model
Class AlignObject

java.lang.Object
  extended by model.AlignObject

public class AlignObject
extends java.lang.Object

This class does the representation of an alignment object.


Constructor Summary
AlignObject()
          Default constructor.
AlignObject(SequenceImpl[] sequences)
          Constructor for AlignObject with sequences as parameter.
 
Method Summary
 void clearGaps()
           
 java.lang.String getFilename()
          Returns the filename.an
 int getHeight()
          Returns the height of the alignment through the number of Sequences.
 int getProteinNumber()
          Returns the number of protein.
 SequenceImpl getSequenceAt(int i)
          Returns the sequence for a certain parameter index.
 SequenceImpl[] getSequences()
          Returns the array of sequence objects.
 int getWidth()
          Returns the width through the maximum of the longest sequence.
 void reloadOnlyAlignment(AlignFrame alignFrame)
           
 void setFilename(java.lang.String filename)
          Sets the filename.
 void setProteinNumber(int proteinNumber)
          Sets the number of protein.
 void setSequences(SequenceImpl[] sequences)
          Sets the array of sequence objects.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

AlignObject

public AlignObject()
Default constructor.


AlignObject

public AlignObject(SequenceImpl[] sequences)
Constructor for AlignObject with sequences as parameter.

Parameters:
sequences -
Method Detail

getHeight

public int getHeight()
Returns the height of the alignment through the number of Sequences.

Returns:
Integer

getWidth

public int getWidth()
Returns the width through the maximum of the longest sequence.

Returns:
Integer

getSequenceAt

public SequenceImpl getSequenceAt(int i)
Returns the sequence for a certain parameter index.

Parameters:
i -
Returns:
sequences SequenceImpl

getFilename

public java.lang.String getFilename()
Returns the filename.an

Returns:
String filename

setFilename

public void setFilename(java.lang.String filename)
Sets the filename.

Parameters:
filename -

getSequences

public SequenceImpl[] getSequences()
Returns the array of sequence objects.

Returns:
SequenceImpl[] sequences

setSequences

public void setSequences(SequenceImpl[] sequences)
Sets the array of sequence objects.

Parameters:
sequences -

getProteinNumber

public int getProteinNumber()
Returns the number of protein.

Returns:
Integer proteinNumber

setProteinNumber

public void setProteinNumber(int proteinNumber)
Sets the number of protein.

Parameters:
proteinNumber -

reloadOnlyAlignment

public void reloadOnlyAlignment(AlignFrame alignFrame)

clearGaps

public void clearGaps()