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java.lang.Object | +--java.awt.Component | +--java.awt.Container | +--javax.swing.JComponent | +--javax.swing.JPanel | +--org.emboss.jemboss.editor.GraphicSequenceCollection
This class can be used to get a grapical representation of a collection of sequences.
Field Summary | |
private java.util.Hashtable |
colorScheme
Colour scheme to use |
private boolean |
drawBlackBox
draw black square around residues |
private boolean |
drawColorBox
colour residues |
private boolean |
drawNumber
draw sequence position number |
private boolean |
drawSequence
draw the sequence |
private java.util.Vector |
graphicName
Vector containing graphical names of sequences |
private java.util.Vector |
graphicSequence
Vector containing graphical sequences |
private int |
hgt
|
private int |
hgtName
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private javax.swing.JScrollPane |
jspSequence
sequence scrollpane |
private int |
len
|
private int |
lenName
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private int |
MAXSEQLENGTH
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private SequenceJPanel |
numberDraw
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private int |
numResiduePerLine
number of residues on each line for print |
private PlotConsensus |
pc
Consensus plot |
private javax.swing.Box |
plotconsSeqBox
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private int |
plotConStrut
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private boolean |
prettPlot
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private java.util.Vector |
removedSeqs
Vector of sequences removed from panel |
private javax.swing.Box |
seqBox
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private javax.swing.Box |
seqNameBox
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private javax.swing.JPanel |
seqNamePanel
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private java.util.Vector |
seqs
Vector containing Sequence objects |
Fields inherited from class javax.swing.JPanel |
|
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.Container |
|
Fields inherited from class java.awt.Component |
BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT |
Fields inherited from interface java.awt.print.Printable |
NO_SUCH_PAGE, PAGE_EXISTS |
Fields inherited from interface java.awt.image.ImageObserver |
ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH |
Constructor Summary | |
GraphicSequenceCollection(java.util.Vector seqs,
java.util.Hashtable colorScheme,
javax.swing.JScrollPane jspSequence,
boolean drawSequence,
boolean drawBlackBox,
boolean drawColorBox,
boolean drawNumber,
javax.swing.JTextField statusField)
|
|
GraphicSequenceCollection(java.util.Vector seqs,
javax.swing.JScrollPane jspSequence,
boolean drawSequence,
boolean drawBlackBox,
boolean drawColorBox,
boolean drawNumber,
javax.swing.JTextField statusField)
|
Method Summary | |
protected void |
addSequence(Sequence seq,
boolean addToSequences,
int ypad,
int fontSize)
Add a sequence to the sequence collection display and to the collection of sequences (seqs) with a specified y-padding. |
protected void |
addSequence(Sequence seq,
boolean addToSequences,
int ypad,
int fontSize,
int index)
Add a sequence at a particular index to the sequence collection display and to the collection of sequences (seqs) with a specified y-padding. |
protected void |
deleteConsensusPlot()
|
protected void |
deleteSequence(java.lang.String name)
Delete a sequence from the sequence collection display and resize the sequence panel display |
void |
drawSequences(java.awt.Graphics2D g2d,
java.awt.print.PageFormat format,
int pageIndex)
|
void |
drawSequences(java.awt.Graphics2D g2d,
java.awt.print.PageFormat format,
int pageIndex,
int numResPerLine)
|
private int |
findMiddle(int newResPos,
int viewWidth,
java.lang.String pat)
Locate the center of a vieport view that contains the defined position to display |
int |
findPattern(java.lang.String pat,
int oldResPosition,
boolean wrapAround)
Search sequences for a pattern and highlight matches. |
protected java.awt.Color |
getColor(java.lang.String s,
int pos,
java.lang.String seqName)
|
int |
getFontSize()
|
java.util.Vector |
getGraphicSequence()
|
int |
getMaxSeqLength()
|
int |
getNameHeight()
|
java.awt.Dimension |
getNameViewSize()
Get the sequence name view size |
int |
getNameWidth()
|
int |
getNumberPages(java.awt.print.PageFormat format)
|
int |
getNumberPages(java.awt.print.PageFormat format,
int numResPerLine)
|
int |
getPanelHeight()
|
java.awt.Dimension |
getPanelSize()
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int |
getPanelWidth()
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java.awt.Dimension |
getPreferredScrollableViewportSize()
|
int |
getResiduesPerLine(java.awt.print.PageFormat format)
|
int |
getResiduesPerPage(java.awt.print.PageFormat format,
int numResPerLine)
|
int |
getScrollableBlockIncrement(java.awt.Rectangle r,
int orientation,
int direction)
|
boolean |
getScrollableTracksViewportHeight()
|
boolean |
getScrollableTracksViewportWidth()
|
int |
getScrollableUnitIncrement(java.awt.Rectangle r,
int orientation,
int direction)
|
protected java.util.Vector |
getSequenceCollection()
|
protected java.awt.Point |
getViewPosition()
|
protected java.awt.Rectangle |
getViewRect()
|
java.awt.Dimension |
getViewSize()
Get the sequence view size |
protected void |
idSort()
|
static void |
main(java.lang.String[] args)
|
protected void |
moveSequence(java.lang.String name,
int i)
|
int |
print(java.awt.Graphics g,
java.awt.print.PageFormat format,
int pageIndex)
|
private Sequence |
removeSequence(java.lang.String name)
|
private int |
searchSequences(int startSearch,
java.lang.String pat)
Search the sequences for the position in that matches the given pattern to search for. |
void |
setColorScheme(java.util.Hashtable colourTable)
|
void |
setDrawBoxes(boolean drawBlackBox)
|
void |
setDrawColor(boolean drawColorBox)
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void |
setFontSizeForCollection(int fs)
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void |
setJScrollPaneViewportView()
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private void |
setMaxSeqLength()
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protected void |
setMaxSequenceLength(int max)
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void |
setNamePanelWidth(int x)
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protected void |
setNumberOfResiduesPerLine(int numResiduePerLine)
|
private void |
setNumberSize()
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void |
setPrettyPlot(boolean bpretty)
|
protected void |
setSequenceSelection(boolean b)
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protected void |
showConsensusPlot(java.io.File matrix,
int wsize)
|
protected void |
showConsensusPlot(Matrix mat,
int wsize)
|
Methods inherited from class javax.swing.JPanel |
getAccessibleContext, getUI, getUIClassID, paramString, setUI, updateUI |
Methods inherited from class javax.swing.JComponent |
addAncestorListener, addNotify, addPropertyChangeListener, addPropertyChangeListener, addVetoableChangeListener, computeVisibleRect, contains, createToolTip, disable, enable, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, fireVetoableChange, getActionForKeyStroke, getActionMap, getAlignmentX, getAlignmentY, getAncestorListeners, getAutoscrolls, getBorder, getBounds, getClientProperty, getComponentGraphics, getConditionForKeyStroke, getDebugGraphicsOptions, getDefaultLocale, getGraphics, getHeight, getInputMap, getInputMap, getInputVerifier, getInsets, getInsets, getListeners, getLocation, getMaximumSize, getMinimumSize, getNextFocusableComponent, getPreferredSize, getPropertyChangeListeners, getPropertyChangeListeners, getRegisteredKeyStrokes, getRootPane, getSize, getToolTipLocation, getToolTipText, getToolTipText, getTopLevelAncestor, getTransferHandler, getVerifyInputWhenFocusTarget, getVetoableChangeListeners, getVisibleRect, getWidth, getX, getY, grabFocus, isDoubleBuffered, isLightweightComponent, isManagingFocus, isMaximumSizeSet, isMinimumSizeSet, isOpaque, isOptimizedDrawingEnabled, isPaintingTile, isPreferredSizeSet, isRequestFocusEnabled, isValidateRoot, paint, paintBorder, paintChildren, paintComponent, paintImmediately, paintImmediately, print, printAll, printBorder, printChildren, printComponent, processComponentKeyEvent, processKeyBinding, processKeyEvent, processMouseMotionEvent, putClientProperty, registerKeyboardAction, registerKeyboardAction, removeAncestorListener, removeNotify, removePropertyChangeListener, removePropertyChangeListener, removeVetoableChangeListener, repaint, repaint, requestDefaultFocus, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, resetKeyboardActions, reshape, revalidate, scrollRectToVisible, setActionMap, setAlignmentX, setAlignmentY, setAutoscrolls, setBackground, setBorder, setDebugGraphicsOptions, setDefaultLocale, setDoubleBuffered, setEnabled, setFont, setForeground, 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, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getContainerListeners, getFocusTraversalKeys, getFocusTraversalPolicy, getLayout, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusCycleRoot, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paintComponents, preferredSize, printComponents, processContainerEvent, processEvent, remove, remove, removeAll, removeContainerListener, setFocusCycleRoot, setFocusTraversalKeys, setFocusTraversalPolicy, setLayout, transferFocusBackward, transferFocusDownCycle, validate, validateTree |
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, getBackground, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusCycleRootAncestor, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getFontMetrics, getForeground, getGraphicsConfiguration, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputContext, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocale, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMouseWheelListeners, getName, getParent, getPeer, getSize, getToolkit, getTreeLock, gotFocus, handleEvent, hasFocus, hide, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, 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, processMouseEvent, processMouseWheelEvent, remove, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, 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 |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Field Detail |
private java.util.Vector removedSeqs
private java.util.Vector seqs
private java.util.Vector graphicSequence
private java.util.Vector graphicName
private java.util.Hashtable colorScheme
private PlotConsensus pc
private int lenName
private int hgtName
private int hgt
private int len
private int MAXSEQLENGTH
private int numResiduePerLine
private SequenceJPanel numberDraw
private javax.swing.JScrollPane jspSequence
private javax.swing.JPanel seqNamePanel
private javax.swing.Box seqBox
private javax.swing.Box seqNameBox
private javax.swing.Box plotconsSeqBox
private boolean drawSequence
private boolean drawBlackBox
private boolean drawColorBox
private boolean drawNumber
private boolean prettPlot
private int plotConStrut
Constructor Detail |
public GraphicSequenceCollection(java.util.Vector seqs, java.util.Hashtable colorScheme, javax.swing.JScrollPane jspSequence, boolean drawSequence, boolean drawBlackBox, boolean drawColorBox, boolean drawNumber, javax.swing.JTextField statusField)
seqs
- vector of sequencescolorScheme
- sequence colour schemejspSequence
- sequence scrollpanedrawSequence
- true to draw the sequencedrawBlackBox
- true to draw black square around residuesdrawColorBox
- true to colour residuesdrawNumber
- true to draw sequence position numberstatusField
- status field in the editorpublic GraphicSequenceCollection(java.util.Vector seqs, javax.swing.JScrollPane jspSequence, boolean drawSequence, boolean drawBlackBox, boolean drawColorBox, boolean drawNumber, javax.swing.JTextField statusField)
Method Detail |
protected java.util.Vector getSequenceCollection()
protected java.awt.Point getViewPosition()
protected java.awt.Rectangle getViewRect()
protected void showConsensusPlot(java.io.File matrix, int wsize)
protected void showConsensusPlot(Matrix mat, int wsize)
protected void deleteConsensusPlot()
protected void setMaxSequenceLength(int max)
private void setMaxSeqLength()
public int getMaxSeqLength()
protected void setSequenceSelection(boolean b)
private void setNumberSize()
protected java.awt.Color getColor(java.lang.String s, int pos, java.lang.String seqName)
private Sequence removeSequence(java.lang.String name)
protected void deleteSequence(java.lang.String name)
protected void moveSequence(java.lang.String name, int i)
protected void idSort()
protected void addSequence(Sequence seq, boolean addToSequences, int ypad, int fontSize, int index)
protected void addSequence(Sequence seq, boolean addToSequences, int ypad, int fontSize)
public java.awt.Dimension getViewSize()
public java.awt.Dimension getNameViewSize()
public java.awt.Dimension getPanelSize()
public int getNameHeight()
public int getNameWidth()
public void setNamePanelWidth(int x)
public int getPanelHeight()
public int getPanelWidth()
public java.util.Vector getGraphicSequence()
public void setDrawBoxes(boolean drawBlackBox)
public void setDrawColor(boolean drawColorBox)
public void setFontSizeForCollection(int fs)
public int getFontSize()
public int findPattern(java.lang.String pat, int oldResPosition, boolean wrapAround)
private int searchSequences(int startSearch, java.lang.String pat)
private int findMiddle(int newResPos, int viewWidth, java.lang.String pat)
public void setColorScheme(java.util.Hashtable colourTable)
public void setPrettyPlot(boolean bpretty)
public void setJScrollPaneViewportView()
public int getNumberPages(java.awt.print.PageFormat format)
public int getNumberPages(java.awt.print.PageFormat format, int numResPerLine)
public int getResiduesPerLine(java.awt.print.PageFormat format)
public int getResiduesPerPage(java.awt.print.PageFormat format, int numResPerLine)
public int print(java.awt.Graphics g, java.awt.print.PageFormat format, int pageIndex) throws java.awt.print.PrinterException
print
in interface java.awt.print.Printable
java.awt.print.PrinterException
protected void setNumberOfResiduesPerLine(int numResiduePerLine)
public void drawSequences(java.awt.Graphics2D g2d, java.awt.print.PageFormat format, int pageIndex)
public void drawSequences(java.awt.Graphics2D g2d, java.awt.print.PageFormat format, int pageIndex, int numResPerLine)
public java.awt.Dimension getPreferredScrollableViewportSize()
getPreferredScrollableViewportSize
in interface javax.swing.Scrollable
public boolean getScrollableTracksViewportHeight()
getScrollableTracksViewportHeight
in interface javax.swing.Scrollable
public boolean getScrollableTracksViewportWidth()
getScrollableTracksViewportWidth
in interface javax.swing.Scrollable
public int getScrollableBlockIncrement(java.awt.Rectangle r, int orientation, int direction)
getScrollableBlockIncrement
in interface javax.swing.Scrollable
public int getScrollableUnitIncrement(java.awt.Rectangle r, int orientation, int direction)
getScrollableUnitIncrement
in interface javax.swing.Scrollable
public static void main(java.lang.String[] args)
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