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java.lang.Object | +--org.acedb.seq.AceSequence
Sequence extracted from an ACeDB database.
Inner classes inherited from class org.biojava.bio.symbol.SymbolList |
SymbolList.EmptySymbolList |
Inner classes inherited from class org.biojava.bio.seq.FeatureHolder |
FeatureHolder.EmptyFeatureHolder |
Field Summary | |
protected AceObject |
seqObj
|
Fields inherited from interface org.biojava.bio.symbol.SymbolList |
EMPTY_LIST |
Fields inherited from interface org.biojava.bio.seq.FeatureHolder |
EMPTY_FEATURE_HOLDER |
Constructor Summary | |
AceSequence(AceObject seqObj)
|
Method Summary | |
int |
countFeatures()
Count how many features are contained. |
Feature |
createFeature(Feature.Template template)
Add a new feature to this sequence. |
Feature |
createFeature(FeatureHolder fh,
Feature.Template template)
Add a new feature to this sequence. |
java.util.Iterator |
features()
Iterate over the features in no well defined order. |
FeatureHolder |
filter(FeatureFilter ff,
boolean recurse)
Return a new FeatureHolder that contains all of the children of this one that passed the filter fc. |
Alphabet |
getAlphabet()
The alphabet that this SymbolList is over. |
Annotation |
getAnnotation()
Should return the associated annotation object. |
java.lang.String |
getName()
The name of this sequence. |
java.lang.String |
getURN()
The URN for this sequence. |
java.util.Iterator |
iterator()
An Iterator over all Symbols in this SymbolList. |
int |
length()
The number of symbols in this SymbolList. |
Feature |
realizeFeature(Feature.Template template)
|
void |
removeFeature(Feature f)
Remove a feature from this FeatureHolder. |
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 class java.lang.Object |
clone,
equals,
finalize,
getClass,
hashCode,
notify,
notifyAll,
toString,
wait,
wait,
wait |
Field Detail |
protected AceObject seqObj
Constructor Detail |
public AceSequence(AceObject seqObj) throws AceException, BioException
Method Detail |
public java.lang.String getName()
The name may contain spaces or odd characters.
public java.lang.String getURN()
urn:sequence/embl:U32766
or
urn:sequence/fasta:sequences.fasta|hox3
.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 Annotation getAnnotation()
public java.util.Iterator iterator()
This is an ordered iterator over the Symbols. It cannot be used to edit the underlying symbols.
public int length()
public Symbol symbolAt(int index)
index
- the ofset into this SymbolListpublic java.util.List toList()
This is an immutable list of symbols. Do not edit it.
public SymbolList subList(int start, int end)
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 SymbolListpublic java.lang.String subStr(int start, int end)
This should use the same rules as seqString.
start
- the first symbol to includeend
- the last symbol to includepublic 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 int countFeatures()
public java.util.Iterator features()
public FeatureHolder filter(FeatureFilter ff, boolean recurse)
fc
- the FeatureFilter to applyrecurse
- true if all features-of-features should be scanned, and a
single flat collection of features returned, or false if
just immediate children should be filtered.public Feature createFeature(FeatureHolder fh, Feature.Template template) throws java.lang.UnsupportedOperationException
Ace sequences are currently immutable. This may be changed in the future. This method will always throw an UnsupportedOperationException.
public Feature createFeature(Feature.Template template) throws java.lang.UnsupportedOperationException
Ace sequences are currently immutable. This may be changed in the future. This method will always throw an UnsupportedOperationException.
public Feature realizeFeature(Feature.Template template)
public void removeFeature(Feature f)
|
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