org.biojava.nbio.structure.align.gui.aligpanel

Class MultipleAlignmentCoordManager

java.lang.Object

org.biojava.nbio.structure.align.gui.aligpanel.MultipleAlignmentCoordManager

public class MultipleAlignmentCoordManager
extends Object

Generalization of the Coodinate Manager to include an arbitrary number of sequences (lines) for MultipleAlignment visualization.

Author:

Aleix Lafita

Field Summary

Fields

Modifier and Type	Field and Description
static int	DEFAULT_CHAR_SIZE Size per character
static int	DEFAULT_LINE_LENGTH Number of chars per line
static int	DEFAULT_LINE_SEPARATION Separation between sequences in the alignment
static int	DEFAULT_RIGHT_SPACER Space on the right side between sequence and legend.
static int	DEFAULT_X_SPACE Left boundary
static int	DEFAULT_Y_SPACE Top boundary
int	DEFAULT_Y_STEP Size of space between rows.
static int	SUMMARY_POS Position at which the alignment summary is printed

Constructor Summary

Constructors

Constructor and Description
MultipleAlignmentCoordManager(int size, int length) Constructor.

Method Summary

Modifier and Type	Method and Description
int	getAligSeq(Point point) Returns the index of the structure, for a given point in the Panel.
Point	getEndLegendPosition(int lineNr, int structure)
Point	getLegendPosition(int lineNr, int structure) Provide the coordinates for where to draw the legend for line X given the structure index.
Point	getPanelPos(int structure, int pos) Get the X position on the Panel of a particular sequence position.
int	getPreferredHeight() Y coordinate size
int	getPreferredWidth() X coordinate size
int	getSeqPos(int aligSeq, Point p) Convert from an X position in the JPanel to the position in the sequence alignment.
int	getSummaryPos()

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_RIGHT_SPACER

public static final int DEFAULT_RIGHT_SPACER

Space on the right side between sequence and legend.

See Also:

Constant Field Values

DEFAULT_LINE_LENGTH

public static final int DEFAULT_LINE_LENGTH

Number of chars per line

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Constant Field Values

DEFAULT_Y_STEP

public final int DEFAULT_Y_STEP

Size of space between rows. Depends on the number of structures aligned.

DEFAULT_CHAR_SIZE

public static final int DEFAULT_CHAR_SIZE

Size per character

See Also:

Constant Field Values

DEFAULT_LINE_SEPARATION

public static final int DEFAULT_LINE_SEPARATION

Separation between sequences in the alignment

See Also:

Constant Field Values

DEFAULT_X_SPACE

public static final int DEFAULT_X_SPACE

Left boundary

See Also:

Constant Field Values

DEFAULT_Y_SPACE

public static final int DEFAULT_Y_SPACE

Top boundary

See Also:

Constant Field Values

SUMMARY_POS

public static final int SUMMARY_POS

Position at which the alignment summary is printed

See Also:

Constant Field Values

Constructor Detail

MultipleAlignmentCoordManager

public MultipleAlignmentCoordManager(int size,
                                     int length)

Constructor.

Parameters:

size - number of structures/sequences aligned (rows).

length - number of aligned residues (columns)

Method Detail

getSummaryPos

public int getSummaryPos()

getPreferredWidth

public int getPreferredWidth()

X coordinate size

Returns:

the preferred width

getPreferredHeight

public int getPreferredHeight()

Y coordinate size

Returns:

the preferred height

getSeqPos

public int getSeqPos(int aligSeq,
                     Point p)

Convert from an X position in the JPanel to the position in the sequence alignment.

Parameters:

aligSeq - sequence number

p - point on panel

Returns:

the sequence position for a point on the Panel

getPanelPos

public Point getPanelPos(int structure,
                         int pos)

Get the X position on the Panel of a particular sequence position.

Parameters:

structure - index of the structure for the sequence position.

pos - sequence position, the aligned position index

Returns:

the point on a panel for a sequence position

getAligSeq

public int getAligSeq(Point point)

Returns the index of the structure, for a given point in the Panel. Returns -1 if not over a position in the sequence alignment.

Parameters:

point - x and y coordinates in the panel

Returns:

which structure a point on the panel corresponds to

getLegendPosition

public Point getLegendPosition(int lineNr,
                               int structure)

Provide the coordinates for where to draw the legend for line X given the structure index.

Parameters:

lineNr - line of the Panel

structure - the structure index

Returns:

get the point where to draw the legend

getEndLegendPosition

public Point getEndLegendPosition(int lineNr,
                                  int structure)