Class SequenceProxyView<C extends Compound>
- java.lang.Object
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- org.biojava.nbio.core.sequence.template.SequenceProxyView<C>
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- All Implemented Interfaces:
Iterable<C>
,Accessioned
,Sequence<C>
,SequenceView<C>
- Direct Known Subclasses:
ComplementSequenceView
,ReversedSequenceView
,RnaSequenceView
public class SequenceProxyView<C extends Compound> extends Object implements SequenceView<C>
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Constructor Summary
Constructors Constructor Description SequenceProxyView()
SequenceProxyView(Sequence<C> sequence)
SequenceProxyView(Sequence<C> sequence, Integer bioStart, Integer bioEnd)
Main constructor for working with SequenceProxyViews
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description int
countCompounds(C... compounds)
Returns the number of times we found a compound in the Sequenceboolean
equals(Object o)
AccessionID
getAccession()
Returns the AccessionID this location is currently bound withList<C>
getAsList()
Returns the Sequence as a List of compoundsInteger
getBioEnd()
1-indexed, inclusive.Integer
getBioStart()
1-indexed, inclusive.C
getCompoundAt(int position)
Returns the Compound at the given biological indexCompoundSet<C>
getCompoundSet()
Gets the compound set used to back this Sequenceint
getIndexOf(C compound)
Scans through the Sequence looking for the first occurrence of the given compoundSequenceView<C>
getInverse()
Does the right thing to get the inverse of the current Sequence.int
getLastIndexOf(C compound)
Scans through the Sequence looking for the last occurrence of the given compoundint
getLength()
Returns the length of the SequenceString
getSequenceAsString()
Returns the String representation of the SequenceSequenceView<C>
getSubSequence(Integer bioStart, Integer bioEnd)
Returns a portion of the sequence from the different positions.Sequence<C>
getViewedSequence()
int
hashCode()
Iterator<C>
iterator()
void
setBioEnd(Integer bioEnd)
void
setBioStart(Integer bioStart)
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Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, toString, wait, wait, wait
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Methods inherited from interface java.lang.Iterable
forEach, spliterator
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Constructor Detail
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SequenceProxyView
public SequenceProxyView()
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SequenceProxyView
public SequenceProxyView(Sequence<C> sequence)
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SequenceProxyView
public SequenceProxyView(Sequence<C> sequence, Integer bioStart, Integer bioEnd)
Main constructor for working with SequenceProxyViews- Parameters:
sequence
- Sequence to proxybioStart
- Start; cannot be less than 1bioEnd
- End; cannot be greater than the sequence length
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Method Detail
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getViewedSequence
public Sequence<C> getViewedSequence()
- Specified by:
getViewedSequence
in interfaceSequenceView<C extends Compound>
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getSequenceAsString
public String getSequenceAsString()
Description copied from interface:Sequence
Returns the String representation of the Sequence- Specified by:
getSequenceAsString
in interfaceSequence<C extends Compound>
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getAsList
public List<C> getAsList()
Description copied from interface:Sequence
Returns the Sequence as a List of compounds
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getCompoundAt
public C getCompoundAt(int position)
Description copied from interface:Sequence
Returns the Compound at the given biological index- Specified by:
getCompoundAt
in interfaceSequence<C extends Compound>
- Parameters:
position
- Biological index (1 to n)- Returns:
- Compound at the specified position
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getIndexOf
public int getIndexOf(C compound)
Description copied from interface:Sequence
Scans through the Sequence looking for the first occurrence of the given compound- Specified by:
getIndexOf
in interfaceSequence<C extends Compound>
- Parameters:
compound
- Compounds to look for- Returns:
- Index of the first position of the compound in the sequence (1 to n)
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getLastIndexOf
public int getLastIndexOf(C compound)
Description copied from interface:Sequence
Scans through the Sequence looking for the last occurrence of the given compound- Specified by:
getLastIndexOf
in interfaceSequence<C extends Compound>
- Parameters:
compound
- Compounds to look for- Returns:
- Index of the last position of the compound in the sequence (1 to n)
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getLength
public int getLength()
Description copied from interface:Sequence
Returns the length of the Sequence
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getCompoundSet
public CompoundSet<C> getCompoundSet()
Description copied from interface:Sequence
Gets the compound set used to back this Sequence- Specified by:
getCompoundSet
in interfaceSequence<C extends Compound>
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getSubSequence
public SequenceView<C> getSubSequence(Integer bioStart, Integer bioEnd)
Description copied from interface:Sequence
Returns a portion of the sequence from the different positions. This is indexed from 1- Specified by:
getSubSequence
in interfaceSequence<C extends Compound>
- Parameters:
bioStart
- Biological index start; must be greater than 0bioEnd
- Biological end; must be less than length + 1- Returns:
- A SequenceView of the offset
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getAccession
public AccessionID getAccession()
Description copied from interface:Accessioned
Returns the AccessionID this location is currently bound with- Specified by:
getAccession
in interfaceAccessioned
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getBioStart
public Integer getBioStart()
Description copied from interface:SequenceView
1-indexed, inclusive.- Specified by:
getBioStart
in interfaceSequenceView<C extends Compound>
- Returns:
- the bioStart
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setBioStart
public void setBioStart(Integer bioStart)
- Parameters:
bioStart
- the bioStart to set
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getBioEnd
public Integer getBioEnd()
Description copied from interface:SequenceView
1-indexed, inclusive.- Specified by:
getBioEnd
in interfaceSequenceView<C extends Compound>
- Returns:
- the bioEnd
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countCompounds
public int countCompounds(C... compounds)
Description copied from interface:Sequence
Returns the number of times we found a compound in the Sequence- Specified by:
countCompounds
in interfaceSequence<C extends Compound>
- Parameters:
compounds
- Vargs of the compounds to count- Returns:
- Number of times a compound was found
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getInverse
public SequenceView<C> getInverse()
Description copied from interface:Sequence
Does the right thing to get the inverse of the current Sequence. This means either reversing the Sequence and optionally complementing the Sequence.- Specified by:
getInverse
in interfaceSequence<C extends Compound>
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