Bases: TASSELpy.net.maizegenetics.util.BitSet.MetaBitSet
Methods
andNot(*args) | this = this ANDNOT other |
capacity(*args) | Returns capacity |
cardinality(*args) | Returns number of set bits |
castTo(pyType) | Casts this object to another java/python type |
clear(*args) | Clears a bit or range of bits, allowing access beyond the current set |
clone(*args) | Creates and returns a copy of this object |
ensureCapacity(*args) | Ensure that the long[] is big enough to hold numBits, expanding it if necessary. |
ensureCapacityWords(*args) | Expand the long[] with the size given as a number of words (64 bit longs). |
equals(*args) | Indicates whether some other object is “equal to” this one |
fastClear(*args) | Clears a bit |
fastFlip(*args) | Flips a bit. |
fastGet(*args) | Returns true or false for the specified bit index |
fastSet(*args) | Sets the bit at the specified index. |
flip(*args) | Flips a bit, expanding the set size if necessary |
flipAndGet(*args) | Flips a bit and returns the resulting bit value. |
get(*args) | Returns true or false for the specified bit index |
getAndSet(*args) | Sets a bit and returns the previous value. |
getArray(size) | Gets an empty wrapped java array that can accept the type of the wrapped |
getBit(*args) | Returns 1 if the bit is set, 0 if not |
getBits(*args) | Expert: returns the long[] storing the bits |
getClass(*args) | Returns the runtime class of this Object. |
getDblArray(rows[, cols]) | Gets an empty wrapped java array that can accept the type of other wrapped java arrays: i.e. |
getIndicesOfSetBits(*args) | Returns the indices of set bits |
getNumWords(*args) | Expert: gets the number of longs in the array that |
hashCode(*args) | Returns a hash code vlaue for the object |
indexOfNthSetBit(*args) | Returns index of the nth set bit |
intersect(*args) | this = this AND other |
intersects(*args) | Returns true if the sets have any elements in common |
isEmpty(*args) | Returns true if there are no set bits |
nextSetBit(*args) | Returns the index of the first set bit starting at the index specified. |
previousSetBit(*args) | Returns the index of the previous set bit starting at the index specified. |
remove(*args) | Remove all elements set in other. |
set(*args) | Sets a bit, expanding the set size if necessary |
setBits(*args) | Expert: sets a new long[] to use as the bit storage |
setLong(*args) | Expert: sets the specified word with given bits |
setNumWords(*args) | Expert: sets the number of longs in the array that are in use |
size(*args) | Returns the current capacity of this set. |
toString(*args) | Returns a string representation of the object |
trimTrailingZeros(*args) | Lowers numWords, the number of words in use, by checking for trailing |
union(*args) | this = this OR other |
wrap_existing_array(arr_instance) | Wraps a java array of this class’s type |
xor(*args) | this = this XOR other |
this = this ANDNOT other
Signature: | xor (BitSet other) |
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Parameters: | other (BitSet) – Another BitSet instance |
Returns number of set bits
Signature: | cardinality () |
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Signature: | cardinality (int index) |
Parameters: | index (int) – index |
Returns: | The number of set bits |
Return type: | long |
Clears a bit or range of bits, allowing access beyond the current set size without changing the size
Signature: | clear (long index) |
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Signature: | clear (int startIndex, int endIndex) |
Signature: | clear (long startIndex, long endIndex) |
Parameters: |
|
Ensure that the long[] is big enough to hold numBits, expanding it if necessary. getNumWords() is unchanged by this call
Signature: | ensureCapacity (long numBits) |
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Parameters: | numBits (long) – The number of bits the BitSet should be able to hold |
Expand the long[] with the size given as a number of words (64 bit longs). getNumWords() is unchanged by this call
Signature: | ensureCapacityWords (int numWords) |
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Parameters: | numWords (int) – The number of words to expand the long[] by |
Clears a bit The index should be less than the BitSet size
Signature: | fastClear (int index) |
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Signature: | fastClear (long index) |
Parameters: | index (long) – index (long or int) |
Flips a bit. The index should be less than the BitSet size
Signature: | fastFlip (int index) |
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Signature: | fastFlip (long index) |
Parameters: | index (long) – The index of the bit to flip (long or int) |
Returns true or false for the specified bit index
Signature: | fastGet (int index) |
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Signature: | fastGet (long index) |
Parameters: | index (long) – index (long or int), should be less than the BitSet size |
Sets the bit at the specified index. The index should be less than the BitSet size
Signature: | fastSet (int index) |
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Signature: | fastSet (long index) |
Parameters: | index (long) – index (long or int) |
Flips a bit, expanding the set size if necessary
Signature: | flip (long index) |
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Signature: | flip (long startIndex, long endIndex) |
Parameters: |
|
Flips a bit and returns the resulting bit value. The index should be less than the BitSet size
Signature: | flipAndGet (int index) |
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Signature: | flipAndGet (long index) |
Parameters: | index (long) – The index to flip and get |
Returns true or false for the specified bit index
Signature: | get (int index) |
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Signature: | get (long index) |
Parameters: | index (long) – index (long or int) |
Sets a bit and returns the previous value. The index should be less than the BitSet size
Signature: | getAndSet (int index) |
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Signature: | getAndSet (long index) |
Parameters: | index (long) – The index to clear and view (long or int) |
Returns 1 if the bit is set, 0 if not
Arguments:
index – index, should be less than the BitSet size
Expert: returns the long[] storing the bits
Signature: | getBits () |
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Signature: | getBits (int startWord, int endWord) |
Signature: | getBits (int index) |
Parameters: |
|
this = this AND other
Signature: | intersect (BitSet other) |
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Parameters: | other (BitSet) – Another BitSet instance |
Returns true if the sets have any elements in common
Signature: | intersects (BitSet other) |
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Parameters: | other (BitSet) – Another BitSet instance |
Returns the index of the first set bit starting at the index specified. -1 is returned if there are no more set bits
Signature: | nextSetBit (long index) |
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Signature: | nextSetBit (int index) |
Parameters: | index (int) – index (long or int) |
Returns: | The next set bit |
Return type: | long |
Returns the index of the previous set bit starting at the index specified. If the bit at the index is set, index is returned, otherwise the next lower numbered set bit is retuned. -1 is returned if there are no more set bits
Signature: | previousSetBit (long index) |
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Signature: | previousSetBit (int index) |
Parameters: | index (int) – index |
Returns: | The previous set bit |
Return type: | long |
Remove all elements set in other. this = this AND_NOT other
Signature: | remove (BitSet other) |
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Parameters: | other (BitSet) – Another BitSEt instance |
Sets a bit, expanding the set size if necessary
Signature: | set (long index) |
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Signature: | set (long startIndex, long endIndex) |
Parameters: |
|
Expert: sets a new long[] to use as the bit storage
Arguments:
bits – long[] to use as the bit storage
Expert: sets the specified word with given bits
Arguments:
wordNum – word index bits – bits
Expert: sets the number of longs in the array that are in use
Arguments:
nWords – The number of longs in the array that should be in use
Returns the current capacity of this set. Included for compatibility. This is not equal to cardinality
Lowers numWords, the number of words in use, by checking for trailing zero words
Signature: | trimTrailingZeros () |
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Bases: TASSELpy.java.lang.Object.Object
Methods
castTo(pyType) | Casts this object to another java/python type |
clone(*args) | Creates and returns a copy of this object |
equals(*args) | Indicates whether some other object is “equal to” this one |
getArray(size) | Gets an empty wrapped java array that can accept the type of the wrapped |
getClass(*args) | Returns the runtime class of this Object. |
getDblArray(rows[, cols]) | Gets an empty wrapped java array that can accept the type of other wrapped java arrays: i.e. |
hashCode(*args) | Returns a hash code vlaue for the object |
toString(*args) | Returns a string representation of the object |
wrap_existing_array(arr_instance) | Wraps a java array of this class’s type |
Bases: TASSELpy.java.lang.Object.Object
Provide generalized annotations (descriptors) for taxon or site
Methods
castTo(pyType) | Casts this object to another java/python type |
clone(*args) | Creates and returns a copy of this object |
equals(*args) | Indicates whether some other object is “equal to” this one |
getAllAnnotationEntries(*args) | Returns all annotation Map.Entries |
getAnnotation(*args) | Returns all annotation value for a given annotation key |
getAnnotationAsMap(*args) | Returns all annotations in TreeMap |
getArray(size) | Gets an empty wrapped java array that can accept the type of the wrapped |
getAverageAnnotation(*args) | Returns average annotation for a given annotation key |
getClass(*args) | Returns the runtime class of this Object. |
getConsensusAnnotation(*args) | Returns consensus value for given annotation key |
getDblArray(rows[, cols]) | Gets an empty wrapped java array that can accept the type of other wrapped java arrays: i.e. |
getQuantAnnotation(*args) | Returns all annotation value for given annotation key |
getTextAnnotation(*args) | Returns all annotation values for a given annotation key |
hashCode(*args) | Returns a hash code vlaue for the object |
toString(*args) | Returns a string representation of the object |
wrap_existing_array(arr_instance) | Wraps a java array of this class’s type |
Returns all annotation Map.Entries
Signatures:
Map.Entry<String, String>[] getAllAnnotationEntries()
Returns:
Array of Map.Entry
Returns all annotation value for a given annotation key
Signature: | getAnnotation (String annoName) |
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Parameters: | annoName (String) – annotation key |
Returns: | array of annotation values (if not present new String[0]) |
Return type: | Object[] |
Returns all annotations in TreeMap
Signatures:
SetMultimap<String,String> getAnnotationAsMap()
Returns:
Map of annotations
Returns average annotation for a given annotation key
Signature: | getAverageAnnotation (String annoName) |
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Parameters: | annoName (String) – annotation key |
Returns: | average value (if not present - return Double.NaN) |
Return type: | double |
Returns consensus value for given annotation key
Signature: | getConsensusAnnotation (String annoName) |
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Parameters: | annoName (String) – annotation key |
Returns: | Consensus value (if not present new String[0]) |
Return type: | String |
Bases: TASSELpy.net.maizegenetics.util.GeneralAnnotation.GeneralAnnotation
Stores general annotations
Methods
Builder | |
castTo(pyType) | Casts this object to another java/python type |
clone(*args) | Creates and returns a copy of this object |
equals(*args) | Indicates whether some other object is “equal to” this one |
getAllAnnotationEntries(*args) | Returns all annotation Map.Entries |
getAnnotation(*args) | Returns all annotation value for a given annotation key |
getAnnotationAsMap(*args) | Returns all annotations in TreeMap |
getArray(size) | Gets an empty wrapped java array that can accept the type of the wrapped |
getAverageAnnotation(*args) | Returns average annotation for a given annotation key |
getBuilder(*args) | Gets a builder for a GeneralAnnotationStorage object |
getClass(*args) | Returns the runtime class of this Object. |
getConsensusAnnotation(*args) | Returns consensus value for given annotation key |
getDblArray(rows[, cols]) | Gets an empty wrapped java array that can accept the type of other wrapped java arrays: i.e. |
getQuantAnnotation(*args) | Returns all annotation value for given annotation key |
getTextAnnotation(*args) | Returns all annotation values for a given annotation key |
hashCode(*args) | Returns a hash code vlaue for the object |
toString(*args) | Returns a string representation of the object |
wrap_existing_array(arr_instance) | Wraps a java array of this class’s type |
Bases: TASSELpy.java.lang.Object.Object
Builder for GeneralAnnotationStorage
Methods
addAnnotation | |
build | |
castTo | |
clone | |
equals | |
getArray | |
getClass | |
getDblArray | |
hashCode | |
toString | |
wrap_existing_array |
Bases: TASSELpy.net.maizegenetics.util.BitSet.BitSet
Methods
andNot(*args) | this = this ANDNOT other |
capacity(*args) | Returns capacity |
cardinality(*args) | Returns number of set bits |
castTo(pyType) | Casts this object to another java/python type |
clear(*args) | Clears a bit or range of bits, allowing access beyond the current set |
clone(*args) | Creates and returns a copy of this object |
ensureCapacity(*args) | Ensure that the long[] is big enough to hold numBits, expanding it if necessary. |
ensureCapacityWords(*args) | Expand the long[] with the size given as a number of words (64 bit longs). |
equals(*args) | Indicates whether some other object is “equal to” this one |
fastClear(*args) | Clears a bit |
fastFlip(*args) | Flips a bit. |
fastGet(*args) | Returns true or false for the specified bit index |
fastSet(*args) | Sets the bit at the specified index. |
flip(*args) | Flips a bit, expanding the set size if necessary |
flipAndGet(*args) | Flips a bit and returns the resulting bit value. |
get(*args) | Returns true or false for the specified bit index |
getAndSet(*args) | Sets a bit and returns the previous value. |
getArray(size) | Gets an empty wrapped java array that can accept the type of the wrapped |
getBit(*args) | Returns 1 if the bit is set, 0 if not |
getBits(*args) | Expert: returns the long[] storing the bits |
getClass(*args) | Returns the runtime class of this Object. |
getDblArray(rows[, cols]) | Gets an empty wrapped java array that can accept the type of other wrapped java arrays: i.e. |
getIndicesOfSetBits(*args) | Returns the indices of set bits |
getNumWords(*args) | Expert: gets the number of longs in the array that |
hashCode(*args) | Returns a hash code vlaue for the object |
indexOfNthSetBit(*args) | Returns index of the nth set bit |
intersect(*args) | this = this AND other |
intersects(*args) | Returns true if the sets have any elements in common |
isEmpty(*args) | Returns true if there are no set bits |
nextSetBit(*args) | Returns the index of the first set bit starting at the index specified. |
previousSetBit(*args) | Returns the index of the previous set bit starting at the index specified. |
remove(*args) | Remove all elements set in other. |
set(*args) | Sets a bit, expanding the set size if necessary |
setBits(*args) | Expert: sets a new long[] to use as the bit storage |
setLong(*args) | Expert: sets the specified word with given bits |
setNumWords(*args) | Expert: sets the number of longs in the array that are in use |
size(*args) | Returns the current capacity of this set. |
toString(*args) | Returns a string representation of the object |
trimTrailingZeros(*args) | Lowers numWords, the number of words in use, by checking for trailing |
union(*args) | this = this OR other |
wrap_existing_array(arr_instance) | Wraps a java array of this class’s type |
xor(*args) | this = this XOR other |
An “open” BitSet implementation that allows direct access to the array of words storing the bits
Unlike java.util.bitset, the fact that bits are packed into an array of longs is part of the interface. This allows efficient implementation of other algorithms by someone other than the author. It also allows one to efficiently implement alternate serialization or interchange formats.
OpenBitSet is faster than java.util.BitSet in most operations and much faster at calculating cardinality of sets and results of set operations. It can also handle sets of larger cardinality (up to 64*2**32-1
The goals of OpenBitSet are the fastest implementation possible, and maximum code reuse. Extra safety and encapsulation may always be built on top, but if that’s built in, the cost can never be removed (and hence people re-implement their own version in order to get better performance). If you want a “safe”, totally encapsulated (and slower and limited) BitSet class (coward), use java.util.BitSet
Signatures:
OpenBitSet(BitSet cloneOBS) OpenBitSet(long[] bits) OpenBitSet(long[] bits, int numWords) OpenBitSet() OpenBitSet(long numBits)
Arguments:
numBits – Specifies the OpenBitSet to be large enough to hold numBits bits – The first 64 bits are in long[0], with bit index 0 at the least significant bit,
and bit index 63 as the most significant. Given a bit index, the word containing it is long[index/64], and it is at bit number index index%64 within that word.
cloneOBS – An instance of a class that implements the BitSet interface
Bases: TASSELpy.java.lang.Object.Object
Methods
castTo(pyType) | Casts this object to another java/python type |
clone(*args) | Creates and returns a copy of this object |
equals(*args) | Indicates whether some other object is “equal to” this one |
getArray(size) | Gets an empty wrapped java array that can accept the type of the wrapped |
getClass(*args) | Returns the runtime class of this Object. |
getDblArray(rows[, cols]) | Gets an empty wrapped java array that can accept the type of other wrapped java arrays: i.e. |
hashCode(*args) | Returns a hash code vlaue for the object |
progress(*args) | Returns the progress of execution |
toString(*args) | Returns a string representation of the object |
wrap_existing_array(arr_instance) | Wraps a java array of this class’s type |
Bases: TASSELpy.java.lang.Object.Object
Interface for classes with data that can be presented in tables
Methods
castTo(pyType) | Casts this object to another java/python type |
clone(*args) | Creates and returns a copy of this object |
equals(*args) | Indicates whether some other object is “equal to” this one |
getArray(size) | Gets an empty wrapped java array that can accept the type of the wrapped |
getClass(*args) | Returns the runtime class of this Object. |
getColumnCount(*args) | Gets the number of columns |
getDblArray(rows[, cols]) | Gets an empty wrapped java array that can accept the type of other wrapped java arrays: i.e. |
getElementCount(*args) | Gets the total number of elements in the dataset |
getRow(*args) | Returns specified row |
getRowCount(*args) | Gets the number of rows |
getTableColumnNames(*args) | Gets the names of the columns |
getTableTitle(*args) | Gets the title of the table |
getValueAt(*args) | Returns value at given row and column |
hashCode(*args) | Returns a hash code vlaue for the object |
toDict() | Outputs the table as a dictionary |
toString(*args) | Returns a string representation of the object |
wrap_existing_array(arr_instance) | Wraps a java array of this class’s type |
Gets the number of columns
Signature: | getColumnCount () |
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Returns: | Number of columns |
Return type: | int |
Gets the total number of elements in the dataset Elements = rowCount*columnCount
Signature: | getElementCount () |
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Returns: | Total number of elements |
Return type: | long |
Returns specified row
Signature: | getRow (long row) |
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Parameters: | row (long) – row number |
Returns: | row |
Return type: | Object[] |
Gets the number of rows
Signature: | getRowCount () |
---|---|
Returns: | Number of rows |
Return type: | long |
Gets the names of the columns
Signature: | getTableColumnNames () |
---|---|
Returns: | Column names |
Return type: | Object[] |
Gets the title of the table
Signature: | getTableTitle () |
---|---|
Returns: | A string title |
Return type: | String |
Bases: TASSELpy.net.maizegenetics.util.BitSet.BitSet
Methods
andNot(*args) | this = this ANDNOT other |
capacity(*args) | Returns capacity |
cardinality(*args) | Returns number of set bits |
castTo(pyType) | Casts this object to another java/python type |
clear(*args) | Clears a bit or range of bits, allowing access beyond the current set |
clone(*args) | Creates and returns a copy of this object |
ensureCapacity(*args) | Ensure that the long[] is big enough to hold numBits, expanding it if necessary. |
ensureCapacityWords(*args) | Expand the long[] with the size given as a number of words (64 bit longs). |
equals(*args) | Indicates whether some other object is “equal to” this one |
fastClear(*args) | Clears a bit |
fastFlip(*args) | Flips a bit. |
fastGet(*args) | Returns true or false for the specified bit index |
fastSet(*args) | Sets the bit at the specified index. |
flip(*args) | Flips a bit, expanding the set size if necessary |
flipAndGet(*args) | Flips a bit and returns the resulting bit value. |
get(*args) | Returns true or false for the specified bit index |
getAndSet(*args) | Sets a bit and returns the previous value. |
getArray(size) | Gets an empty wrapped java array that can accept the type of the wrapped |
getBit(*args) | Returns 1 if the bit is set, 0 if not |
getBits(*args) | Expert: returns the long[] storing the bits |
getClass(*args) | Returns the runtime class of this Object. |
getDblArray(rows[, cols]) | Gets an empty wrapped java array that can accept the type of other wrapped java arrays: i.e. |
getIndicesOfSetBits(*args) | Returns the indices of set bits |
getInstance(*args) | Get instance of UnmodifiableBitSet from a BitSet |
getNumWords(*args) | Expert: gets the number of longs in the array that |
hashCode(*args) | Returns a hash code vlaue for the object |
indexOfNthSetBit(*args) | Returns index of the nth set bit |
intersect(*args) | this = this AND other |
intersects(*args) | Returns true if the sets have any elements in common |
isEmpty(*args) | Returns true if there are no set bits |
nextSetBit(*args) | Returns the index of the first set bit starting at the index specified. |
previousSetBit(*args) | Returns the index of the previous set bit starting at the index specified. |
remove(*args) | Remove all elements set in other. |
set(*args) | Sets a bit, expanding the set size if necessary |
setBits(*args) | Expert: sets a new long[] to use as the bit storage |
setLong(*args) | Expert: sets the specified word with given bits |
setNumWords(*args) | Expert: sets the number of longs in the array that are in use |
size(*args) | Returns the current capacity of this set. |
toString(*args) | Returns a string representation of the object |
trimTrailingZeros(*args) | Lowers numWords, the number of words in use, by checking for trailing |
union(*args) | this = this OR other |
wrap_existing_array(arr_instance) | Wraps a java array of this class’s type |
xor(*args) | this = this XOR other |