charite.christo.strap
Class StrapView

java.lang.Object
  charite.christo.strap.StrapView

All Implemented Interfaces:

ChRunnable, Disposable, PaintHook, PreferredSize, ProcessEv, StrapListener, TooltipProvider, java.awt.event.ActionListener, java.util.EventListener

public final class StrapView
extends java.lang.Object
implements ChRunnable, StrapListener, Disposable, PreferredSize, java.awt.event.ActionListener, PaintHook, TooltipProvider, ProcessEv

HELP The central view of the STRAP application is the alignment panel. It shows the names and sequences of loaded proteins. The user can add and remove white space to align the sequences, so-called alignment gaps. Usually, only one sequence alignment panel is shown but additional alignment views can be opened ITEM:StrapAlign#ACTION_newPan. In any case only one alignment is present in one STRAP instance. Nevertheless, STRAP can be run several times in parallel and data exchange between STRAP sessions is conducted by Drag-n-Drop.

Shading: Three residue shadings are available in the tool-bar: "charge", "hydropathy" and "chemical". Alternatively, secondary structure can be highlighted: Helices are painted red and sheets yellow. Further GUI controls are in the context-menu.

Editing: Manipulation of the multiple sequence alignment is performed with the keyboard. STRAP has many sophisticated keyboard commands. Please see ITEM:StrapKeyStroke.

Cursor: The cursor position is highlighted in all views with the following symbol: ICON:IC_CURSOR16. Usually only the alignment row containing the cursor is changed when for example a gap is introduced by pressing the space bar. It is often necessary to add white space to a number of sequences and not only to one sequence. The number of adjacent rows edited simultaneously can be set by hitting "#" and subsequently typing a number.

Stacking proteins: Usually, each row contains exactly one protein. The proteins can be dragged up or down in the row header to change their order. A number of proteins can be stacked into one single row to be manipulated simultaneously while only the sequence of one protein is shown: DIALOG:DialogManyInOneRow.
Residue selections are highlighted in the multiple sequence alignment. When the mouse is over a highlighted residue a WIKI:Tooltip with additional information appears. Right-click opens the context meny and CTRL+left-click selects the selection. It can also be selected by dragging a rectangular region.

Scrolling: The horizontal scroll-bar outlines the entire alignment and shows selections and plots. It can be enlarged with the mouse. If there are many proteins the vertical scroll-bar is visible. But also the horizontal scroll-bar can scroll vertically. Try mouse wheel turning with and without SHIFT and CTRL.

Field Summary

static int	BUT_3D
static int	BUT_ALIGN
static int	BUT_ALIGN_CTRL
static int	BUT_ALIGN_UNDO
static int	BUT_EXPORT
static int	BUT_FEATURE
static int	BUT_INFER3D_ALL
static int	BUT_LAF
static int	BUT_LIST_HET
static int	BUT_NUCL
static int	BUT_SEQVISTA
static int	BUT_WARN_MARCHING_ANTS
static int	CURSOR_COLUMN
static java.lang.String	KEY_AP
static java.lang.String	KEY_RH
static int	MCSV_CHARACTERS
static int	MCSV_FREQ
static int	MCSV_RESSEL_RECT
static int	TOG_BRIGHTER
static int	TOG_MAXIMIZE
static int	TOG_PLOT_ENTIRE_PANEL
static int	TOG_PROTECT_COL
static int	TOG_SHADE_ONLY_SELECTED

Fields inherited from interface charite.christo.ChRunnable

APPEND, COLUMN_TITLE, DOWNLOAD_FINISHED, GET_PANEL, ICON, INTERPRET_LINE, IS_DRAG4XY, ITEM_TEXT, MODIFY_RENDERER_COMPONENT, PROGRESS, REPAINT_CURSOR, SAY_DOWNLOADING, SET_ICON_IMAGE, SET_TREE_VALUE, SHOW_IN_FRAME, TAB_TEXT, TIP_TEXT

Fields inherited from interface charite.christo.Disposable

NONE

Constructor Summary

StrapView(boolean real)

Method Summary

void	actionPerformed(java.awt.event.ActionEvent ev)
void	addProtein(int afterRow, Protein p)
static ChButton	button(int t)
static ChCombo	choiceShading()
int	col2x(int col)
int	countColumns()
int	countRows()
void	dispose()
int	findRow(Protein p)
javax.swing.JComponent	getAlignmentPane()
static javax.swing.JComponent	getAlignmentPane(StrapView v)
int	getCursorAminoAcid()
int	getCursorColumn()
Protein	getCursorProtein()
int	getCursorRow()
HScrollBar	getHorizontalSB()
javax.swing.JComponent	getPanel()
java.awt.Dimension	getPreferredSize(javax.swing.JComponent c)
Protein	getProtein(int row)
Protein[]	getProteins()
Protein[]	getProteinsInRow(int row)
java.awt.Rectangle	getRectRubberBand()
javax.swing.JComponent	getRowHeader()
int	getSpaceBetweenRows()
Protein[]	getVisibleProteins()
java.awt.Rectangle	getVisibleRowsAndCols()
java.awt.Rectangle	getVisibleXYWH()
void	handleEvent(StrapEvent ev)
int	modificationCount()
void	mouseEnterDrogTarget(java.lang.Object target)
boolean	paintHook(javax.swing.JComponent c, java.awt.Graphics g, boolean after)
void	paintRegion(java.awt.Graphics gAwt, int colLeft, int colRight, int rowTop, int rowBot, int options)
void	processEv(java.awt.AWTEvent ev)
java.lang.String	provideTip(java.lang.Object objOrEv)
void	removeProteins(Protein... pp)
int	row2y(int row)
java.lang.Object	run(java.lang.String id, java.lang.Object arg)
void	saveRestore(boolean save, java.lang.Object key)
static void	setButAlign(int nProt)
boolean	setCursor(int opt, Protein p, int idxOrCol)
void	setRectRubberBand(int col, int row, int numCol, int numRow)
static void	setReduceHeight()
void	setReduceHeight(int h)
static void	setResSelection(boolean toClipbrd, Protein protein, int col1, int col2, boolean[] selRes, StrapView view0)
static void	setRowHeaderType(java.lang.String t)
void	setSpaceBetweenRows(int space)
void	showMinRows(int n)
static ChSlider	sliderSimilarity()
java.lang.Thread	thread_setCursor(int opt, Protein p, int idxOrCol)
static java.lang.Thread	thread_setRowHeaderType(java.lang.String t)
int	x2col(int x)
int	y2row(int y)

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

KEY_AP

public static final java.lang.String KEY_AP

See Also:

Constant Field Values

KEY_RH

public static final java.lang.String KEY_RH

See Also:

Constant Field Values

BUT_INFER3D_ALL

public static final int BUT_INFER3D_ALL

See Also:

Constant Field Values

BUT_LIST_HET

public static final int BUT_LIST_HET

See Also:

Constant Field Values

BUT_NUCL

public static final int BUT_NUCL

See Also:

Constant Field Values

BUT_SEQVISTA

public static final int BUT_SEQVISTA

See Also:

Constant Field Values

BUT_3D

public static final int BUT_3D

See Also:

Constant Field Values

BUT_EXPORT

public static final int BUT_EXPORT

See Also:

Constant Field Values

BUT_ALIGN

public static final int BUT_ALIGN

See Also:

Constant Field Values

BUT_ALIGN_CTRL

public static final int BUT_ALIGN_CTRL

See Also:

Constant Field Values

BUT_ALIGN_UNDO

public static final int BUT_ALIGN_UNDO

See Also:

Constant Field Values

BUT_LAF

public static final int BUT_LAF

See Also:

Constant Field Values

BUT_FEATURE

public static final int BUT_FEATURE

See Also:

Constant Field Values

BUT_WARN_MARCHING_ANTS

public static final int BUT_WARN_MARCHING_ANTS

See Also:

Constant Field Values

TOG_MAXIMIZE

public static final int TOG_MAXIMIZE

See Also:

Constant Field Values

TOG_BRIGHTER

public static final int TOG_BRIGHTER

See Also:

Constant Field Values

TOG_SHADE_ONLY_SELECTED

public static final int TOG_SHADE_ONLY_SELECTED

See Also:

Constant Field Values

TOG_PLOT_ENTIRE_PANEL

public static final int TOG_PLOT_ENTIRE_PANEL

See Also:

Constant Field Values

TOG_PROTECT_COL

public static final int TOG_PROTECT_COL

See Also:

Constant Field Values

MCSV_RESSEL_RECT

public static final int MCSV_RESSEL_RECT

See Also:

Constant Field Values

MCSV_CHARACTERS

public static final int MCSV_CHARACTERS

See Also:

Constant Field Values

MCSV_FREQ

public static final int MCSV_FREQ

See Also:

Constant Field Values

CURSOR_COLUMN

public static final int CURSOR_COLUMN

See Also:

Constant Field Values

Constructor Detail

StrapView

public StrapView(boolean real)

Method Detail

dispose

public void dispose()

Specified by:

dispose in interface Disposable

countRows

public int countRows()

getProtein

public Protein getProtein(int row)

modificationCount

public int modificationCount()

findRow

public int findRow(Protein p)

addProtein

public void addProtein(int afterRow,
                       Protein p)

getProteinsInRow

public Protein[] getProteinsInRow(int row)

removeProteins

public void removeProteins(Protein... pp)

getProteins

public Protein[] getProteins()

getVisibleProteins

public Protein[] getVisibleProteins()

sliderSimilarity

public static ChSlider sliderSimilarity()

choiceShading

public static ChCombo choiceShading()

button

public static ChButton button(int t)

run

public java.lang.Object run(java.lang.String id,
                            java.lang.Object arg)

Specified by:

run in interface ChRunnable

countColumns

public int countColumns()

getVisibleRowsAndCols

public java.awt.Rectangle getVisibleRowsAndCols()

row2y

public int row2y(int row)

col2x

public int col2x(int col)

x2col

public int x2col(int x)

y2row

public int y2row(int y)

getPreferredSize

public java.awt.Dimension getPreferredSize(javax.swing.JComponent c)

Specified by:

getPreferredSize in interface PreferredSize

getPanel

public javax.swing.JComponent getPanel()

getSpaceBetweenRows

public int getSpaceBetweenRows()

setSpaceBetweenRows

public void setSpaceBetweenRows(int space)

getVisibleXYWH

public java.awt.Rectangle getVisibleXYWH()

setReduceHeight

public static void setReduceHeight()

showMinRows

public void showMinRows(int n)

setReduceHeight

public void setReduceHeight(int h)

provideTip

public java.lang.String provideTip(java.lang.Object objOrEv)

Specified by:

provideTip in interface TooltipProvider

paintHook

public boolean paintHook(javax.swing.JComponent c,
                         java.awt.Graphics g,
                         boolean after)

Specified by:

paintHook in interface PaintHook

after - This method is called once before and once after super.paintComponent.

Returns:

means do not call super.paintComponent

getAlignmentPane

public static javax.swing.JComponent getAlignmentPane(StrapView v)

getAlignmentPane

public javax.swing.JComponent getAlignmentPane()

getHorizontalSB

public HScrollBar getHorizontalSB()

paintRegion

public void paintRegion(java.awt.Graphics gAwt,
                        int colLeft,
                        int colRight,
                        int rowTop,
                        int rowBot,
                        int options)

handleEvent

public void handleEvent(StrapEvent ev)

Specified by:

handleEvent in interface StrapListener

processEv

public void processEv(java.awt.AWTEvent ev)

Specified by:

processEv in interface ProcessEv

See Also:

EvAdapter

actionPerformed

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

Specified by:

actionPerformed in interface java.awt.event.ActionListener

getRowHeader

public javax.swing.JComponent getRowHeader()

thread_setRowHeaderType

public static java.lang.Thread thread_setRowHeaderType(java.lang.String t)

setRowHeaderType

public static void setRowHeaderType(java.lang.String t)

mouseEnterDrogTarget

public void mouseEnterDrogTarget(java.lang.Object target)

setButAlign

public static void setButAlign(int nProt)

setResSelection

public static void setResSelection(boolean toClipbrd,
                                   Protein protein,
                                   int col1,
                                   int col2,
                                   boolean[] selRes,
                                   StrapView view0)

getCursorAminoAcid

public int getCursorAminoAcid()

getCursorColumn

public int getCursorColumn()

getCursorRow

public int getCursorRow()

getCursorProtein

public Protein getCursorProtein()

thread_setCursor

public java.lang.Thread thread_setCursor(int opt,
                                         Protein p,
                                         int idxOrCol)

setCursor

public boolean setCursor(int opt,
                         Protein p,
                         int idxOrCol)

saveRestore

public void saveRestore(boolean save,
                        java.lang.Object key)

setRectRubberBand

public void setRectRubberBand(int col,
                              int row,
                              int numCol,
                              int numRow)

getRectRubberBand

public java.awt.Rectangle getRectRubberBand()