charite.christo.interfaces
Interface ResidueSelection

All Known Implementing Classes:

AbstractResidueSelection

public interface ResidueSelection

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_convertToResidueAnnotation
• Sequence features: Sequence features like glycosylation are residue annotations obtained from remote servers.

Field Summary

static ResidueSelection[]

NONE

Method Summary

Protein	getProtein() Usually, the protein reference which is stored in an instance variable is returned.
boolean[]	getSelectedAminoacids()
int	getSelectedAminoacidsOffset()
boolean	setProtein(Protein p) Usually, an instance variable is set with the given protein.
void	setSelectedAminoacids(boolean[] bb, int offset) The selected residues might be initialized.

Field Detail

NONE

static final ResidueSelection[] NONE

Method Detail

setProtein

boolean setProtein(Protein p)

Usually, an instance variable is set with the given protein.

Parameters:

p - a reference to the protein object.

getProtein

Protein getProtein()

Usually, the protein reference which is stored in an instance variable is returned.

Returns:

a reference to the protein object.

getSelectedAminoacids

boolean[] getSelectedAminoacids()

Returns:

true for each selected residue.

getSelectedAminoacidsOffset

int getSelectedAminoacidsOffset()

setSelectedAminoacids

void setSelectedAminoacids(boolean[] bb,
                           int offset)

The selected residues might be initialized. Usually the method body can be kept empty.