public class AlignmentFrame extends javax.swing.JInternalFrame implements AlignmentListener, DisplayPropertiesListener, ActivityColorListener
javax.swing.JInternalFrame.AccessibleJInternalFrame, javax.swing.JInternalFrame.JDesktopIconjavax.swing.JComponent.AccessibleJComponent| Modifier and Type | Field and Description |
|---|---|
protected boolean |
columnFiltering |
protected boolean |
columnSorting |
static int |
MaxPriority |
closable, CONTENT_PANE_PROPERTY, desktopIcon, FRAME_ICON_PROPERTY, frameIcon, GLASS_PANE_PROPERTY, iconable, IS_CLOSED_PROPERTY, IS_ICON_PROPERTY, IS_MAXIMUM_PROPERTY, IS_SELECTED_PROPERTY, isClosed, isIcon, isMaximum, isSelected, LAYERED_PANE_PROPERTY, maximizable, MENU_BAR_PROPERTY, resizable, ROOT_PANE_PROPERTY, rootPane, rootPaneCheckingEnabled, title, TITLE_PROPERTYlistenerList, TOOL_TIP_TEXT_KEY, ui, UNDEFINED_CONDITION, WHEN_ANCESTOR_OF_FOCUSED_COMPONENT, WHEN_FOCUSED, WHEN_IN_FOCUSED_WINDOWaccessibleContext, BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT| Constructor and Description |
|---|
AlignmentFrame(AlignmentTree tree) |
AlignmentFrame(AlignmentTree tree,
java.util.Map<java.lang.String,java.awt.Color> activityColorMap) |
| Modifier and Type | Method and Description |
|---|---|
void |
activityBackgroundChanged(DisplayProperties displayProperties) |
void |
activityColorChanged(java.lang.String encodedActivity,
java.awt.Color color) |
void |
activityColorMappingChanged(java.awt.Color color) |
void |
addColumnFilter(ColumnFilter filter,
int column) |
void |
addColumnSort(ColumnSort columnSort,
int column) |
void |
alignmentNameChanged(Alignment alignment) |
void |
alignmentSeqActivityChanged(Alignment alignment,
Sequence sequence) |
void |
alignmentSeqDeleted(Alignment alignment,
int i,
Sequence sequence) |
void |
alignmentSeqSwapped(Alignment alignment,
int i,
int j) |
void |
displayAnnViewChanged(DisplayProperties displayProperties,
Sequence sequence,
boolean show) |
void |
displayFontChanged(DisplayProperties displayProperties) |
void |
displayGroupEditingChanged(DisplayProperties displayProperties) |
void |
displayHighlightsChanged(DisplayProperties displayProperties,
Sequence sequence) |
void |
displayHighlightsChanged(DisplayProperties displayProperties,
Sequence[] sequenceArray) |
void |
displayOverwriteChanged(DisplayProperties displayProperties) |
void |
displayRenderGapsChanged(DisplayProperties displayProperties) |
void |
displaySeqSelectChanged(DisplayProperties displayProperties,
Sequence sequence,
boolean select) |
java.util.Map<java.lang.String,java.lang.String> |
getCharActivityMap() |
java.util.Map<java.lang.String,java.awt.Color> |
getEncodedActivityColorMap() |
int |
getEncodingLength() |
int |
getNextFreePriority() |
int |
getNoColumnSorts() |
boolean |
hasAnyActivities(java.lang.String s) |
void |
incrementColumnSorts() |
boolean |
isValidEncodedActivity(java.lang.String encodedActivity) |
void |
removeColumnFilter(int column) |
void |
removeColumnSort(int column) |
void |
removed(int priority) |
void |
revalidateAndRepaintAll() |
void |
setAllSequenceCollapsed(boolean collapsed,
boolean repaint) |
void |
setAllSequencesHidden(boolean hidden) |
void |
setColumnFiltering(boolean columnFiltering) |
void |
setColumnFiltering(boolean columnFiltering,
boolean setMenu) |
void |
setColumnSorting(boolean columnSorting) |
void |
setColumnSorting(boolean columnSorting,
boolean setMenu) |
void |
setSequenceCollapsed(int idx,
boolean collapsed,
boolean repaint) |
void |
updateCollapsed() |
void |
updateSort() |
addImpl, addInternalFrameListener, createRootPane, dispose, doDefaultCloseAction, fireInternalFrameEvent, getAccessibleContext, getContentPane, getDefaultCloseOperation, getDesktopIcon, getDesktopPane, getFocusCycleRootAncestor, getFocusOwner, getFrameIcon, getGlassPane, getInternalFrameListeners, getJMenuBar, getLastCursor, getLayer, getLayeredPane, getMenuBar, getMostRecentFocusOwner, getNormalBounds, getRootPane, getTitle, getUI, getUIClassID, getWarningString, hide, isClosable, isClosed, isFocusCycleRoot, isIcon, isIconifiable, isMaximizable, isMaximum, isResizable, isRootPaneCheckingEnabled, isSelected, moveToBack, moveToFront, pack, paintComponent, paramString, remove, removeInternalFrameListener, reshape, restoreSubcomponentFocus, setClosable, setClosed, setContentPane, setCursor, setDefaultCloseOperation, setDesktopIcon, setFocusCycleRoot, setFrameIcon, setGlassPane, setIcon, setIconifiable, setJMenuBar, setLayer, setLayer, setLayeredPane, setLayout, setMaximizable, setMaximum, setMenuBar, setNormalBounds, setResizable, setRootPane, setRootPaneCheckingEnabled, setSelected, setTitle, setUI, show, toBack, toFront, updateUIaddAncestorListener, addNotify, addVetoableChangeListener, computeVisibleRect, contains, createToolTip, disable, enable, firePropertyChange, firePropertyChange, firePropertyChange, fireVetoableChange, getActionForKeyStroke, getActionMap, getAlignmentX, getAlignmentY, getAncestorListeners, getAutoscrolls, getBaseline, getBaselineResizeBehavior, getBorder, getBounds, getClientProperty, getComponentGraphics, getComponentPopupMenu, getConditionForKeyStroke, getDebugGraphicsOptions, getDefaultLocale, getFontMetrics, getGraphics, getHeight, getInheritsPopupMenu, getInputMap, getInputMap, getInputVerifier, getInsets, getInsets, getListeners, getLocation, getMaximumSize, getMinimumSize, getNextFocusableComponent, getPopupLocation, getPreferredSize, getRegisteredKeyStrokes, getSize, getToolTipLocation, getToolTipText, getToolTipText, getTopLevelAncestor, getTransferHandler, getVerifyInputWhenFocusTarget, getVetoableChangeListeners, getVisibleRect, getWidth, getX, getY, grabFocus, isDoubleBuffered, isLightweightComponent, isManagingFocus, isOpaque, isOptimizedDrawingEnabled, isPaintingForPrint, isPaintingOrigin, isPaintingTile, isRequestFocusEnabled, isValidateRoot, paint, paintBorder, paintChildren, paintImmediately, paintImmediately, print, printAll, printBorder, printChildren, printComponent, processComponentKeyEvent, processKeyBinding, processKeyEvent, processMouseEvent, processMouseMotionEvent, putClientProperty, registerKeyboardAction, registerKeyboardAction, removeAncestorListener, removeNotify, removeVetoableChangeListener, repaint, repaint, requestDefaultFocus, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, resetKeyboardActions, 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, setUI, setVerifyInputWhenFocusTarget, setVisible, unregisterKeyboardAction, updateadd, 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, invalidate, isAncestorOf, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paintComponents, preferredSize, printComponents, processContainerEvent, processEvent, remove, removeAll, removeContainerListener, setComponentZOrder, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, transferFocusDownCycle, validate, validateTreeaction, add, addComponentListener, addFocusListener, addHierarchyBoundsListener, addHierarchyListener, addInputMethodListener, addKeyListener, addMouseListener, addMouseMotionListener, addMouseWheelListener, bounds, checkImage, checkImage, coalesceEvents, contains, createImage, createImage, createVolatileImage, createVolatileImage, disableEvents, dispatchEvent, enable, enableEvents, enableInputMethods, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getBackground, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, 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, 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, processComponentEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processMouseWheelEvent, remove, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, resize, resize, setBounds, setBounds, setComponentOrientation, setDropTarget, setFocusable, setFocusTraversalKeysEnabled, setIgnoreRepaint, setLocale, setLocation, setLocation, setName, setSize, setSize, show, size, toString, transferFocus, transferFocusBackward, transferFocusUpCycleprotected boolean columnFiltering
protected boolean columnSorting
public static final int MaxPriority
public AlignmentFrame(AlignmentTree tree, java.util.Map<java.lang.String,java.awt.Color> activityColorMap)
public AlignmentFrame(AlignmentTree tree)
public java.util.Map<java.lang.String,java.awt.Color> getEncodedActivityColorMap()
public void incrementColumnSorts()
public int getNextFreePriority()
public void removed(int priority)
public int getNoColumnSorts()
public void addColumnSort(ColumnSort columnSort, int column)
public void removeColumnSort(int column)
public void updateSort()
public void removeColumnFilter(int column)
public void addColumnFilter(ColumnFilter filter, int column)
public void updateCollapsed()
public void revalidateAndRepaintAll()
public void setColumnFiltering(boolean columnFiltering)
public void setColumnFiltering(boolean columnFiltering,
boolean setMenu)
public void setColumnSorting(boolean columnSorting)
public void setColumnSorting(boolean columnSorting,
boolean setMenu)
public void setAllSequenceCollapsed(boolean collapsed,
boolean repaint)
public void setAllSequencesHidden(boolean hidden)
public void setSequenceCollapsed(int idx,
boolean collapsed,
boolean repaint)
public void displayAnnViewChanged(DisplayProperties displayProperties, Sequence sequence, boolean show)
displayAnnViewChanged in interface DisplayPropertiesListenerpublic void displaySeqSelectChanged(DisplayProperties displayProperties, Sequence sequence, boolean select)
displaySeqSelectChanged in interface DisplayPropertiesListenerpublic void displayFontChanged(DisplayProperties displayProperties)
displayFontChanged in interface DisplayPropertiesListenerpublic void displayRenderGapsChanged(DisplayProperties displayProperties)
displayRenderGapsChanged in interface DisplayPropertiesListenerpublic void displayGroupEditingChanged(DisplayProperties displayProperties)
displayGroupEditingChanged in interface DisplayPropertiesListenerpublic void displayOverwriteChanged(DisplayProperties displayProperties)
displayOverwriteChanged in interface DisplayPropertiesListenerpublic void displayHighlightsChanged(DisplayProperties displayProperties, Sequence sequence)
displayHighlightsChanged in interface DisplayPropertiesListenerpublic void displayHighlightsChanged(DisplayProperties displayProperties, Sequence[] sequenceArray)
displayHighlightsChanged in interface DisplayPropertiesListenerpublic void activityBackgroundChanged(DisplayProperties displayProperties)
activityBackgroundChanged in interface DisplayPropertiesListenerpublic void alignmentNameChanged(Alignment alignment)
alignmentNameChanged in interface AlignmentListenerpublic void alignmentSeqDeleted(Alignment alignment, int i, Sequence sequence)
alignmentSeqDeleted in interface AlignmentListenerpublic void alignmentSeqSwapped(Alignment alignment, int i, int j)
alignmentSeqSwapped in interface AlignmentListenerpublic void alignmentSeqActivityChanged(Alignment alignment, Sequence sequence)
alignmentSeqActivityChanged in interface AlignmentListenerpublic void activityColorMappingChanged(java.awt.Color color)
activityColorMappingChanged in interface ActivityColorListenerpublic void activityColorChanged(java.lang.String encodedActivity,
java.awt.Color color)
activityColorChanged in interface ActivityColorListenerpublic boolean isValidEncodedActivity(java.lang.String encodedActivity)
public int getEncodingLength()
public boolean hasAnyActivities(java.lang.String s)
public java.util.Map<java.lang.String,java.lang.String> getCharActivityMap()