public class AlignmentFrame extends javax.swing.JInternalFrame implements AlignmentListener, DisplayPropertiesListener, ActivityColorListener
javax.swing.JInternalFrame.AccessibleJInternalFrame, javax.swing.JInternalFrame.JDesktopIcon
javax.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_PROPERTY
listenerList, TOOL_TIP_TEXT_KEY, ui, UNDEFINED_CONDITION, WHEN_ANCESTOR_OF_FOCUSED_COMPONENT, WHEN_FOCUSED, WHEN_IN_FOCUSED_WINDOW
accessibleContext, 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, updateUI
addAncestorListener, 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, update
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, invalidate, isAncestorOf, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paintComponents, preferredSize, printComponents, processContainerEvent, processEvent, remove, removeAll, removeContainerListener, setComponentZOrder, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, transferFocusDownCycle, validate, validateTree
action, 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, transferFocusUpCycle
protected 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 DisplayPropertiesListener
public void displaySeqSelectChanged(DisplayProperties displayProperties, Sequence sequence, boolean select)
displaySeqSelectChanged
in interface DisplayPropertiesListener
public void displayFontChanged(DisplayProperties displayProperties)
displayFontChanged
in interface DisplayPropertiesListener
public void displayRenderGapsChanged(DisplayProperties displayProperties)
displayRenderGapsChanged
in interface DisplayPropertiesListener
public void displayGroupEditingChanged(DisplayProperties displayProperties)
displayGroupEditingChanged
in interface DisplayPropertiesListener
public void displayOverwriteChanged(DisplayProperties displayProperties)
displayOverwriteChanged
in interface DisplayPropertiesListener
public void displayHighlightsChanged(DisplayProperties displayProperties, Sequence sequence)
displayHighlightsChanged
in interface DisplayPropertiesListener
public void displayHighlightsChanged(DisplayProperties displayProperties, Sequence[] sequenceArray)
displayHighlightsChanged
in interface DisplayPropertiesListener
public void activityBackgroundChanged(DisplayProperties displayProperties)
activityBackgroundChanged
in interface DisplayPropertiesListener
public void alignmentNameChanged(Alignment alignment)
alignmentNameChanged
in interface AlignmentListener
public void alignmentSeqDeleted(Alignment alignment, int i, Sequence sequence)
alignmentSeqDeleted
in interface AlignmentListener
public void alignmentSeqSwapped(Alignment alignment, int i, int j)
alignmentSeqSwapped
in interface AlignmentListener
public void alignmentSeqActivityChanged(Alignment alignment, Sequence sequence)
alignmentSeqActivityChanged
in interface AlignmentListener
public void activityColorMappingChanged(java.awt.Color color)
activityColorMappingChanged
in interface ActivityColorListener
public void activityColorChanged(java.lang.String encodedActivity, java.awt.Color color)
activityColorChanged
in interface ActivityColorListener
public 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()