charite.christo.strap
Class DialogPlot

java.lang.Object
  java.awt.Component
      java.awt.Container
          javax.swing.JComponent
              javax.swing.JTabbedPane
                  charite.christo.strap.AbstractDialogJTabbedPane
                      charite.christo.strap.DialogPlot

All Implemented Interfaces:

Colored, Disposable, HasModiCount, IsEnabled, HasProtein, ResidueSelection, StrapListener, ValueOfResidue, VisibleIn123, ValueOfAlignPosition, java.awt.event.ActionListener, java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, java.util.EventListener, javax.accessibility.Accessible, javax.swing.SwingConstants

public class DialogPlot
extends AbstractDialogJTabbedPane
implements ValueOfResidue, ValueOfAlignPosition, ResidueSelection, java.awt.event.ActionListener, IsEnabled, VisibleIn123, StrapListener, HasModiCount

HELP With this dialog numeric data is plotted along the sequence/alignment.

1. Plotting values assigned to amino acids such as sequence hydrophobicity profile
2. Values belonging to columns of the multiple sequence alignment such as sequence variable

Values are assigned to each column of the sequence alignment and a diagram is plotted in the alignment pane and the horizontal scrollbar. PACKAGE:charite.christo.strap.extensions. The values are calculated by a class which implements ValueOfAlignPosition or ValueOfResidue. The user chooses a Java class COMBO:CountResidues and some proteins and selects the toggle ICON:IC_SHOW. SEE_DIALOG:DialogPlot SEE_DIALOG:DialogBarChart

See Also:

Serialized Form

Nested Class Summary

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

Fields inherited from class javax.swing.JTabbedPane

SCROLL_TAB_LAYOUT, WRAP_TAB_LAYOUT

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.protein.ResidueSelection

NAME_BACKBONE, NAME_CURSOR, NAME_MOUSE_OVER, NAME_STANDARD, NONE

Fields inherited from interface charite.christo.protein.VisibleIn123

ANYWHERE, ARROW_HEADS, BIT_SHIFT_LINE, HTML, JALVIEW, NO_FLASH, SB, SEQUENCE, STRUCTURE, STYLE_BACKGROUND, STYLE_CIRCLE, STYLE_CURSOR, STYLE_DOTTED, STYLE_HIDDEN, STYLE_IMAGE, STYLE_IMAGE_LUCID, STYLE_LOWER_HALF_BACKGROUND, STYLE_UNDERLINE, STYLE_UPPER_HALF_BACKGROUND

Fields inherited from interface charite.christo.Disposable

NONE

Fields inherited from interface javax.swing.SwingConstants

BOTTOM, CENTER, EAST, HORIZONTAL, LEADING, LEFT, NEXT, NORTH, NORTH_EAST, NORTH_WEST, PREVIOUS, RIGHT, SOUTH, SOUTH_EAST, SOUTH_WEST, TOP, TRAILING, VERTICAL, WEST

Fields inherited from interface java.awt.image.ImageObserver

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

Constructor Summary

DialogPlot()

Method Summary

void	actionPerformed(java.awt.event.ActionEvent ev)
void	dispose()
java.awt.Color	getColor()
Protein	getProtein()
Protein[]	getProteins()
boolean[]	getSelectedAminoacids()
int	getSelectedAminoacidsOffset()
int	getStyle()
double[]	getValues() Plugin that returns a numeric value for each amino acid of the protein or null.
int	getVisibleWhere() e.g.
void	handleEvent(StrapEvent ev)
boolean	isEnabled(java.lang.Object o)
int	modificationCount()
void	setColor(java.awt.Color c)
void	setProtein(Protein p)
void	setProteins(Protein... proteins)
void	setSelectedAminoacids(boolean[] bb, int offset) The method body may be kept empty.
void	setStyle(int s)
void	setVisibleWhere(int w)
void	setVoAP(java.lang.Object o)
void	setVoR(java.lang.Object o)

Methods inherited from class charite.christo.strap.AbstractDialogJTabbedPane

fireStateChanged, isDisposed

Methods inherited from class javax.swing.JTabbedPane

add, add, add, add, add, addChangeListener, addTab, addTab, addTab, getAccessibleContext, getBackgroundAt, getBoundsAt, getChangeListeners, getComponentAt, getDisabledIconAt, getDisplayedMnemonicIndexAt, getForegroundAt, getIconAt, getMnemonicAt, getModel, getSelectedComponent, getSelectedIndex, getTabComponentAt, getTabCount, getTabLayoutPolicy, getTabPlacement, getTabRunCount, getTitleAt, getToolTipText, getToolTipTextAt, getUI, getUIClassID, indexAtLocation, indexOfComponent, indexOfTab, indexOfTab, indexOfTabComponent, insertTab, isEnabledAt, remove, remove, removeAll, removeChangeListener, removeTabAt, setBackgroundAt, setComponentAt, setDisabledIconAt, setDisplayedMnemonicIndexAt, setEnabledAt, setForegroundAt, setIconAt, setMnemonicAt, setModel, setSelectedComponent, setSelectedIndex, setTabComponentAt, setTabLayoutPolicy, setTabPlacement, setTitleAt, setToolTipTextAt, 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, getMaximumSize, getMinimumSize, getNextFocusableComponent, getPopupLocation, getPreferredSize, getRegisteredKeyStrokes, getRootPane, getSize, getToolTipLocation, getToolTipText, getTopLevelAncestor, getTransferHandler, getVerifyInputWhenFocusTarget, getVetoableChangeListeners, getVisibleRect, getWidth, getX, getY, grabFocus, isDoubleBuffered, isLightweightComponent, isManagingFocus, isOpaque, isOptimizedDrawingEnabled, isPaintingForPrint, isPaintingTile, isRequestFocusEnabled, isValidateRoot, paint, 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

addContainerListener, addPropertyChangeListener, addPropertyChangeListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalKeys, getFocusTraversalPolicy, getLayout, getMousePosition, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paintComponents, preferredSize, printComponents, 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, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isMaximumSizeSet, isMinimumSizeSet, isPreferredSizeSet, isShowing, 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

Constructor Detail

DialogPlot

public DialogPlot()

Method Detail

setVoR

public void setVoR(java.lang.Object o)

setVoAP

public void setVoAP(java.lang.Object o)

getColor

public java.awt.Color getColor()

Specified by:

getColor in interface Colored

Specified by:

getColor in interface VisibleIn123

setColor

public void setColor(java.awt.Color c)

Specified by:

setColor in interface Colored

actionPerformed

public void actionPerformed(java.awt.event.ActionEvent ev)

Specified by:

actionPerformed in interface java.awt.event.ActionListener

isEnabled

public final boolean isEnabled(java.lang.Object o)

Specified by:

isEnabled in interface IsEnabled

getProtein

public Protein getProtein()

Specified by:

getProtein in interface HasProtein

Specified by:

getProtein in interface ResidueSelection

getProteins

public Protein[] getProteins()

Specified by:

getProteins in interface ValueOfAlignPosition

setProteins

public void setProteins(Protein... proteins)

Specified by:

setProteins in interface ValueOfAlignPosition

setProtein

public void setProtein(Protein p)

Specified by:

setProtein in interface ResidueSelection

Specified by:

setProtein in interface ValueOfResidue

getValues

public double[] getValues()

Description copied from interface: ValueOfResidue

Plugin that returns a numeric value for each amino acid of the protein or null. These are plotted in the alignment pane. It should notify changes by dispatching a JAVADOC:StrapEvent of type JAVADOC:StrapEvent#VALUE_OF_RESIDUE_CHANGED

Specified by:

getValues in interface ValueOfResidue

Specified by:

getValues in interface ValueOfAlignPosition

dispose

public void dispose()

Specified by:

dispose in interface Disposable

Overrides:

dispose in class AbstractDialogJTabbedPane

modificationCount

public int modificationCount()

Specified by:

modificationCount in interface HasModiCount

setSelectedAminoacids

public void setSelectedAminoacids(boolean[] bb,
                                  int offset)

Description copied from interface: ResidueSelection

The method body may be kept empty.

Specified by:

setSelectedAminoacids in interface ResidueSelection

getSelectedAminoacidsOffset

public int getSelectedAminoacidsOffset()

Specified by:

getSelectedAminoacidsOffset in interface ResidueSelection

Returns:

A possible offset. For example {true,true} with offset 6 means that that the 6th and 7th residue is selected.

getSelectedAminoacids

public boolean[] getSelectedAminoacids()

Specified by:

getSelectedAminoacids in interface ResidueSelection

Returns:

true for each selected residue.

setStyle

public void setStyle(int s)

Specified by:

setStyle in interface VisibleIn123

getStyle

public int getStyle()

Specified by:

getStyle in interface VisibleIn123

getVisibleWhere

public int getVisibleWhere()

Description copied from interface: VisibleIn123

e.g. STRUCTURE | SEQUENCE means visible in 3d and 1d

Specified by:

getVisibleWhere in interface VisibleIn123

setVisibleWhere

public void setVisibleWhere(int w)

Specified by:

setVisibleWhere in interface VisibleIn123

handleEvent

public final void handleEvent(StrapEvent ev)

Specified by:

handleEvent in interface StrapListener