public class MultipleAlignmentCoordManager
extends java.lang.Object
Modifier and Type | Field | 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 | Description |
---|---|
MultipleAlignmentCoordManager(int size,
int length) |
Constructor.
|
Modifier and Type | Method | Description |
---|---|---|
int |
getAligSeq(java.awt.Point point) |
Returns the index of the structure, for a given point in the Panel.
|
java.awt.Point |
getEndLegendPosition(int lineNr,
int structure) |
|
java.awt.Point |
getLegendPosition(int lineNr,
int structure) |
Provide the coordinates for where to draw the legend for
line X given the structure index.
|
java.awt.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,
java.awt.Point p) |
Convert from an X position in the JPanel to the position
in the sequence alignment.
|
int |
getSummaryPos() |
public static final int DEFAULT_RIGHT_SPACER
public static final int DEFAULT_LINE_LENGTH
public final int DEFAULT_Y_STEP
public static final int DEFAULT_CHAR_SIZE
public static final int DEFAULT_LINE_SEPARATION
public static final int DEFAULT_X_SPACE
public static final int DEFAULT_Y_SPACE
public static final int SUMMARY_POS
public MultipleAlignmentCoordManager(int size, int length)
size
- number of structures/sequences aligned (rows).length
- number of aligned residues (columns)public int getSummaryPos()
public int getPreferredWidth()
public int getPreferredHeight()
public int getSeqPos(int aligSeq, java.awt.Point p)
aligSeq
- sequence numberp
- point on panelpublic java.awt.Point getPanelPos(int structure, int pos)
structure
- index of the structure for the sequence position.pos
- sequence position, the aligned position indexpublic int getAligSeq(java.awt.Point point)
point
- x and y coordinates in the panelpublic java.awt.Point getLegendPosition(int lineNr, int structure)
lineNr
- line of the Panelstructure
- the structure indexpublic java.awt.Point getEndLegendPosition(int lineNr, int structure)