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A sequence of symbols that belong to an alphabet.
This uses biological coordinates (1 to length).
Nested Class Summary | |
static class |
SymbolList.EmptySymbolList
The empty immutable implementation. |
Field Summary | |
static ChangeType |
EDIT
Signals that the SymbolList is being edited. |
static SymbolList |
EMPTY_LIST
A useful object that represents an empty symbol list, to avoid returning null. |
Method Summary | |
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.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. |
SymbolList |
subList(int start,
int end)
Return a new SymbolList for the symbols start to end inclusive. |
java.lang.String |
subStr(int start,
int end)
Return a region of this symbol list as a String. |
Symbol |
symbolAt(int index)
Return the symbol at index, counting from 1. |
java.util.List |
toList()
Returns a List of symbols. |
Methods inherited from interface org.biojava.utils.Changeable |
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener |
Field Detail |
public static final ChangeType EDIT
public static final SymbolList EMPTY_LIST
Method Detail |
public Alphabet getAlphabet()
Every symbol within this SymbolList is a member of this alphabet.
alphabet.contains(symbol) == true
for each symbol that is within this sequence.
public int length()
public Symbol symbolAt(int index) throws java.lang.IndexOutOfBoundsException
index
- the offset into this SymbolList
java.lang.IndexOutOfBoundsException
- if index is less than 1, or greater than
the length of the symbol listpublic java.util.List toList()
This is an immutable list of symbols. Do not edit it.
public java.util.Iterator iterator()
This is an ordered iterator over the Symbols. It cannot be used to edit the underlying symbols.
public SymbolList subList(int start, int end) throws java.lang.IndexOutOfBoundsException
The resulting SymbolList will count from 1 to (end-start + 1) inclusive, and refer to the symbols start to end of the original sequence.
start
- the first symbol of the new SymbolListend
- the last symbol (inclusive) of the new SymbolList
java.lang.IndexOutOfBoundsException
public java.lang.String seqString()
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.
public java.lang.String subStr(int start, int end) throws java.lang.IndexOutOfBoundsException
This should use the same rules as seqString.
start
- the first symbol to includeend
- the last symbol to include
java.lang.IndexOutOfBoundsException
- if either start or end are not within the
SymbolListpublic void edit(Edit edit) throws java.lang.IndexOutOfBoundsException, IllegalAlphabetException, ChangeVetoException
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
- the Edit to perform
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
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