charite.christo.strap
Class DrawGappedSequence
java.lang.Object
charite.christo.strap.DrawGappedSequence
public class DrawGappedSequence
- extends java.lang.Object
A gapped sequence with colorshading is drawn.
Not used for the main alignment view in Strap.
It is used for the Dialoges DialogAlign
and DialogAlignOneToAll
.
Method Summary |
void |
draw(java.awt.Component component,
java.awt.Graphics gAwt,
java.awt.Point origin,
int idxOfFirstAA,
byte[] seq,
int fromCol,
int toCol,
Protein p,
java.awt.Color[] shadeAminos,
long mode)
|
void |
draw(java.awt.Component component,
java.awt.Graphics g,
java.awt.Point origin,
Protein p,
java.awt.Color[] shadeAminos,
long mode)
Draws a gapped sequence into the graphics context. |
void |
drawBlastMidline(byte[] b1,
byte[] b2,
int colFrom,
int colTo,
byte[][] matrix,
java.awt.Graphics g,
int x0,
int y0)
|
static DrawGappedSequence |
instance()
|
void |
setConservation(short[][] frequenciesOfAminos,
int minFrequency)
|
Methods inherited from class java.lang.Object |
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
SHADE_SEC_STRU
public static final int SHADE_SEC_STRU
- See Also:
- Constant Field Values
AA2NT
public static final int AA2NT
- See Also:
- Constant Field Values
NUCLEOTIDES
public static final int NUCLEOTIDES
- See Also:
- Constant Field Values
DrawGappedSequence
public DrawGappedSequence()
instance
public static DrawGappedSequence instance()
draw
public void draw(java.awt.Component component,
java.awt.Graphics g,
java.awt.Point origin,
Protein p,
java.awt.Color[] shadeAminos,
long mode)
- Draws a gapped sequence into the graphics context.
- Parameters:
component
- any component and is used for the management of images of
selections (ImageObserver). May be null.origin
- point where to start to draw,shadeAminos
- An array of Color of length 256. E.g. Alanin will be
drawn in the color shadeAminos['A'], May be null.
draw
public void draw(java.awt.Component component,
java.awt.Graphics gAwt,
java.awt.Point origin,
int idxOfFirstAA,
byte[] seq,
int fromCol,
int toCol,
Protein p,
java.awt.Color[] shadeAminos,
long mode)
setConservation
public void setConservation(short[][] frequenciesOfAminos,
int minFrequency)
drawBlastMidline
public void drawBlastMidline(byte[] b1,
byte[] b2,
int colFrom,
int colTo,
byte[][] matrix,
java.awt.Graphics g,
int x0,
int y0)
'The most important classes are StrapAlign, Protein and StrapEvent.'