public class ChunkedSymbolList extends AbstractSymbolList implements Serializable
AbstractSymbolList.EditScreener, AbstractSymbolList.EditTranslater
EDIT, EMPTY_LIST
Constructor and Description |
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ChunkedSymbolList(SymbolList[] chunks,
int chunkSize,
int length,
Alphabet alpha) |
Modifier and Type | Method and Description |
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void |
edit(Edit edit)
Apply an edit to the SymbolList as specified by the edit object.
|
protected void |
finalize() |
Alphabet |
getAlphabet()
The alphabet that this SymbolList is over.
|
int |
length()
The number of symbols in this SymbolList.
|
SymbolList |
subList(int start,
int end)
Return a new SymbolList for the symbols start to end inclusive.
|
Symbol |
symbolAt(int pos)
Return the symbol at index, counting from 1.
|
equals, hashCode, iterator, seqString, subStr, toList, toString
addChangeListener, addChangeListener, generateChangeSupport, getChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListener
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener
public ChunkedSymbolList(SymbolList[] chunks, int chunkSize, int length, Alphabet alpha)
public 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 int length()
SymbolList
length
in interface SymbolList
public Symbol symbolAt(int pos)
SymbolList
symbolAt
in interface SymbolList
pos
- the offset into this SymbolListpublic SymbolList subList(int start, int end)
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
subList
in class AbstractSymbolList
start
- the first symbol of the new SymbolListend
- the last symbol (inclusive) of the new SymbolListpublic void edit(Edit edit) throws 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
in class AbstractSymbolList
edit
- the Edit to performIllegalAlphabetException
- if the SymbolList to insert has an
incompatible alphabetChangeVetoException
- if either the SymboList does not support the
edit, or if the change was vetoedCopyright © 2020 BioJava. All rights reserved.