JAligner

jaligner
Class Alignment

java.lang.Object
  extended byjaligner.Alignment

public final class Alignment
extends java.lang.Object

Holds the output of a pairwise sequences alignment.

Author:
Ahmed Moustafa (ahmed@users.sf.net)

Field Summary
static char GAP
          Gap character
 
Constructor Summary
Alignment()
          Constructor for Alignment
 
Method Summary
 float calculateScore()
          Calculate the score of the alignment, not using the score field (the function only uses sequence1, sequence2, matrix and gap penalties).
 boolean checkScore()
          Check if the calculated score matches the field score.
 float getExtend()
           
 int getGaps()
           
 int getIdentity()
           
 char[] getMarkupLine()
           
 Matrix getMatrix()
           
 java.lang.String getName1()
           
 java.lang.String getName2()
           
 float getOpen()
           
 Sequence getOriginalSequence1()
          Returns original Sequence #1
 Sequence getOriginalSequence2()
          Returns original Sequence #2
 float getScore()
           
 char[] getSequence1()
           
 char[] getSequence2()
           
 int getSimilarity()
           
 int getStart1()
           
 int getStart2()
           
 java.lang.String getSummary()
          Returns a summary for alignment
 void setExtend(float extend)
           
 void setGaps(int gaps)
           
 void setIdentity(int identity)
           
 void setMarkupLine(char[] markupLine)
           
 void setMatrix(Matrix matrix)
           
 void setName1(java.lang.String name1)
           
 void setName2(java.lang.String name2)
           
 void setOpen(float open)
           
 void setOriginalSequence1(Sequence originalSequence1)
           
 void setOriginalSequence2(Sequence originalSequence2)
           
 void setScore(float score)
           
 void setSequence1(char[] sequence1)
           
 void setSequence2(char[] sequence2)
           
 void setSimilarity(int similarity)
           
 void setStart1(int start1)
           
 void setStart2(int start2)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

GAP

public static final char GAP
Gap character

See Also:
Constant Field Values
Constructor Detail

Alignment

public Alignment()
Constructor for Alignment

Method Detail

getExtend

public float getExtend()
Returns:
Returns the extend.

setExtend

public void setExtend(float extend)
Parameters:
extend - The extend to set.

getMatrix

public Matrix getMatrix()
Returns:
Returns the matrix.

setMatrix

public void setMatrix(Matrix matrix)
Parameters:
matrix - The matrix to set.

getName1

public java.lang.String getName1()
Returns:
Returns the name1.

setName1

public void setName1(java.lang.String name1)
Parameters:
name1 - The name1 to set.

getName2

public java.lang.String getName2()
Returns:
Returns the name2.

setName2

public void setName2(java.lang.String name2)
Parameters:
name2 - The name2 to set.

getOpen

public float getOpen()
Returns:
Returns the open.

setOpen

public void setOpen(float open)
Parameters:
open - The open to set.

getScore

public float getScore()
Returns:
Returns the score.

setScore

public void setScore(float score)
Parameters:
score - The score to set.

getSequence1

public char[] getSequence1()
Returns:
Returns the sequence1.

setSequence1

public void setSequence1(char[] sequence1)
Parameters:
sequence1 - The sequence1 to set.

getSequence2

public char[] getSequence2()
Returns:
Returns the sequence2.

setSequence2

public void setSequence2(char[] sequence2)
Parameters:
sequence2 - The sequence2 to set.

getStart1

public int getStart1()
Returns:
Returns the start1.

setStart1

public void setStart1(int start1)
Parameters:
start1 - The start1 to set.

getStart2

public int getStart2()
Returns:
Returns the start2.

setStart2

public void setStart2(int start2)
Parameters:
start2 - The start2 to set.

getGaps

public int getGaps()
Returns:
Returns the gaps.

setGaps

public void setGaps(int gaps)
Parameters:
gaps - The gaps to set.

getIdentity

public int getIdentity()
Returns:
Returns the identity.

setIdentity

public void setIdentity(int identity)
Parameters:
identity - The identity to set.

getMarkupLine

public char[] getMarkupLine()
Returns:
Returns the markupLine.

setMarkupLine

public void setMarkupLine(char[] markupLine)
Parameters:
markupLine - The markupLine to set.

getSimilarity

public int getSimilarity()
Returns:
Returns the similarity.

setSimilarity

public void setSimilarity(int similarity)
Parameters:
similarity - The similarity to set.

getSummary

public java.lang.String getSummary()
Returns a summary for alignment

Returns:
String alignment summary

calculateScore

public float calculateScore()
Calculate the score of the alignment, not using the score field (the function only uses sequence1, sequence2, matrix and gap penalties).

Returns:
the calculated score (By: Bram Minnaert)

checkScore

public boolean checkScore()
Check if the calculated score matches the field score.

Returns:
true if equal, else false. (By: Bram Minnaert)

getOriginalSequence1

public Sequence getOriginalSequence1()
Returns original Sequence #1

Returns:
original Sequence #1

setOriginalSequence1

public void setOriginalSequence1(Sequence originalSequence1)
Parameters:
originalSequence1 -

getOriginalSequence2

public Sequence getOriginalSequence2()
Returns original Sequence #2

Returns:
original Sequence #2

setOriginalSequence2

public void setOriginalSequence2(Sequence originalSequence2)
Parameters:
originalSequence2 -

JAligner

Ahmed Moustafa (ahmed@users.sf.net)SourceForge.net
The source code of JAligner is licensed under The GNU General Public License (GPL)