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java.lang.Objectorg.biojava3.core.sequence.loader.StringProxySequenceReader<C>
C
- public class StringProxySequenceReader<C extends Compound>
An example of a ProxySequenceReader that is created from a String. Used for testing
Constructor Summary | |
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StringProxySequenceReader(String sequence,
CompoundSet<C> compoundSet)
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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 |
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 |
String |
getSequenceAsString(Integer bioBegin,
Integer bioEnd,
Strand strand)
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SequenceView<C> |
getSubSequence(Integer bioBegin,
Integer bioEnd)
Returns a portion of the sequence from the different positions. |
Iterator<C> |
iterator()
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void |
setCompoundSet(CompoundSet<C> compoundSet)
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void |
setContents(String sequence)
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String |
toString()
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Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Constructor Detail |
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public StringProxySequenceReader(String sequence, CompoundSet<C> compoundSet)
Method Detail |
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public void setCompoundSet(CompoundSet<C> compoundSet)
setCompoundSet
in interface SequenceReader<C extends Compound>
public void setContents(String sequence)
setContents
in interface SequenceReader<C extends Compound>
public int getLength()
Sequence
getLength
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 String toString()
toString
in class Object
public String getSequenceAsString()
Sequence
getSequenceAsString
in interface Sequence<C extends Compound>
public List<C> getAsList()
Sequence
getAsList
in interface Sequence<C extends Compound>
public String getSequenceAsString(Integer bioBegin, Integer bioEnd, Strand strand)
public SequenceView<C> getSubSequence(Integer bioBegin, 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 + 1
public Iterator<C> iterator()
iterator
in interface Iterable<C extends Compound>
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 count
public SequenceView<C> getInverse()
Sequence
getInverse
in interface Sequence<C extends Compound>
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