charite.christo.strap
Class ResidueAnnotation

java.lang.Object
  charite.christo.strap.ResidueAnnotation

All Implemented Interfaces:

ChRunnable, Colored, Disposable, HasImage, HasModiCount, HasName, HasPropertyMap, HasRenderer, HasRendererModiCount, HasWeakRef, HasProtein, ResidueSelection, SelectorOfNucleotides, VisibleIn123

public final class ResidueAnnotation
extends java.lang.Object
implements HasWeakRef, HasName, ResidueSelection, SelectorOfNucleotides, VisibleIn123, Colored, Disposable, HasRendererModiCount, HasImage, HasPropertyMap, ChRunnable, HasModiCount

HELP Residue annotations, allow the assignment of information to specific amino acids or nucleotides of proteins. They are special types of residue selections. A residue annotation has a list of entries each having a type, modifiable text. The user can change these entries and add new entries. Depending on the type, the entries contain different information:

• Rendering commands for 3D-viewers,
• Expressions to select certain atoms for the rendering commands to act upon.
• LaTeX-code for the PDF-output,
• Hyperlinks, PUBMED-references, database references,
• Free text notes and remarks.

More detailed information is found in ITEM:ResidueAnnotationView A ResidueAnnotation can be created in different ways:

• A residue selection can be created by dragging the mouse over the sequence. Right-click opens the context menu of the residue selection. With the menu item BUTTON:ResidueSelectionPopup#ACTION_MK_RESANO a residue annotation can be created that has the same amino acid positions.
Alternatively, use the context menu of the alignment panel to create an annotation for the protein under the mouse pointer.

Residue annotations which are highlighted in the alignment can be selected in two different ways: By CTRL left-click or by dragging a rectangular box. Selected residue annotations have WIKI:Marching_ants.

Sequence Features: Features like phosporylation sites and active sites are special annotations which are retrieved from a computational service and are therefore not saved to hard disk. Their color cannot be changed.

Background Images

INCLUDE_DOC:ChIcon SEE_DIALOG:DialogResidueAnnotationChanges SEE_DIALOG:DialogResidueAnnotationList SEE_CLASS:ResidueAnnotationView SEE_CLASS:ActivateDeactivate SEE_CLASS:AddAnnotation

Nested Class Summary

static class

ResidueAnnotation.Entry

Field Summary

static java.lang.String	ATOMS
static java.lang.String	BALLOON
static java.lang.String	BG_IMAGE
static java.lang.String	COLOR
static java.lang.String	DISABLED
static long	ENTRY_NOT_SAVED
static java.lang.String	GROUP
static java.lang.String	HYPERREFS
static java.lang.String[]	MAIN_KEYS
static java.lang.String	NAME
static ResidueAnnotation[]	NONE
static java.lang.String[]	OTHER_KEYS
static java.lang.String	POS
static java.lang.String	SPECIFIC_VIEW3D
static java.lang.String	STYLE
static java.lang.String	TEXSHADE
static java.lang.String	VIEW3D

Fields inherited from interface charite.christo.protein.ResidueSelection

NAME_BACKBONE, NAME_CURSOR, NAME_MOUSE_OVER, NAME_STANDARD

Fields inherited from interface charite.christo.protein.VisibleIn123

ANYWHERE, ARROW_HEADS, BIT_SHIFT_LINE, HTML, JALVIEW, NO_FLASH, SB, SEQUENCE, STRUCTURE, STYLE_BACKGROUND, STYLE_CIRCLE, STYLE_CURSOR, STYLE_DOTTED, STYLE_HIDDEN, STYLE_IMAGE, STYLE_IMAGE_LUCID, STYLE_LOWER_HALF_BACKGROUND, STYLE_UNDERLINE, STYLE_UPPER_HALF_BACKGROUND

Fields inherited from interface charite.christo.HasRenderer

JLIST, STRIKE_THROUGH

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

Constructor Summary

ResidueAnnotation(Protein p)

Method Summary

void	addE(long options, java.lang.String key, java.lang.String value, boolean isEnabled, int row)
void	addE(java.lang.String key0, java.lang.String value)
void	addEnS(java.lang.String key0, java.lang.String value)
void	dispose()
boolean	featureEndsWithAminoName()
java.awt.Color	getColor()
java.lang.String	getCssClass()
ResidueAnnotation.Entry[]	getEntries()
java.lang.String	getFeatureName()
javax.swing.ImageIcon	getIcon()
java.lang.String	getID()
java.awt.Image	getImage(java.awt.Component observer)
java.lang.String	getName() A ResidueAnnotation-object has a name.
java.util.Map	getPropertyMap(boolean create)
Protein	getProtein() ResidueAnnotation-Objects belong to a certain protein
java.lang.Object	getRenderer(long options, long[] rendOptions)
long	getRendererModiCount()
boolean[]	getSelectedAminoacids()
int	getSelectedAminoacidsOffset()
boolean[]	getSelectedNucleotides()
int	getSelectedNucleotidesOffset() The goal is to reduce the size of the returned boolean array.
java.lang.CharSequence	getSrcText()
int	getStyle() Rendering style
java.lang.String	getValue(java.lang.String key) Return the 1st value with the key.
int	getVisibleWhere() e.g.
java.lang.Object	getWeakRef()
long	getWhenCreated()
int	getWhereFeatureLoadedFrom()
boolean	isAmino()
boolean	isEnabled()
static void	loadResidueAnnotation(Protein p, java.io.File file)
static java.lang.String	mapKey(java.lang.String k)
int	modificationCount()
void	readFeatureAnnotations()
void	removeEntry(ResidueAnnotation.Entry e)
java.lang.Object	run(java.lang.String id, java.lang.Object arg)
static java.io.File	save(Protein p, java.io.File dir)
void	setColor(java.awt.Color c) sets the color
void	setEnabled(boolean b)
void	setEnabled(boolean b, java.lang.String key)
void	setFeatureName(java.lang.String name, int featureSrc)
void	setProtein(Protein p)
void	setRendererText(java.lang.String s)
void	setSelectedAminoacids(boolean[] bb, int offset) The method body may be kept empty.
void	setSelectedAminoacids(java.lang.String selection) e.g.
void	setSelectedNucleotides(java.lang.String selection)
void	setSrcText(java.lang.CharSequence t)
void	setStyle(int i) Rendering style
void	setValue(java.lang.String key, java.lang.CharSequence textValue) Adds a new key-value-pair
void	setVisibleWhere(int where)
boolean	verifyDropRows(boolean drop, java.lang.String data, int row, java.awt.Point screen)

Methods inherited from class java.lang.Object

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

Field Detail

NAME

public static final java.lang.String NAME

See Also:

Constant Field Values

POS

public static final java.lang.String POS

See Also:

Constant Field Values

GROUP

public static final java.lang.String GROUP

See Also:

Constant Field Values

ATOMS

public static final java.lang.String ATOMS

See Also:

Constant Field Values

STYLE

public static final java.lang.String STYLE

See Also:

Constant Field Values

TEXSHADE

public static final java.lang.String TEXSHADE

HYPERREFS

public static final java.lang.String HYPERREFS

COLOR

public static final java.lang.String COLOR

See Also:

Constant Field Values

BG_IMAGE

public static final java.lang.String BG_IMAGE

See Also:

Constant Field Values

VIEW3D

public static final java.lang.String VIEW3D

See Also:

Constant Field Values

SPECIFIC_VIEW3D

public static final java.lang.String SPECIFIC_VIEW3D

See Also:

Constant Field Values

DISABLED

public static final java.lang.String DISABLED

See Also:

Constant Field Values

BALLOON

public static final java.lang.String BALLOON

See Also:

Constant Field Values

MAIN_KEYS

public static final java.lang.String[] MAIN_KEYS

OTHER_KEYS

public static final java.lang.String[] OTHER_KEYS

NONE

public static final ResidueAnnotation[] NONE

ENTRY_NOT_SAVED

public static final long ENTRY_NOT_SAVED

See Also:

Constant Field Values

Constructor Detail

ResidueAnnotation

public ResidueAnnotation(Protein p)

Method Detail

getWeakRef

public java.lang.Object getWeakRef()

Specified by:

getWeakRef in interface HasWeakRef

modificationCount

public int modificationCount()

Specified by:

modificationCount in interface HasModiCount

getWhenCreated

public long getWhenCreated()

dispose

public void dispose()

Specified by:

dispose in interface Disposable

getProtein

public Protein getProtein()

ResidueAnnotation-Objects belong to a certain protein

Specified by:

getProtein in interface HasProtein

Specified by:

getProtein in interface ResidueSelection

Specified by:

getProtein in interface SelectorOfNucleotides

setProtein

public void setProtein(Protein p)

Specified by:

setProtein in interface ResidueSelection

Specified by:

setProtein in interface SelectorOfNucleotides

getName

public java.lang.String getName()

A ResidueAnnotation-object has a name.

Specified by:

getName in interface HasName

getID

public java.lang.String getID()

setSelectedAminoacids

public void setSelectedAminoacids(boolean[] bb,
                                  int offset)

Description copied from interface: ResidueSelection

The method body may be kept empty.

Specified by:

setSelectedAminoacids in interface ResidueSelection

setSelectedAminoacids

public void setSelectedAminoacids(java.lang.String selection)

e.g. s.setSelectedAminoacids("3-5");

setSelectedNucleotides

public void setSelectedNucleotides(java.lang.String selection)

getSelectedAminoacidsOffset

public int getSelectedAminoacidsOffset()

Specified by:

getSelectedAminoacidsOffset in interface ResidueSelection

Returns:

A possible offset. For example {true,true} with offset 6 means that that the 6th and 7th residue is selected.

getSelectedAminoacids

public boolean[] getSelectedAminoacids()

Specified by:

getSelectedAminoacids in interface ResidueSelection

Returns:

true for each selected residue.

getSelectedNucleotidesOffset

public int getSelectedNucleotidesOffset()

Description copied from interface: SelectorOfNucleotides

The goal is to reduce the size of the returned boolean array. if e.g. the 100th nt is selected getOffset() can return 99 and getSelectedNucleotides() can return new boolean[]{true}. BitSet would not have been a solution because the following causses OutOfMemoryError: new BitSet().set(1000*1000*1000,true);

Specified by:

getSelectedNucleotidesOffset in interface SelectorOfNucleotides

getSelectedNucleotides

public boolean[] getSelectedNucleotides()

Specified by:

getSelectedNucleotides in interface SelectorOfNucleotides

getStyle

public int getStyle()

Rendering style

Specified by:

getStyle in interface VisibleIn123

setStyle

public void setStyle(int i)

Rendering style

Specified by:

setStyle in interface VisibleIn123

setColor

public void setColor(java.awt.Color c)

sets the color

Specified by:

setColor in interface Colored

getColor

public java.awt.Color getColor()

Specified by:

getColor in interface Colored

Specified by:

getColor in interface VisibleIn123

getVisibleWhere

public int getVisibleWhere()

Description copied from interface: VisibleIn123

e.g. STRUCTURE | SEQUENCE means visible in 3d and 1d

Specified by:

getVisibleWhere in interface VisibleIn123

setVisibleWhere

public void setVisibleWhere(int where)

Specified by:

setVisibleWhere in interface VisibleIn123

getImage

public java.awt.Image getImage(java.awt.Component observer)

Specified by:

getImage in interface HasImage

run

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

Specified by:

run in interface ChRunnable

getIcon

public javax.swing.ImageIcon getIcon()

setRendererText

public void setRendererText(java.lang.String s)

getRenderer

public java.lang.Object getRenderer(long options,
                                    long[] rendOptions)

Specified by:

getRenderer in interface HasRenderer

getRendererModiCount

public long getRendererModiCount()

Specified by:

getRendererModiCount in interface HasRendererModiCount

getValue

public java.lang.String getValue(java.lang.String key)

Return the 1st value with the key.

isAmino

public boolean isAmino()

setValue

public void setValue(java.lang.String key,
                     java.lang.CharSequence textValue)

Adds a new key-value-pair

setEnabled

public void setEnabled(boolean b)

setEnabled

public void setEnabled(boolean b,
                       java.lang.String key)

getEntries

public ResidueAnnotation.Entry[] getEntries()

removeEntry

public void removeEntry(ResidueAnnotation.Entry e)

addE

public void addE(java.lang.String key0,
                 java.lang.String value)

addEnS

public void addEnS(java.lang.String key0,
                   java.lang.String value)

addE

public void addE(long options,
                 java.lang.String key,
                 java.lang.String value,
                 boolean isEnabled,
                 int row)

isEnabled

public boolean isEnabled()

loadResidueAnnotation

public static void loadResidueAnnotation(Protein p,
                                         java.io.File file)

save

public static java.io.File save(Protein p,
                                java.io.File dir)

getPropertyMap

public java.util.Map getPropertyMap(boolean create)

Specified by:

getPropertyMap in interface HasPropertyMap

readFeatureAnnotations

public void readFeatureAnnotations()

setFeatureName

public void setFeatureName(java.lang.String name,
                           int featureSrc)

getFeatureName

public java.lang.String getFeatureName()

getWhereFeatureLoadedFrom

public int getWhereFeatureLoadedFrom()

getCssClass

public java.lang.String getCssClass()

getSrcText

public java.lang.CharSequence getSrcText()

setSrcText

public void setSrcText(java.lang.CharSequence t)

featureEndsWithAminoName

public boolean featureEndsWithAminoName()

verifyDropRows

public boolean verifyDropRows(boolean drop,
                              java.lang.String data,
                              int row,
                              java.awt.Point screen)

mapKey

public static java.lang.String mapKey(java.lang.String k)