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java.lang.Objectorg.biojava.utils.AbstractChangeable
org.biojava.bio.symbol.AbstractSymbolList
org.biojava.bio.seq.impl.AssembledSymbolList
public class AssembledSymbolList
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.
Nested Class Summary |
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Nested classes/interfaces inherited from class org.biojava.bio.symbol.AbstractSymbolList |
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AbstractSymbolList.EditScreener, AbstractSymbolList.EditTranslater |
Field Summary |
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Fields inherited from interface org.biojava.bio.symbol.SymbolList |
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EDIT, EMPTY_LIST |
Constructor Summary | |
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AssembledSymbolList()
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Method Summary | |
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Alphabet |
getAlphabet()
The alphabet that this SymbolList is over. |
Set |
getComponentLocationSet()
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int |
length()
The number of symbols in this SymbolList. |
void |
putComponent(ComponentFeature f)
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void |
putComponent(Location l,
SymbolList sl)
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void |
removeComponent(Location loc)
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void |
setLength(int len)
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SymbolList |
subList(int start,
int end)
Return a new SymbolList for the symbols start to end inclusive. |
String |
subStr(int start,
int end)
Return a region of this symbol list as a String. |
Symbol |
symbolAt(int pos)
Return the symbol at index, counting from 1. |
Methods inherited from class org.biojava.bio.symbol.AbstractSymbolList |
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edit, equals, hashCode, iterator, seqString, toList, toString |
Methods inherited from class org.biojava.utils.AbstractChangeable |
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addChangeListener, addChangeListener, generateChangeSupport, getChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListener |
Methods inherited from class java.lang.Object |
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clone, finalize, getClass, notify, notifyAll, wait, wait, wait |
Methods inherited from interface org.biojava.utils.Changeable |
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addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener |
Constructor Detail |
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public AssembledSymbolList()
Method Detail |
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public void setLength(int len)
public void putComponent(ComponentFeature f)
public void putComponent(Location l, SymbolList sl)
IllegalArgumentException
- if sl would introduce a circularity
into the tree of componentspublic void removeComponent(Location loc)
public Set getComponentLocationSet()
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.
public int length()
SymbolList
public Symbol symbolAt(int pos)
SymbolList
pos
- the offset into this SymbolList
public 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 String subStr(int start, int end)
SymbolList
This should use the same rules as seqString.
subStr
in interface SymbolList
subStr
in class AbstractSymbolList
start
- the first symbol to includeend
- the last symbol to include
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