public static final class SimilarityPairFeature.EmptyPairwiseAlignment extends Unchangeable implements Alignment
EmptyPairwiseAlignment
empty pairwise alignment
which has labels to empty symbol lists.Alignment.SymbolListIterator
EDIT, EMPTY_LIST
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.
|
addChangeListener, addChangeListener, addForwarder, getForwarders, getListeners, isUnchanging, removeChangeListener, removeChangeListener, removeForwarder
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener
public java.util.List getLabels()
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.
public Symbol symbolAt(java.lang.Object label, int index) throws java.util.NoSuchElementException
Alignment
symbolAt
in interface Alignment
label
- the SymbolList to retrieve fromindex
- the index of the column to retrievejava.util.NoSuchElementException
- if there is no row for 'label'public SymbolList symbolListForLabel(java.lang.Object label) throws java.util.NoSuchElementException
Alignment
symbolListForLabel
in interface Alignment
label
- the object from which to retrieve the symbol listjava.util.NoSuchElementException
- if there is no row for 'label'public Alignment subAlignment(java.util.Set labels, Location loc) throws java.util.NoSuchElementException
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.
subAlignment
in interface Alignment
labels
- the Set of sequences to include by labelloc
- the Location to includejava.util.NoSuchElementException
- if labels contains any item that is not a labelpublic int length()
SymbolList
length
in interface SymbolList
public java.util.Iterator iterator()
SymbolList
This is an ordered iterator over the Symbols. It cannot be used to edit the underlying symbols.
iterator
in interface SymbolList
public SymbolList subList(int index1, int index2) throws java.lang.IndexOutOfBoundsException
SymbolList
The resulting SymbolList will count from 1 to (end-start + 1) inclusive, and refer to the symbols start to end of the original sequence.
subList
in interface SymbolList
index1
- the first symbol of the new SymbolListindex2
- the last symbol (inclusive) of the new SymbolListjava.lang.IndexOutOfBoundsException
public Symbol symbolAt(int index) throws java.lang.IndexOutOfBoundsException
SymbolList
symbolAt
in interface SymbolList
index
- the offset into this SymbolListjava.lang.IndexOutOfBoundsException
- if index is less than 1, or greater than
the length of the symbol listpublic Alphabet getAlphabet()
SymbolList
Every symbol within this SymbolList is a member of this alphabet.
alphabet.contains(symbol) == true
for each symbol that is within this sequence.
getAlphabet
in interface SymbolList
public java.util.List toList()
SymbolList
This is an immutable list of symbols. Do not edit it.
toList
in interface SymbolList
public java.lang.String seqString()
SymbolList
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.
seqString
in interface SymbolList
public java.lang.String subStr(int index1, int index2) throws java.lang.IndexOutOfBoundsException
SymbolList
This should use the same rules as seqString.
subStr
in interface SymbolList
index1
- the first symbol to includeindex2
- the last symbol to includejava.lang.IndexOutOfBoundsException
- if either start or end are not within the
SymbolListpublic void edit(Edit edit) throws java.lang.IndexOutOfBoundsException, IllegalAlphabetException, ChangeVetoException
SymbolList
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:
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());
edit
in interface SymbolList
edit
- the Edit to performjava.lang.IndexOutOfBoundsException
- if the edit does not lie within the
SymbolListIllegalAlphabetException
- if the SymbolList to insert has an
incompatible alphabetChangeVetoException
- if either the SymboList does not support the
edit, or if the change was vetoedpublic java.util.Iterator symbolListIterator()
Alignment
symbolListIterator
in interface Alignment