv)
void	removeProtein(Protein p)
java.lang.Object	run(java.lang.String id, java.lang.Object arg)
void	setHideDistantDNS(boolean b)
void	showListOfHeterosAndNucleotides(Protein p)

Methods inherited from class charite.christo.ChPanel

cp, getDndDateien, getMaximumSize, getPreferredScrollableViewportSize, getPreferredSize, getScrollableBlockIncrement, getScrollableTracksViewportHeight, getScrollableTracksViewportWidth, getScrollableUnitIncrement, getToolTipLocation, getWhenPainted, invalidate, isAlreadyPainted, isEnabled, isShowing, isValidateRoot, paint, processEvent, removeAll

Methods inherited from class javax.swing.JPanel

getAccessibleContext, getUI, getUIClassID, setUI, updateUI

Methods inherited from class javax.swing.JComponent

addAncestorListener, addNotify, addVetoableChangeListener, computeVisibleRect, contains, createToolTip, disable, enable, firePropertyChange, firePropertyChange, firePropertyChange, getActionForKeyStroke, getActionMap, getAlignmentX, getAlignmentY, getAncestorListeners, getAutoscrolls, getBaseline, getBaselineResizeBehavior, getBorder, getBounds, getClientProperty, getComponentPopupMenu, getConditionForKeyStroke, getDebugGraphicsOptions, getDefaultLocale, getFontMetrics, getGraphics, getHeight, getInheritsPopupMenu, getInputMap, getInputMap, getInputVerifier, getInsets, getInsets, getListeners, getLocation, getMinimumSize, getNextFocusableComponent, getPopupLocation, getRegisteredKeyStrokes, getRootPane, getSize, getToolTipText, getTopLevelAncestor, getTransferHandler, getVerifyInputWhenFocusTarget, getVetoableChangeListeners, getVisibleRect, getWidth, getX, getY, grabFocus, isDoubleBuffered, isLightweightComponent, isManagingFocus, isOpaque, isOptimizedDrawingEnabled, isPaintingForPrint, isPaintingTile, isRequestFocusEnabled, paintImmediately, paintImmediately, print, printAll, putClientProperty, registerKeyboardAction, registerKeyboardAction, removeAncestorListener, removeNotify, removeVetoableChangeListener, repaint, repaint, requestDefaultFocus, requestFocus, requestFocus, requestFocusInWindow, resetKeyboardActions, reshape, revalidate, scrollRectToVisible, setActionMap, setAlignmentX, setAlignmentY, setAutoscrolls, setBackground, setBorder, setComponentPopupMenu, setDebugGraphicsOptions, setDefaultLocale, setDoubleBuffered, setEnabled, setFocusTraversalKeys, setFont, setForeground, setInheritsPopupMenu, setInputMap, setInputVerifier, setMaximumSize, setMinimumSize, setNextFocusableComponent, setOpaque, setPreferredSize, setRequestFocusEnabled, setToolTipText, setTransferHandler, setVerifyInputWhenFocusTarget, setVisible, unregisterKeyboardAction, update

Methods inherited from class java.awt.Container

add, add, add, add, add, addContainerListener, addPropertyChangeListener, addPropertyChangeListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalKeys, getFocusTraversalPolicy, getLayout, getMousePosition, insets, isAncestorOf, isFocusCycleRoot, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paintComponents, preferredSize, printComponents, remove, remove, removeContainerListener, setComponentZOrder, setFocusCycleRoot, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setLayout, transferFocusBackward, transferFocusDownCycle, validate

Methods inherited from class java.awt.Component

action, add, addComponentListener, addFocusListener, addHierarchyBoundsListener, addHierarchyListener, addInputMethodListener, addKeyListener, addMouseListener, addMouseMotionListener, addMouseWheelListener, bounds, checkImage, checkImage, contains, createImage, createImage, createVolatileImage, createVolatileImage, dispatchEvent, enable, enableInputMethods, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getBackground, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusCycleRootAncestor, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getForeground, getGraphicsConfiguration, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputContext, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocale, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMousePosition, getMouseWheelListeners, getName, getParent, getPeer, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getToolkit, getTreeLock, gotFocus, handleEvent, hasFocus, hide, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isMaximumSizeSet, isMinimumSizeSet, isPreferredSizeSet, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, postEvent, prepareImage, prepareImage, remove, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, resize, resize, setBounds, setBounds, setComponentOrientation, setCursor, setDropTarget, setFocusable, setFocusTraversalKeysEnabled, setIgnoreRepaint, setLocale, setLocation, setLocation, setName, setSize, setSize, show, show, size, toString, transferFocus, transferFocusUpCycle

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

KEY_INITIALLY_SHOW

public static final java.lang.String KEY_INITIALLY_SHOW

See Also:

Constant Field Values

KEY_BIO_MOLECULES

public static final java.lang.String KEY_BIO_MOLECULES

See Also:

Constant Field Values

KEY_INTERPRET_AFTER_LOADING

public static final java.lang.String KEY_INTERPRET_AFTER_LOADING

See Also:

Constant Field Values

ID_DISPOSED

public static final java.lang.String ID_DISPOSED

See Also:

Constant Field Values

ID_PROTEIN_VIEWER

public static final java.lang.String ID_PROTEIN_VIEWER

See Also:

Constant Field Values

SPIN

public static final java.lang.String SPIN

See Also:

Constant Field Values

KEY_MSG_NO_PROTEIN

public static final java.lang.String KEY_MSG_NO_PROTEIN

See Also:

Constant Field Values

Constructor Detail

Protein3d

public Protein3d()

Method Detail

isPreview

public boolean isPreview()

dispose

public void dispose()

Specified by:

dispose in interface Disposable

getProteins

public Protein[] getProteins()

addProteins

public void addProteins(Protein... pp0)

afterAddProteins

public void afterAddProteins(Protein... pp)

removeProtein

public void removeProtein(Protein p)

isProteinShown

public boolean isProteinShown(Protein p)

eachProteinInDifferentColor

public boolean eachProteinInDifferentColor(boolean asChain,
                                           boolean testOnly)

getRotationAndTranslationOfView

public Matrix3D getRotationAndTranslationOfView()

run

public java.lang.Object run(java.lang.String id,
                            java.lang.Object arg)

Specified by:

run in interface ChRunnable

isNucleotideChainVisible

public boolean isNucleotideChainVisible(HeteroCompound ha)

showListOfHeterosAndNucleotides

public void showListOfHeterosAndNucleotides(Protein p)

paintComponent

public void paintComponent(java.awt.Graphics g)

Overrides:

paintComponent in class ChPanel

paintChildren

public void paintChildren(java.awt.Graphics g)

Overrides:

paintChildren in class ChPanel

paintHook

public boolean paintHook(javax.swing.JComponent component,
                         java.awt.Graphics g,
                         boolean after)

Specified by:

paintHook in interface PaintHook

after - This method is called once before and once after super.paintComponent.

Returns:

means do not call super.paintComponent

getToolTipText

public java.lang.String getToolTipText(java.awt.event.MouseEvent ev)

Overrides:

getToolTipText in class ChPanel

provideTip

public java.lang.String provideTip(java.lang.Object objOrEv)

Specified by:

provideTip in interface TooltipProvider

enableDisable

public void enableDisable()

addOrRemoveButton

public void addOrRemoveButton(int pos,
                              javax.swing.JComponent b,
                              int where)

setHideDistantDNS

public void setHideDistantDNS(boolean b)

processEv

public void processEv(java.awt.AWTEvent ev)

Specified by:

processEv in interface ProcessEv

See Also:

EvAdapter

getProteinAtMouse

public Protein getProteinAtMouse()

getResidueIndexAtMouse

public int getResidueIndexAtMouse()

highlightAminoAcid

public void highlightAminoAcid(Protein p,
                               int idx)

highlightAminoAcid

public void highlightAminoAcid(float[] xyz)

chain2color

public static java.awt.Color chain2color(int i)

docuColorChooser

public static javax.swing.JComponent docuColorChooser()

getView

public Protein3d.PView getView(Protein prot)