org.biojava.bio.seq.homol

Class SimilarityPairFeature.EmptyPairwiseAlignment

java.lang.Object

org.biojava.utils.Unchangeable

org.biojava.bio.seq.homol.SimilarityPairFeature.EmptyPairwiseAlignment

All Implemented Interfaces:

Alignment, SymbolList, Changeable

Enclosing interface:

SimilarityPairFeature

public static final class SimilarityPairFeature.EmptyPairwiseAlignment
extends Unchangeable
implements Alignment

EmptyPairwiseAlignment empty pairwise alignment which has labels to empty symbol lists.

Nested Class Summary

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

Method Summary

Methods

Modifier and Type	Method and Description
void	edit(Edit edit) Apply an edit to the SymbolList as specified by the edit object.
Alphabet	getAlphabet() The alphabet that this SymbolList is over.
java.util.List	getLabels() The list of SymbolLists in the alignment.
java.util.Iterator	iterator() An Iterator over all Symbols in this SymbolList.
int	length() The number of symbols in this SymbolList.
java.lang.String	seqString() Stringify this symbol list.
Alignment	subAlignment(java.util.Set labels, Location loc) Make a view onto this alignment.
SymbolList	subList(int index1, int index2) Return a new SymbolList for the symbols start to end inclusive.
java.lang.String	subStr(int index1, int index2) Return a region of this symbol list as a String.
Symbol	symbolAt(int index) Return the symbol at index, counting from 1.
Symbol	symbolAt(java.lang.Object label, int index) 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.
java.util.List	toList() Returns a List of symbols.

Methods inherited from class org.biojava.utils.Unchangeable

addChangeListener, addChangeListener, addForwarder, getForwarders, getListeners, isUnchanging, removeChangeListener, removeChangeListener, removeForwarder

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Method Detail

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 index)
                throws java.util.NoSuchElementException

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

index - the index of the column to retrieve

Returns:

the symbol in the symbol list associated with the label at the given column

Throws:

java.util.NoSuchElementException - if there is no row for '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'

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

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

iterator

public java.util.Iterator iterator()

Description copied from interface: SymbolList

An Iterator over all Symbols in this SymbolList.

This is an ordered iterator over the Symbols. It cannot be used to edit the underlying symbols.

Specified by:

iterator in interface SymbolList

Returns:

an iterator

subList

public SymbolList subList(int index1,
                 int index2)
                   throws java.lang.IndexOutOfBoundsException

Description copied from interface: SymbolList

Return a new SymbolList for the symbols start to end inclusive.

The resulting SymbolList will count from 1 to (end-start + 1) inclusive, and refer to the symbols start to end of the original sequence.

Specified by:

subList in interface SymbolList

Parameters:

index1 - the first symbol of the new SymbolList

index2 - the last symbol (inclusive) of the new SymbolList

Throws:

java.lang.IndexOutOfBoundsException

symbolAt

public Symbol symbolAt(int index)
                throws java.lang.IndexOutOfBoundsException

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

Throws:

java.lang.IndexOutOfBoundsException - if index is less than 1, or greater than the length of the symbol list

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

toList

public java.util.List toList()

Description copied from interface: SymbolList

Returns a List of symbols.

This is an immutable list of symbols. Do not edit it.

Specified by:

toList in interface SymbolList

Returns:

a List of Symbols

seqString

public java.lang.String seqString()

Description copied from interface: SymbolList

Stringify this symbol list.

It is expected that this will use the symbol's token to render each symbol. It should be parsable back into a SymbolList using the default token parser for this alphabet.

Specified by:

seqString in interface SymbolList

Returns:

a string representation of the symbol list

subStr

public java.lang.String subStr(int index1,
                      int index2)
                        throws java.lang.IndexOutOfBoundsException

Description copied from interface: SymbolList

Return a region of this symbol list as a String.

This should use the same rules as seqString.

Specified by:

subStr in interface SymbolList

Parameters:

index1 - the first symbol to include

index2 - the last symbol to include

Returns:

the string representation

Throws:

java.lang.IndexOutOfBoundsException - if either start or end are not within the SymbolList

edit

public void edit(Edit edit)
          throws java.lang.IndexOutOfBoundsException,
                 IllegalAlphabetException,
                 ChangeVetoException

Description copied from interface: SymbolList

Apply an edit to the SymbolList as specified by the edit object.

Description

All edits can be broken down into a series of operations that change contiguous blocks of the sequence. This represent a one of those operations.

When applied, this Edit will replace 'length' number of symbols starting a position 'pos' by the SymbolList 'replacement'. This allow to do insertions (length=0), deletions (replacement=SymbolList.EMPTY_LIST) and replacements (length>=1 and replacement.length()>=1).

The pos and pos+length should always be valid positions on the SymbolList to:

• be edited (between 0 and symL.length()+1).
• To append to a sequence, pos=symL.length()+1, pos=0.
• To insert something at the beginning of the sequence, set pos=1 and length=0.

Examples

 SymbolList seq = DNATools.createDNA("atcaaaaacgctagc");
 System.out.println(seq.seqString());

 // delete 5 bases from position 4
 Edit ed = new Edit(4, 5, SymbolList.EMPTY_LIST);
 seq.edit(ed);
 System.out.println(seq.seqString());

 // delete one base from the start
 ed = new Edit(1, 1, SymbolList.EMPTY_LIST);
 seq.edit(ed);

 // delete one base from the end
 ed = new Edit(seq.length(), 1, SymbolList.EMPTY_LIST);
 seq.edit(ed);
 System.out.println(seq.seqString());

 // overwrite 2 bases from position 3 with "tt"
 ed = new Edit(3, 2, DNATools.createDNA("tt"));
 seq.edit(ed);
 System.out.println(seq.seqString());

 // add 6 bases to the start
 ed = new Edit(1, 0, DNATools.createDNA("aattgg");
 seq.edit(ed);
 System.out.println(seq.seqString());

 // add 4 bases to the end
 ed = new Edit(seq.length() + 1, 0, DNATools.createDNA("tttt"));
 seq.edit(ed);
 System.out.println(seq.seqString());

 // full edit
 ed = new Edit(3, 2, DNATools.createDNA("aatagaa");
 seq.edit(ed);
 System.out.println(seq.seqString());
 

Specified by:

edit in interface SymbolList

Parameters:

edit - the Edit to perform

Throws:

java.lang.IndexOutOfBoundsException - if the edit does not lie within the SymbolList

IllegalAlphabetException - if the SymbolList to insert has an incompatible alphabet

ChangeVetoException - if either the SymboList does not support the edit, or if the change was vetoed

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