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java.lang.Object | +--org.biojava.bio.seq.ViewSequence
A view onto another Sequence object. This class allows new features and annotations to be overlayed onto an existing Sequence without modifying it.
Inner classes inherited from class org.biojava.bio.symbol.SymbolList |
SymbolList.EmptySymbolList |
Inner classes inherited from class org.biojava.bio.seq.FeatureHolder |
FeatureHolder.EmptyFeatureHolder |
Inner classes inherited from class org.biojava.bio.seq.FeatureHolder |
FeatureHolder.EmptyFeatureHolder |
Fields inherited from interface org.biojava.bio.symbol.SymbolList |
EMPTY_LIST |
Fields inherited from interface org.biojava.bio.seq.FeatureHolder |
EMPTY_FEATURE_HOLDER |
Fields inherited from interface org.biojava.bio.seq.FeatureHolder |
EMPTY_FEATURE_HOLDER |
Constructor Summary | |
ViewSequence(Sequence seq)
Construct a view onto an existing sequence. |
|
ViewSequence(Sequence seq,
FeatureRealizer fr)
Construct a view onto a sequence, using a specific FeatureRealizer |
Method Summary | |
int |
countFeatures()
Count how many features are contained. |
Feature |
createFeature(Feature.Template template)
Create a new Feature, and add it to this FeatureHolder. |
Feature |
createFeature(FeatureHolder fh,
Feature.Template template)
Deprecated. Please use 1-arg createFeature instead. |
java.util.Iterator |
features()
Iterate over the features in no well defined order. |
FeatureHolder |
filter(FeatureFilter fc,
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(FeatureHolder parent,
Feature.Template template)
Realize a feature template. |
void |
removeFeature(Feature f)
Remove a feature from this sequence. |
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 indx)
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 |
Constructor Detail |
public ViewSequence(Sequence seq)
public ViewSequence(Sequence seq, FeatureRealizer fr)
Method Detail |
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 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 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 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 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 Symbol symbolAt(int indx)
index
- the ofset into this SymbolListpublic java.util.List toList()
This is an immutable list of symbols. Do not edit it.
public java.lang.String getURN()
urn:sequence/embl:U32766
or
urn:sequence/fasta:sequences.fasta|hox3
.public java.lang.String getName()
The name may contain spaces or odd characters.
public int countFeatures()
public java.util.Iterator features()
public FeatureHolder filter(FeatureFilter fc, 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 void removeFeature(Feature f)
public Annotation getAnnotation()
public Feature realizeFeature(FeatureHolder parent, Feature.Template template) throws BioException
createFeature
method of either
this FeatureHolder
or one of our child Features.public Feature createFeature(Feature.Template template) throws BioException
public Feature createFeature(FeatureHolder fh, Feature.Template template) throws BioException
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