Class ChunkedSymbolList
- All Implemented Interfaces:
Serializable
,SymbolList
,Changeable
- Author:
- David Huen, Matthew Pocock, George Waldon
- See Also:
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Nested Class Summary
Nested classes/interfaces inherited from class org.biojava.bio.symbol.AbstractSymbolList
AbstractSymbolList.EditScreener, AbstractSymbolList.EditTranslater
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Field Summary
Fields inherited from interface org.biojava.bio.symbol.SymbolList
EDIT, EMPTY_LIST
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Constructor Summary
ConstructorsConstructorDescriptionChunkedSymbolList
(SymbolList[] chunks, int chunkSize, int length, Alphabet alpha) -
Method Summary
Modifier and TypeMethodDescriptionvoid
Apply an edit to the SymbolList as specified by the edit object.protected void
finalize()
The alphabet that this SymbolList is over.int
length()
The number of symbols in this SymbolList.subList
(int start, int end) Return a new SymbolList for the symbols start to end inclusive.symbolAt
(int pos) Return the symbol at index, counting from 1.Methods inherited from class org.biojava.bio.symbol.AbstractSymbolList
equals, hashCode, iterator, seqString, subStr, toList, toString
Methods inherited from class org.biojava.utils.AbstractChangeable
addChangeListener, addChangeListener, generateChangeSupport, getChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListener
Methods inherited from interface org.biojava.utils.Changeable
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener
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Constructor Details
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ChunkedSymbolList
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Method Details
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finalize
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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 interfaceSymbolList
- Returns:
- the alphabet
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length
Description copied from interface:SymbolList
The number of symbols in this SymbolList.- Specified by:
length
in interfaceSymbolList
- Returns:
- the length
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symbolAt
Description copied from interface:SymbolList
Return the symbol at index, counting from 1.- Specified by:
symbolAt
in interfaceSymbolList
- Parameters:
pos
- the offset into this SymbolList- Returns:
- the Symbol at that index
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subList
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 interfaceSymbolList
- Overrides:
subList
in classAbstractSymbolList
- Parameters:
start
- the first symbol of the new SymbolListend
- the last symbol (inclusive) of the new SymbolList
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edit
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 interfaceSymbolList
- Overrides:
edit
in classAbstractSymbolList
- Parameters:
edit
- the Edit to perform- Throws:
IllegalAlphabetException
- if the SymbolList to insert has an incompatible alphabetChangeVetoException
- if either the SymboList does not support the edit, or if the change was vetoed
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