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java.lang.Objectorg.biojava3.core.sequence.storage.BitSequenceReader.BitArrayWorker<C>
C
- The Compound
to usepublic abstract static class BitSequenceReader.BitArrayWorker<C extends Compound>
The logic of working with a bit has been separated out into this class
to help developers create the bit data structures without having to
put the code into an intermediate format and to also use the format
without the need to copy this code.
This class behaves just like a Sequence
without the interface
Field Summary | |
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static int |
BYTES_PER_INT
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Constructor Summary | |
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BitSequenceReader.BitArrayWorker(CompoundSet<C> compoundSet,
int length)
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BitSequenceReader.BitArrayWorker(CompoundSet<C> compoundSet,
int[] sequence)
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BitSequenceReader.BitArrayWorker(Sequence<C> sequence)
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BitSequenceReader.BitArrayWorker(String sequence,
CompoundSet<C> compoundSet)
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Method Summary | |
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protected abstract byte |
bitMask()
This method should return the bit mask to be used to extract the bytes you are interested in working with. |
protected int |
bitsPerCompound()
Returns how many bits are used to represent a compound e.g. |
protected abstract int |
compoundsPerDatatype()
Should return the maximum amount of compounds we can encode per int |
boolean |
equals(Object o)
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protected abstract Map<C,Integer> |
generateCompoundsToIndex()
Returns what the value of a compound is in the backing bit storage i.e. |
protected abstract List<C> |
generateIndexToCompounds()
Should return the inverse information that generateCompoundsToIndex()
returns i.e. |
C |
getCompoundAt(int position)
Returns the compound at the specified biological index |
CompoundSet<C> |
getCompoundSet()
Returns the compound set backing this store |
protected Map<C,Integer> |
getCompoundsToIndexLookup()
Returns a map which converts from compound to an integer representation |
protected List<C> |
getIndexToCompoundsLookup()
Returns a list of compounds the index position of which is used to translate from the byte representation into a compound. |
int |
getLength()
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int |
hashCode()
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void |
populate(Sequence<C> sequence)
Loops through the Compounds in a Sequence and passes them onto setCompoundAt(Compound, int) |
void |
populate(String sequence)
Loops through the chars in a String and passes them onto setCompoundAt(char, int) |
protected byte |
processUnknownCompound(C compound,
int position)
Since bit encoding only supports a finite number of bases it is more than likely when processing sequence you will encounter a compound which is not covered by the encoding e.g. |
int |
seqArraySize(int length)
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void |
setCompoundAt(char base,
int position)
Converts from char to Compound and sets it at the given biological index |
void |
setCompoundAt(C compound,
int position)
Sets the compound at the specified biological index |
Methods inherited from class java.lang.Object |
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clone, finalize, getClass, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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public static final int BYTES_PER_INT
Constructor Detail |
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public BitSequenceReader.BitArrayWorker(Sequence<C> sequence)
public BitSequenceReader.BitArrayWorker(String sequence, CompoundSet<C> compoundSet)
public BitSequenceReader.BitArrayWorker(CompoundSet<C> compoundSet, int length)
public BitSequenceReader.BitArrayWorker(CompoundSet<C> compoundSet, int[] sequence)
Method Detail |
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protected abstract byte bitMask()
protected abstract int compoundsPerDatatype()
protected abstract List<C> generateIndexToCompounds()
generateCompoundsToIndex()
returns i.e. if the Compound C returns 1 from compoundsToIndex then we
should find that compound here in position 1
protected abstract Map<C,Integer> generateCompoundsToIndex()
protected int bitsPerCompound()
public int seqArraySize(int length)
public void populate(Sequence<C> sequence)
setCompoundAt(Compound, int)
public void populate(String sequence)
setCompoundAt(char, int)
public void setCompoundAt(char base, int position)
public void setCompoundAt(C compound, int position)
public C getCompoundAt(int position)
protected byte processUnknownCompound(C compound, int position) throws IllegalStateException
compound
- Compound process
IllegalStateException
- Done whenever this method is invokedprotected List<C> getIndexToCompoundsLookup()
protected Map<C,Integer> getCompoundsToIndexLookup()
public CompoundSet<C> getCompoundSet()
public int getLength()
public int hashCode()
hashCode
in class Object
public boolean equals(Object o)
equals
in class Object
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