apollo.gui.detailviewers.sequencealigner
Class BaseEditorPanel

java.lang.Object
  java.awt.Component
      java.awt.Container
          javax.swing.JComponent
              javax.swing.JPanel
                  apollo.gui.detailviewers.sequencealigner.SeqAlignPanel
                      apollo.gui.detailviewers.sequencealigner.BaseEditorPanel

All Implemented Interfaces:

BaseScrollable, java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, javax.accessibility.Accessible, javax.swing.Scrollable

public class BaseEditorPanel
extends SeqAlignPanel

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class apollo.gui.detailviewers.sequencealigner.SeqAlignPanel

SeqAlignPanel.AutoscrollThread, SeqAlignPanel.ScrollMouseListener

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

javax.swing.JPanel.AccessibleJPanel

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

javax.swing.JComponent.AccessibleJComponent

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

java.awt.Container.AccessibleAWTContainer

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

java.awt.Component.AccessibleAWTComponent, java.awt.Component.BltBufferStrategy, java.awt.Component.FlipBufferStrategy

Field Summary

protected AnnotationEditor	annotationEditor
protected BaseFineEditor	baseFineEditor
protected javax.swing.JMenuItem	createExonMenuItem
protected javax.swing.JMenuItem	deleteExonMenuItem
protected javax.swing.JMenuItem	deletionMenuItem
protected javax.swing.JMenuItem	findSequenceMenuItem
protected SequenceI[]	frame
protected java.util.Vector	hitZones
protected javax.swing.JMenuItem	insertionMenuItem
protected javax.swing.JLabel	locationLabel
protected static org.apache.log4j.Logger	logger
protected javax.swing.JMenuItem	makeIntronMenuItem
protected javax.swing.JMenuItem	merge3PrimeMenuItem
protected javax.swing.JMenuItem	merge5PrimeMenuItem
protected javax.swing.JMenuItem	noAdjustmentMenuItem
protected int	padAmt
protected javax.swing.JLabel	relativeLocationLabel
protected javax.swing.JPopupMenu	rightClickMenu
protected int	selectBeginPos
protected int	selectCurrentPos
SeqFeatureI	selectedFeature
protected int	selectedTier
protected java.awt.Color	selectionBoxColor
static int	SEQ_SELECT_DRAG
protected java.awt.Color	seqSelectColor
protected javax.swing.JMenuItem	sequenceMenuItem
protected javax.swing.JMenu	sequencingErrorSubMenu
protected javax.swing.JMenuItem	set3PrimeMenuItem
protected javax.swing.JMenuItem	set5PrimeMenuItem
protected boolean	showHitZones
protected int[]	splices
protected javax.swing.JMenuItem	startTranslationMenuItem
protected javax.swing.JMenuItem	substitutionMenuItem
protected java.util.Vector	translatedHitZones
protected javax.swing.JMenuItem	translationSlipMenuItem
protected javax.swing.JMenuItem	translationStutterMenuItem

Fields inherited from class apollo.gui.detailviewers.sequencealigner.SeqAlignPanel

cols, END_BOUNDARY, EXON, highestBase, horizontalMode, INTRON, lowestBase, NO_BOUNDARY, NO_TYPE, reverseStrand, rowMargin, sequences, START_BOUNDARY, START_CODON, STOP_CODON, stripeWidth

Fields inherited from class javax.swing.JComponent

accessibleContext, listenerList, TOOL_TIP_TEXT_KEY, ui, 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 java.awt.image.ImageObserver

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

Constructor Summary

BaseEditorPanel(GuiCurationState curationState, BaseFineEditor baseFineEditor, boolean reverseStrand, int lowestBase, int highestBase, SeqFeatureI annotFeatureSet)
Need lowestBase for offset of sequence

Method Summary

int	addFeature(SeqFeatureI feature) Adds feature to an existing SeqWrapper if it doesnt overlap with it, otherwise creates a new SeqWrapper for it,
int	addResult(SeqFeatureI result) Adds a result to this panel so that it can be displayed.
int	addResults(java.util.Set<SeqFeatureI> results) Adds all results in a set to this panel so that they can be displayed.
int	attachAnnot(AnnotatedFeatureI annot) can be transcript or 1 level annot
void	attachTranscripts(java.util.Vector transcripts) Expects a vector of Transcripts or 1 level annots.
protected void	changeEnd(SeqFeatureI feature, int base_offset, int limit_5prime, int limit_3prime)
protected void	changeStart(SeqFeatureI feature, int base_offset, int limit_5prime, int limit_3prime)
protected void	createRightClickMenu()
void	detachTranscript(Transcript trans)
void	displayRightClickMenu(int xLoc, int yLoc)
void	formatRightClickMenu()
java.awt.Color[][]	getColorArray() The inner array is an array of 2 colors, for alternating exon colors.
int	getRowMargin() FIXME: Returns the row margin property value, whatever that is...
SeqFeatureI	getSelectedFeature()
int	getSelectedTier()
java.awt.Color	getSelectionBoxColor()
java.awt.Color	getSeqSelectColor()
boolean	getShowHitZones()
java.util.Vector	getTranslatedHitZones(int frame)
protected boolean	isSequencingErrorPosition(int dnapos)
protected boolean	notTooSmall(int start_pos, int end_pos)
int	selectHighPos()
int	selectLowPos()
void	setHitZones(java.util.Vector hitZones)
void	setShowHitZones(boolean showHitZones)
void	setTranslatedHitZones(java.util.Vector hitZones, int frame)
protected void	showFindDialog()
protected void	showGoToDialog()

Methods inherited from class apollo.gui.detailviewers.sequencealigner.SeqAlignPanel

addAlignFeature, addNotify, addTier, attachFeatureToSequence, attachRendererToTier, basePairToPos, clear, createGraphics, getBackgroundColor1, getBackgroundColor2, getBoundaryType, getCharAt, getCharHeight, getCharWidth, getColForPixelPosition, getColForPosition, getColumnCount, getExonRangeIndex, getExonRangeIndex, getFeatureAtIndex, getFeatureAtPosition, getFeatureCount, getFeatureForPixelPosition, getFeatureForPixelPosition, getFeatureSetAtPosition, getFeaturesInRange, getHighestBase, getLowestBase, getPixelLocForColAndRow, getPixelLocForPosition, getPosRectangleForPixels, getPreferredScrollableViewportSize, getRangeAtPosition, getRangeIndex, getRectangleForCharPosition, getRectangleForTierPosition, getRendererAt, getReverseStrand, getRowCount, getRowForPixelPosition, getRowForPosition, getRowHeight, getRowWidth, getScrollableBlockIncrement, getScrollableTracksViewportHeight, getScrollableTracksViewportWidth, getScrollableUnitIncrement, getSequenceCount, getSequenceForTier, getSeqWrapperForTier, getStripeWidth, getTierCount, getTierForFeature, getTierForPixelPosition, getTypeAtPosition, getVisibleBase, getVisibleBaseCount, haltThread, handleAutoscroll, moveSequence, padPerChar, paint, posToBasePair, posToResidue, reformat, removeFeature, repaint, repaint, residueToBasePair, residueToPos, scrollToBase, scrollToFeature, scrollToPosition, scrollToRow, setAutoscroll, setHorizontalMode, setReverseStrand, setStripeWidth, setVisibilityForSequence, validate, validateTree

Methods inherited from class javax.swing.JPanel

getAccessibleContext, getUI, getUIClassID, paramString, setUI, updateUI

Methods inherited from class javax.swing.JComponent

addAncestorListener, addVetoableChangeListener, computeVisibleRect, contains, createToolTip, disable, enable, firePropertyChange, firePropertyChange, firePropertyChange, fireVetoableChange, getActionForKeyStroke, getActionMap, getAlignmentX, getAlignmentY, getAncestorListeners, getAutoscrolls, 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, getRootPane, getSize, getToolTipLocation, getToolTipText, getToolTipText, getTopLevelAncestor, getTransferHandler, getVerifyInputWhenFocusTarget, getVetoableChangeListeners, getVisibleRect, getWidth, getX, getY, grabFocus, isDoubleBuffered, isLightweightComponent, isManagingFocus, isOpaque, isOptimizedDrawingEnabled, isPaintingTile, isRequestFocusEnabled, isValidateRoot, paintBorder, paintChildren, paintComponent, 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, 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, setUI, setVerifyInputWhenFocusTarget, setVisible, unregisterKeyboardAction, update

Methods inherited from class java.awt.Container

add, add, add, add, add, addContainerListener, addImpl, 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, processContainerEvent, processEvent, remove, remove, removeAll, removeContainerListener, setComponentZOrder, setFocusCycleRoot, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setLayout, transferFocusBackward, transferFocusDownCycle

Methods inherited from class java.awt.Component

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, 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, processComponentEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processMouseWheelEvent, remove, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, 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

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

logger

protected static final org.apache.log4j.Logger logger

SEQ_SELECT_DRAG

public static final int SEQ_SELECT_DRAG

See Also:

Constant Field Values

padAmt

protected int padAmt

selectedFeature

public SeqFeatureI selectedFeature

selectedTier

protected int selectedTier

annotationEditor

protected AnnotationEditor annotationEditor

baseFineEditor

protected BaseFineEditor baseFineEditor

locationLabel

protected javax.swing.JLabel locationLabel

relativeLocationLabel

protected javax.swing.JLabel relativeLocationLabel

rightClickMenu

protected javax.swing.JPopupMenu rightClickMenu

makeIntronMenuItem

protected javax.swing.JMenuItem makeIntronMenuItem

createExonMenuItem

protected javax.swing.JMenuItem createExonMenuItem

merge5PrimeMenuItem

protected javax.swing.JMenuItem merge5PrimeMenuItem

merge3PrimeMenuItem

protected javax.swing.JMenuItem merge3PrimeMenuItem

set5PrimeMenuItem

protected javax.swing.JMenuItem set5PrimeMenuItem

set3PrimeMenuItem

protected javax.swing.JMenuItem set3PrimeMenuItem

deleteExonMenuItem

protected javax.swing.JMenuItem deleteExonMenuItem

startTranslationMenuItem

protected javax.swing.JMenuItem startTranslationMenuItem

translationSlipMenuItem

protected javax.swing.JMenuItem translationSlipMenuItem

translationStutterMenuItem

protected javax.swing.JMenuItem translationStutterMenuItem

insertionMenuItem

protected javax.swing.JMenuItem insertionMenuItem

deletionMenuItem

protected javax.swing.JMenuItem deletionMenuItem

substitutionMenuItem

protected javax.swing.JMenuItem substitutionMenuItem

noAdjustmentMenuItem

protected javax.swing.JMenuItem noAdjustmentMenuItem

sequencingErrorSubMenu

protected javax.swing.JMenu sequencingErrorSubMenu

findSequenceMenuItem

protected javax.swing.JMenuItem findSequenceMenuItem

sequenceMenuItem

protected javax.swing.JMenuItem sequenceMenuItem

seqSelectColor

protected java.awt.Color seqSelectColor

selectionBoxColor

protected java.awt.Color selectionBoxColor

frame

protected SequenceI[] frame

selectBeginPos

protected int selectBeginPos

selectCurrentPos

protected int selectCurrentPos

splices

protected int[] splices

hitZones

protected java.util.Vector hitZones

translatedHitZones

protected java.util.Vector translatedHitZones

showHitZones

protected boolean showHitZones

Constructor Detail

BaseEditorPanel

public BaseEditorPanel(GuiCurationState curationState,
                       BaseFineEditor baseFineEditor,
                       boolean reverseStrand,
                       int lowestBase,
                       int highestBase,
                       SeqFeatureI annotFeatureSet)

Need lowestBase for offset of sequence

Method Detail

setShowHitZones

public void setShowHitZones(boolean showHitZones)

getShowHitZones

public boolean getShowHitZones()

addResults

public int addResults(java.util.Set<SeqFeatureI> results)

Adds all results in a set to this panel so that they can be displayed.

Parameters:

Set - reults - each result should be !isAnnot

Returns:

int tier - the number of results added

setHitZones

public void setHitZones(java.util.Vector hitZones)

setTranslatedHitZones

public void setTranslatedHitZones(java.util.Vector hitZones,
                                  int frame)

getTranslatedHitZones

public java.util.Vector getTranslatedHitZones(int frame)

selectLowPos

public int selectLowPos()

selectHighPos

public int selectHighPos()

getRowMargin

public int getRowMargin()

Description copied from class: SeqAlignPanel

FIXME: Returns the row margin property value, whatever that is...

Overrides:

getRowMargin in class SeqAlignPanel

Returns:

the rowMargin property

getColorArray

public java.awt.Color[][] getColorArray()

The inner array is an array of 2 colors, for alternating exon colors. The "outer" array represents transcript coloring. Transcripts can have different exon coloring pairs(see SelectableDNARenderer's exonColorIndex and transcriptColorIndex). This now takes in 2 colors from Config edeFeatureColor. It no longer is setting up 4 colors for alternating transcripts as well as exons. Easy enough to reinstate if desired.

getSelectedFeature

public SeqFeatureI getSelectedFeature()

getSelectedTier

public int getSelectedTier()

addFeature

public int addFeature(SeqFeatureI feature)

Adds feature to an existing SeqWrapper if it doesnt overlap with it, otherwise creates a new SeqWrapper for it,

Returns:

The element number in sequences, which is synonomous with tier number

showFindDialog

protected void showFindDialog()

showGoToDialog

protected void showGoToDialog()

notTooSmall

protected boolean notTooSmall(int start_pos,
                              int end_pos)

changeStart

protected void changeStart(SeqFeatureI feature,
                           int base_offset,
                           int limit_5prime,
                           int limit_3prime)

changeEnd

protected void changeEnd(SeqFeatureI feature,
                         int base_offset,
                         int limit_5prime,
                         int limit_3prime)

createRightClickMenu

protected void createRightClickMenu()

formatRightClickMenu

public void formatRightClickMenu()

displayRightClickMenu

public void displayRightClickMenu(int xLoc,
                                  int yLoc)

detachTranscript

public void detachTranscript(Transcript trans)

attachAnnot

public int attachAnnot(AnnotatedFeatureI annot)

can be transcript or 1 level annot

addResult

public int addResult(SeqFeatureI result)

Adds a result to this panel so that it can be displayed.

Parameters:

SeqFeatureI - result - should be !isAnnot

Returns:

int tier - the tier on which the result was placed

attachTranscripts

public void attachTranscripts(java.util.Vector transcripts)

Expects a vector of Transcripts or 1 level annots. This also creates the 3 amino acid sequences. This method is essential for BaseEditorPanel initialization.

getSeqSelectColor

public java.awt.Color getSeqSelectColor()

getSelectionBoxColor

public java.awt.Color getSelectionBoxColor()

isSequencingErrorPosition

protected boolean isSequencingErrorPosition(int dnapos)