org.biojava3.core.sequence.loader
C
- public class SequenceFileProxyLoader<C extends Compound> extends java.lang.Object implements ProxySequenceReader<C>
Constructor and Description |
---|
SequenceFileProxyLoader(java.io.File file,
SequenceParserInterface sequenceParser,
long sequenceStartIndex,
int sequenceLength,
CompoundSet<C> compoundSet) |
Modifier and Type | Method and 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.
|
boolean |
isInitialized() |
java.util.Iterator<C> |
iterator() |
void |
setCompoundSet(CompoundSet<C> compoundSet) |
void |
setContents(java.lang.String sequence) |
void |
setInitialized(boolean initialized) |
java.lang.String |
toString() |
public SequenceFileProxyLoader(java.io.File file, SequenceParserInterface sequenceParser, long sequenceStartIndex, int sequenceLength, CompoundSet<C> compoundSet)
file
- The file where the sequence will be foundsequenceParser
- The parser to use to load the sequencesequenceStartIndex
- The file offset to the start of the sequencesequenceLength
- The length of the sequencecompoundSet
- public void setCompoundSet(CompoundSet<C> compoundSet)
setCompoundSet
in interface SequenceReader<C extends Compound>
compoundSet
- public void setContents(java.lang.String sequence)
setContents
in interface SequenceReader<C extends Compound>
sequence
- public int getLength()
Sequence
public C getCompoundAt(int position)
Sequence
getCompoundAt
in interface Sequence<C extends Compound>
position
- public int getIndexOf(C compound)
Sequence
getIndexOf
in interface Sequence<C extends Compound>
compound
- public int getLastIndexOf(C compound)
Sequence
getLastIndexOf
in interface Sequence<C extends Compound>
compound
- public 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.lang.String getSequenceAsString(java.lang.Integer bioBegin, java.lang.Integer bioEnd, Strand strand)
bioBegin
- bioEnd
- strand
- public java.util.List<C> getAsList()
Sequence
public SequenceView<C> getSubSequence(java.lang.Integer bioBegin, java.lang.Integer bioEnd)
Sequence
getSubSequence
in interface Sequence<C extends Compound>
bioBegin
- bioEnd
- public java.util.Iterator<C> iterator()
public CompoundSet<C> getCompoundSet()
Sequence
getCompoundSet
in interface Sequence<C extends Compound>
public boolean isInitialized()
public void setInitialized(boolean initialized)
initialized
- the initialized to setpublic AccessionID getAccession()
Accessioned
getAccession
in interface Accessioned
public int countCompounds(C... compounds)
Sequence
countCompounds
in interface Sequence<C extends Compound>
compounds
- public SequenceView<C> getInverse()
Sequence
getInverse
in interface Sequence<C extends Compound>