charite.christo.protein
Interface ResidueSelection

All Superinterfaces:

HasProtein

All Known Implementing Classes:

BasicResidueSelection, DialogPlot, Distance3DToCursor, Distance3DToHetero, ResidueAnnotation

public interface ResidueSelection
extends HasProtein

HELP PACKAGE:charite.christo.strap. Residue selections are objects attached to proteins which select one or more amino acid positions from the amino acid sequence. They usually have color, style attributes and a balloon message. They may be shown in the alignment (1D) and in the built in 3D-wire-frame (3D) and the scrollbar view-port (VP). Selections are created in different ways:

• Mouse selection: Dragging the mouse in the alignment pane selects a continuous chain of residues which may be pasted e.g. into a BLAST web form.
• The dialog DIALOG:charite.christo.strap.DialogHighlightPattern. All occurrences of the patterns will be highlighted in the selected color.
• 3D-Visualizations: Clicking a 3D-backbone atom creates selections.
• Some dialogs create selection objects:
  1. DIALOG:DialogDotPlot.
  2. DIALOG:DialogSelectionOfResiduesMain.
• User extension: Users familiar with Java-Programming may implement their own algorithms. See DIALOG:charite.christo.strap.StrapHotswap.
• Residue annotations: Annotations are residue selections that can contain text attributes. They are saved to HD. Simple selections can easily be transfered into residue annotations using ITEM:ResidueSelectionPopup#ACTION_MK_RESANO
• Sequence features: Sequence features like glycosylation are residue annotations obtained from remote servers.

Field Summary

static java.lang.String	NAME_BACKBONE
static java.lang.String	NAME_CURSOR
static java.lang.String	NAME_MOUSE_OVER
static java.lang.String	NAME_STANDARD
static ResidueSelection[]	NONE

Method Summary

Protein	getProtein()
boolean[]	getSelectedAminoacids()
int	getSelectedAminoacidsOffset()
void	setProtein(Protein p)
void	setSelectedAminoacids(boolean[] bb, int offset) The method body may be kept empty.

Field Detail

NAME_MOUSE_OVER

static final java.lang.String NAME_MOUSE_OVER

See Also:

Constant Field Values

NAME_BACKBONE

static final java.lang.String NAME_BACKBONE

See Also:

Constant Field Values

NAME_CURSOR

static final java.lang.String NAME_CURSOR

See Also:

Constant Field Values

NAME_STANDARD

static final java.lang.String NAME_STANDARD

See Also:

Constant Field Values

NONE

static final ResidueSelection[] NONE

Method Detail

setProtein

void setProtein(Protein p)

getProtein

Protein getProtein()

Specified by:

getProtein in interface HasProtein

getSelectedAminoacids

boolean[] getSelectedAminoacids()

Returns:

true for each selected residue.

getSelectedAminoacidsOffset

int getSelectedAminoacidsOffset()

Returns:

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

setSelectedAminoacids

void setSelectedAminoacids(boolean[] bb,
                           int offset)

The method body may be kept empty.