Package org.biojava.bio.seq.impl
Class AssembledSymbolList
java.lang.Object
org.biojava.utils.AbstractChangeable
org.biojava.bio.symbol.AbstractSymbolList
org.biojava.bio.seq.impl.AssembledSymbolList
- All Implemented Interfaces:
SymbolList
,Changeable
Support class for applications which need to patch together sections
of sequence into a single SymbolList. This class isn't intended
for direct use in user code -- instead, it is a helper for people
implementing the full BioJava assembly model. See SimpleAssembly
for an example.
- Since:
- 1.1
- Author:
- Thomas Down, Greg Cox, Matthew Pocock
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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
Constructors -
Method Summary
Modifier and TypeMethodDescriptionThe alphabet that this SymbolList is over.int
length()
The number of symbols in this SymbolList.void
void
putComponent
(Location l, SymbolList sl) void
removeComponent
(Location loc) void
setLength
(int len) 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 pos) Return the symbol at index, counting from 1.Methods inherited from class org.biojava.bio.symbol.AbstractSymbolList
edit, equals, hashCode, iterator, seqString, toList, toString
Methods inherited from class org.biojava.utils.AbstractChangeable
addChangeListener, addChangeListener, generateChangeSupport, getChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListener
Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, wait, wait, wait
Methods inherited from interface org.biojava.utils.Changeable
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener
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Constructor Details
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AssembledSymbolList
public AssembledSymbolList()
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Method Details
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setLength
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putComponent
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putComponent
- Throws:
IllegalArgumentException
- if sl would introduce a circularity into the tree of components
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removeComponent
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getComponentLocationSet
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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.- Returns:
- the alphabet
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length
Description copied from interface:SymbolList
The number of symbols in this SymbolList.- Returns:
- the length
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symbolAt
Description copied from interface:SymbolList
Return the symbol at index, counting from 1.- 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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subStr
Description copied from interface:SymbolList
Return a region of this symbol list as a String.This should use the same rules as seqString.
- Specified by:
subStr
in interfaceSymbolList
- Overrides:
subStr
in classAbstractSymbolList
- Parameters:
start
- the first symbol to includeend
- the last symbol to include- Returns:
- the string representation
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