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

Class AFPChainCoordManager

java.lang.Object

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

public class AFPChainCoordManager
extends Object

Field Summary

Fields

Modifier and Type	Field	Description
static final int	DEFAULT_CHAR_SIZE	size per character
static final int	DEFAULT_LINE_LENGTH	number of chars per line
static final int	DEFAULT_LINE_SEPARATION	separation of line 1 and 2 in alignment
static final int	DEFAULT_RIGHT_SPACER	Space on the right side between sequence and legend.
static final int	DEFAULT_X_SPACE	left boundary
static final int	DEFAULT_Y_SPACE	top boundary
static final int	DEFAULT_Y_STEP	size of space between rows
static final int	SUMMARY_POS	Position at which the alignment summary is printed

Constructor Summary

Constructors

Constructor	Description
AFPChainCoordManager()

Method Summary

Modifier and Type	Method	Description
int	getAligSeq(Point point)	returns the AligSeq (0 or 1) for a point returns -1 if not over an alig seq.
Point	getEndLegendPosition(int lineNr, int chainNr)
Point	getLegendPosition(int lineNr, int chainNr)	provide the coordinates for where to draw the legend for line X and if it is chain 1 or 2
Point	getPanelPos(int aligSeq, int i)	get the position of the sequence position on the Panel
int	getPreferredHeight()	Y coordinate size
int	getPreferredWidth()	X coordinate size
int	getSeqPos(int aligSeq, Point p)	Convert from a X position in the JPanel to alignment position
int	getSummaryPos()
void	setAFPChain(AFPChain afpChain)

Methods inherited from class java.lang.Object

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

Field Details

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

See Also:

• Constant Field Values

DEFAULT_Y_STEP

public static final int DEFAULT_Y_STEP

size of space between rows

See Also:

• Constant Field Values

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 of line 1 and 2 in 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 Details

AFPChainCoordManager

public AFPChainCoordManager()

Method Details

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 a X position in the JPanel to alignment position

Parameters:

aligSeq - sequence 0 or 1

p - point on panel

Returns:

the sequence position for a point on the Panel

getPanelPos

public Point getPanelPos(int aligSeq,
 int i)

get the position of the sequence position on the Panel

Parameters:

aligSeq - 0 or 1 for which of the two sequences to ask for.

i - sequence position

Returns:

the point on a panel for a sequence position

setAFPChain

public void setAFPChain(AFPChain afpChain)

getAligSeq

public int getAligSeq(Point point)

returns the AligSeq (0 or 1) for a point returns -1 if not over an alig seq.

Parameters:

point -

Returns:

which of the two sequences a point on the panel corresponds to

getLegendPosition

public Point getLegendPosition(int lineNr,
 int chainNr)

provide the coordinates for where to draw the legend for line X and if it is chain 1 or 2

Parameters:

lineNr - which line is this for

chainNr - is it chain 0 or 1

Returns:

get the point where to draw the legend

getEndLegendPosition

public Point getEndLegendPosition(int lineNr,
 int chainNr)