'STRAP:multiple sequence alignments '

charite.christo.strap
Class DrawGappedSequence

java.lang.Object
  extended by 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.


Field Summary
static int AA2NT
           
static int NUCLEOTIDES
           
static int SHADE_SEC_STRU
           
 
Constructor Summary
DrawGappedSequence()
           
 
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
 

Field Detail

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
Constructor Detail

DrawGappedSequence

public DrawGappedSequence()
Method Detail

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)

'STRAP:multiple sequence alignments '

'The most important classes are StrapAlign, Protein and StrapEvent.'