uk.ac.man.bioinf.sequence.alignment
Class AlignmentColumn
java.lang.Object
|
+--uk.ac.man.bioinf.sequence.alignment.AlignmentColumn
- public class AlignmentColumn
- extends Object
AlignmentColumn.java
The Sequence and SequenceAlignment classes have been created to be fail-fast. They
throw exceptions if attempts are made to access and element outside
of the range of the sequence. Additionally the alignment allows
sequences to start at any place within the alignment which is very
nice, but has the disadvantage of being a little fiddly to use in some
circumstances. This class addresses this problem. Essentially it is
a mask over a sequence alignment. It can be moved to any column of
the alignment, and will then return the elements down that
column. It takes care of the offsets, and returns a simple gap
Element if a request is made for an Element from before a sequence
starts or after a sequence finishes, so long as the row > 0 and <
alignment.getLength().
Created: Wed Jun 7 14:23:43 2000
- Version:
- $Id: AlignmentColumn.java,v 1.3 2001/04/11 17:04:43 lord Exp $
- Author:
- Phillip Lord
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
AlignmentColumn
public AlignmentColumn()
AlignmentColumn
public AlignmentColumn(SequenceAlignment alignment)
setAlignment
public void setAlignment(SequenceAlignment alignment)
getAlignment
public SequenceAlignment getAlignment()
setColumn
public void setColumn(int column)
getColumn
public int getColumn()
getElementAtRow
public Element getElementAtRow(int row)
throws NoSuchSequenceException,
IllegalStateException
- Get the element for this column at the given row. This will
return a Gap element if in front or after the sequence.
- Parameters:
row
- the row
- Returns:
- the element
- Throws:
NoSuchSequenceException
- if row < 1 or row > getNumberSequences()
IllegalStateException
- if the alignment has not been set