org.biojava.bio.symbol
Class SimpleAlignment

java.lang.Object
  extended by org.biojava.utils.AbstractChangeable
      extended by org.biojava.bio.symbol.AbstractSymbolList
          extended by org.biojava.bio.symbol.SimpleAlignment
All Implemented Interfaces:
java.io.Serializable, Alignment, SymbolList, Changeable

public class SimpleAlignment
extends AbstractSymbolList
implements Alignment, java.io.Serializable

A simple implementation of an Alignment.

This is a simple-stupid implementation that is made from a set of same-lengthed SymbolList objects each with an associated label. It does not handle differently lengthed sequences and doesn't contain any gap-editing concepts.

Author:
Matthew Pocock, Greg Cox, Nimesh Singh
See Also:
Serialized Form

Nested Class Summary
 
Nested classes/interfaces inherited from class org.biojava.bio.symbol.AbstractSymbolList
AbstractSymbolList.EditScreener, AbstractSymbolList.EditTranslater
 
Nested classes/interfaces inherited from interface org.biojava.bio.symbol.Alignment
Alignment.SymbolListIterator
 
Field Summary
 
Fields inherited from interface org.biojava.bio.symbol.Alignment
CONTENT
 
Fields inherited from interface org.biojava.bio.symbol.SymbolList
EDIT, EMPTY_LIST
 
Constructor Summary
SimpleAlignment(java.util.Map labelToResList)
          Generate an alignment from a list of SymbolLists.
 
Method Summary
protected  void finalize()
           
 Alphabet getAlphabet()
          The alphabet that this SymbolList is over.
 java.util.List getLabels()
           The list of SymbolLists in the alignment.
 int length()
          The number of symbols in this SymbolList.
 Alignment subAlignment(java.util.Set labels, Location loc)
           Make a view onto this alignment.
 Symbol symbolAt(int index)
          Return the symbol at index, counting from 1.
 Symbol symbolAt(java.lang.Object label, int column)
          Retrieve a symbol by label and column.
 SymbolList symbolListForLabel(java.lang.Object label)
          Retrieve a single row of the alignment by label.
 java.util.Iterator symbolListIterator()
          Creates an Iterator over the SymbolLists in the alignment.
 
Methods inherited from class org.biojava.bio.symbol.AbstractSymbolList
edit, equals, hashCode, iterator, seqString, subList, subStr, toList, toString
 
Methods inherited from class org.biojava.utils.AbstractChangeable
addChangeListener, addChangeListener, generateChangeSupport, getChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListener
 
Methods inherited from class java.lang.Object
clone, getClass, notify, notifyAll, wait, wait, wait
 
Methods inherited from interface org.biojava.bio.symbol.SymbolList
edit, iterator, seqString, subList, subStr, toList
 
Methods inherited from interface org.biojava.utils.Changeable
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener
 

Constructor Detail

SimpleAlignment

public SimpleAlignment(java.util.Map labelToResList)
                throws java.lang.IllegalArgumentException
Generate an alignment from a list of SymbolLists.

The SymbolLists must all be of the same length.

Parameters:
labelToResList - the label-to-symbol list mapping
Throws:
java.lang.IllegalArgumentException - if the SymbolLists are not the same length
Method Detail

finalize

protected void finalize()
                 throws java.lang.Throwable
Overrides:
finalize in class java.lang.Object
Throws:
java.lang.Throwable

length

public int length()
Description copied from interface: SymbolList
The number of symbols in this SymbolList.

Specified by:
length in interface SymbolList
Returns:
the length

getAlphabet

public Alphabet getAlphabet()
Description copied from interface: SymbolList
The alphabet that this SymbolList is over.

Every symbol within this SymbolList is a member of this alphabet. alphabet.contains(symbol) == true for each symbol that is within this sequence.

Specified by:
getAlphabet in interface SymbolList
Returns:
the alphabet

symbolAt

public Symbol symbolAt(int index)
Description copied from interface: SymbolList
Return the symbol at index, counting from 1.

Specified by:
symbolAt in interface SymbolList
Parameters:
index - the offset into this SymbolList
Returns:
the Symbol at that index

getLabels

public java.util.List getLabels()
Description copied from interface: Alignment

The list of SymbolLists in the alignment.

The index in the list is the same as the index in the alignment. Each SymbolList object will only be in the alignment once. However, a single underlying SymbolList may have more than one view within an alignment, each represented by a different GappedSymbolList.

Specified by:
getLabels in interface Alignment
Returns:
the List of all SymbolLists in the alignment

symbolAt

public Symbol symbolAt(java.lang.Object label,
                       int column)
Description copied from interface: Alignment
Retrieve a symbol by label and column.

Specified by:
symbolAt in interface Alignment
Parameters:
label - the SymbolList to retrieve from
column - the index of the column to retrieve
Returns:
the symbol in the symbol list associated with the label at the given column

subAlignment

public Alignment subAlignment(java.util.Set labels,
                              Location loc)
                       throws java.util.NoSuchElementException
Description copied from interface: Alignment

Make a view onto this alignment.

If labels is null, then each label will be kept. Otherwise, only those in labels will be kept. If loc is null, then the entire length of the alignment will be kept. If loc is not null, then only the columns within the location will be kept.

Specified by:
subAlignment in interface Alignment
Parameters:
labels - the Set of sequences to include by label
loc - the Location to include
Returns:
a sub Alignment
Throws:
java.util.NoSuchElementException - if labels contains any item that is not a label

symbolListForLabel

public SymbolList symbolListForLabel(java.lang.Object label)
                              throws java.util.NoSuchElementException
Description copied from interface: Alignment
Retrieve a single row of the alignment by label.

Specified by:
symbolListForLabel in interface Alignment
Parameters:
label - the object from which to retrieve the symbol list
Returns:
a SymbolList that contains each token in a row of the alignment
Throws:
java.util.NoSuchElementException - if there is no row for 'label'

symbolListIterator

public java.util.Iterator symbolListIterator()
Description copied from interface: Alignment
Creates an Iterator over the SymbolLists in the alignment. This should be similar to iterating over the labels and then fetching each SymbolList, but the order is not guaranteed to be the same.

Specified by:
symbolListIterator in interface Alignment
Returns:
an Iterator