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java.lang.Objectorg.biojava3.core.sequence.template.SequenceProxyView<C>
public class SequenceProxyView<C extends Compound>
Constructor Summary | |
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SequenceProxyView()
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SequenceProxyView(Sequence<C> sequence)
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SequenceProxyView(Sequence<C> sequence,
Integer bioStart,
Integer bioEnd)
Main constructor for working with SequenceProxyViews |
Method Summary | |
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int |
countCompounds(C... compounds)
Returns the number of times we found a compound in the Sequence |
AccessionID |
getAccession()
Returns the AccessionID this location is currently bound with |
List<C> |
getAsList()
Returns the Sequence as a List of compounds |
Integer |
getBioEnd()
1-indexed, inclusive. |
Integer |
getBioStart()
1-indexed, inclusive. |
C |
getCompoundAt(int position)
Returns the Compound at the given biological index |
CompoundSet<C> |
getCompoundSet()
Gets the compound set used to back this Sequence |
int |
getIndexOf(C compound)
Scans through the Sequence looking for the first occurrence of the given compound |
SequenceView<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 compound |
int |
getLength()
Returns the length of the Sequence |
String |
getSequenceAsString()
Returns the String representation of the Sequence |
SequenceView<C> |
getSubSequence(Integer bioStart,
Integer bioEnd)
Returns a portion of the sequence from the different positions. |
Sequence<C> |
getViewedSequence()
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Iterator<C> |
iterator()
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void |
setBioEnd(Integer bioEnd)
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void |
setBioStart(Integer bioStart)
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Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public SequenceProxyView()
public SequenceProxyView(Sequence<C> sequence)
public SequenceProxyView(Sequence<C> sequence, Integer bioStart, Integer bioEnd)
sequence
- Sequence to proxybioStart
- Start; cannot be less than 1bioEnd
- End; cannot be greater than the sequence lengthMethod Detail |
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public Sequence<C> getViewedSequence()
getViewedSequence
in interface SequenceView<C extends Compound>
public String getSequenceAsString()
Sequence
getSequenceAsString
in interface Sequence<C extends Compound>
public List<C> getAsList()
Sequence
getAsList
in interface Sequence<C extends Compound>
public C getCompoundAt(int position)
Sequence
getCompoundAt
in interface Sequence<C extends Compound>
position
- Biological index (1 to n)
public int getIndexOf(C compound)
Sequence
getIndexOf
in interface Sequence<C extends Compound>
compound
- Compounds to look for
public int getLastIndexOf(C compound)
Sequence
getLastIndexOf
in interface Sequence<C extends Compound>
compound
- Compounds to look for
public int getLength()
Sequence
getLength
in interface Sequence<C extends Compound>
public CompoundSet<C> getCompoundSet()
Sequence
getCompoundSet
in interface Sequence<C extends Compound>
public SequenceView<C> getSubSequence(Integer bioStart, Integer bioEnd)
Sequence
getSubSequence
in interface Sequence<C extends Compound>
bioStart
- Biological index start; must be greater than 0bioEnd
- Biological end; must be less than length + 1
public Iterator<C> iterator()
iterator
in interface Iterable<C extends Compound>
public AccessionID getAccession()
Accessioned
getAccession
in interface Accessioned
public Integer getBioStart()
SequenceView
getBioStart
in interface SequenceView<C extends Compound>
public void setBioStart(Integer bioStart)
bioStart
- the bioStart to setpublic Integer getBioEnd()
SequenceView
getBioEnd
in interface SequenceView<C extends Compound>
public void setBioEnd(Integer bioEnd)
bioEnd
- the bioEnd to setpublic int countCompounds(C... compounds)
Sequence
countCompounds
in interface Sequence<C extends Compound>
compounds
- Vargs of the compounds to count
public SequenceView<C> getInverse()
Sequence
getInverse
in interface Sequence<C extends Compound>
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