Interface SymbolList
- All Superinterfaces:
Changeable
- All Known Subinterfaces:
Alignment
,ARAlignment
,GappedSequence
,GappedSymbolList
,RichSequence
,Sequence
,StatePath
,UnequalLengthAlignment
- All Known Implementing Classes:
AbstractSymbolList
,AbstractULAlignment
,AbstractULAlignment.SubULAlignment
,AlignmentPair
,AssembledSymbolList
,ChunkedSymbolList
,CircularView
,DummySequence
,DummySymbolList
,FlexibleAlignment
,InfinitelyAmbiguousSymbolList
,NewAssembledSymbolList
,NewSimpleAssembly
,PackedSymbolList
,PhredSequence
,RelabeledAlignment
,RevCompSequence
,SimilarityPairFeature.EmptyPairwiseAlignment
,SimpleAlignment
,SimpleAssembly
,SimpleGappedSequence
,SimpleGappedSymbolList
,SimpleRichSequence
,SimpleSequence
,SimpleStatePath
,SimpleSymbolList
,SubSequence
,ThinRichSequence
,ViewSequence
This uses biological coordinates (1 to length).
- Author:
- Matthew Pocock, Mark Schreiber, Francois Pepin
-
Field Summary
FieldsModifier and TypeFieldDescriptionstatic final ChangeType
Signals that the SymbolList is being edited.static final SymbolList
A useful object that represents an empty symbol list, to avoid returning null. -
Method Summary
Modifier and TypeMethodDescriptionvoid
Apply an edit to the SymbolList as specified by the edit object.The alphabet that this SymbolList is over.iterator()
An Iterator over all Symbols in this SymbolList.int
length()
The number of symbols in this SymbolList.Stringify this symbol list.subList
(int start, int end) Return a new SymbolList for the symbols start to end inclusive.subStr
(int start, int end) Return a region of this symbol list as a String.symbolAt
(int index) Return the symbol at index, counting from 1.toList()
Returns a List of symbols.Methods inherited from interface org.biojava.utils.Changeable
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener
-
Field Details
-
EDIT
Signals that the SymbolList is being edited. The getChange field of the event should contain the SymbolList.Edit object describing the change. -
EMPTY_LIST
A useful object that represents an empty symbol list, to avoid returning null.
-
-
Method Details
-
getAlphabet
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.- Returns:
- the alphabet
-
length
int length()The number of symbols in this SymbolList.- Returns:
- the length
-
symbolAt
Return the symbol at index, counting from 1.- Parameters:
index
- the offset into this SymbolList- Returns:
- the Symbol at that index
- Throws:
IndexOutOfBoundsException
- if index is less than 1, or greater than the length of the symbol list
-
toList
Returns a List of symbols.This is an immutable list of symbols. Do not edit it.
- Returns:
- a List of Symbols
-
iterator
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.
- Returns:
- an iterator
-
subList
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.
- Parameters:
start
- the first symbol of the new SymbolListend
- the last symbol (inclusive) of the new SymbolList- Throws:
IndexOutOfBoundsException
-
seqString
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.
- Returns:
- a string representation of the symbol list
-
subStr
Return a region of this symbol list as a String.This should use the same rules as seqString.
- Parameters:
start
- the first symbol to includeend
- the last symbol to include- Returns:
- the string representation
- Throws:
IndexOutOfBoundsException
- if either start or end are not within the SymbolList
-
edit
void edit(Edit edit) throws IndexOutOfBoundsException, IllegalAlphabetException, ChangeVetoException 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());
- Parameters:
edit
- the Edit to perform- Throws:
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 vetoed
-