C
- java.lang.Iterable<C>
, Accessioned
, ProxySequenceReader<C>
, Sequence<C>
, SequenceReader<C>
GenbankProxySequenceReader
public class StringProxySequenceReader<C extends Compound> extends java.lang.Object implements ProxySequenceReader<C>
Constructor | Description |
---|---|
StringProxySequenceReader() |
|
StringProxySequenceReader(java.lang.String sequence,
CompoundSet<C> compoundSet) |
Modifier and Type | Method | Description |
---|---|---|
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
|
java.util.List<C> |
getAsList() |
Returns the Sequence as a List of compounds
|
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
|
java.lang.String |
getSequenceAsString() |
Returns the String representation of the Sequence
|
java.lang.String |
getSequenceAsString(java.lang.Integer bioBegin,
java.lang.Integer bioEnd,
Strand strand) |
|
SequenceView<C> |
getSubSequence(java.lang.Integer bioBegin,
java.lang.Integer bioEnd) |
Returns a portion of the sequence from the different positions.
|
java.util.Iterator<C> |
iterator() |
|
void |
setCompoundSet(CompoundSet<C> compoundSet) |
|
void |
setContents(java.lang.String sequence) |
|
void |
setContents(java.lang.String sequence,
java.util.ArrayList features) |
|
java.lang.String |
toString() |
public StringProxySequenceReader()
public StringProxySequenceReader(java.lang.String sequence, CompoundSet<C> compoundSet) throws CompoundNotFoundException
CompoundNotFoundException
public void setCompoundSet(CompoundSet<C> compoundSet)
setCompoundSet
in interface SequenceReader<C extends Compound>
public void setContents(java.lang.String sequence) throws CompoundNotFoundException
setContents
in interface SequenceReader<C extends Compound>
CompoundNotFoundException
public void setContents(java.lang.String sequence, java.util.ArrayList features) throws CompoundNotFoundException
CompoundNotFoundException
public int getLength()
Sequence
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 forpublic int getLastIndexOf(C compound)
Sequence
getLastIndexOf
in interface Sequence<C extends Compound>
compound
- Compounds to look forpublic java.lang.String toString()
toString
in class java.lang.Object
public java.lang.String getSequenceAsString()
Sequence
getSequenceAsString
in interface Sequence<C extends Compound>
public java.util.List<C> getAsList()
Sequence
public java.lang.String getSequenceAsString(java.lang.Integer bioBegin, java.lang.Integer bioEnd, Strand strand)
public SequenceView<C> getSubSequence(java.lang.Integer bioBegin, java.lang.Integer bioEnd)
Sequence
getSubSequence
in interface Sequence<C extends Compound>
bioBegin
- Biological index start; must be greater than 0bioEnd
- Biological end; must be less than length + 1public java.util.Iterator<C> iterator()
public CompoundSet<C> getCompoundSet()
Sequence
getCompoundSet
in interface Sequence<C extends Compound>
public AccessionID getAccession()
Accessioned
getAccession
in interface Accessioned
public int countCompounds(C... compounds)
Sequence
countCompounds
in interface Sequence<C extends Compound>
compounds
- Vargs of the compounds to countpublic SequenceView<C> getInverse()
Sequence
getInverse
in interface Sequence<C extends Compound>