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beagle_beaglejniwrapper(3) [debian man page]

beagle.BeagleJNIWrapper(3)					     HMSBEAGLE						beagle.BeagleJNIWrapper(3)

NAME

       beagle.BeagleJNIWrapper -

SYNOPSIS

   Public Member Functions
       native ResourceDetails[] getResourceList ()
       native int createInstance (int tipCount, int partialsBufferCount, int compactBufferCount, int stateCount, int patternCount, int
	   eigenBufferCount, int matrixBufferCount, int categoryCount, int scaleBufferCount, final int[] resourceList, int resourceCount, long
	   preferenceFlags, long requirementFlags, InstanceDetails returnInfo)
       native int finalize (int instance)
       native int setPatternWeights (int instance, final double[] patternWeights)
       native int setTipStates (int instance, int tipIndex, final int[] inStates)
       native int getTipStates (int instance, int tipIndex, final int[] inStates)
       native int setTipPartials (int instance, int tipIndex, final double[] inPartials)
       native int setPartials (int instance, int bufferIndex, final double[] inPartials)
       native int getPartials (int instance, int bufferIndex, int scaleIndex, final double[] outPartials)
       native int setEigenDecomposition (int instance, int eigenIndex, final double[] eigenVectors, final double[] inverseEigenValues, final
	   double[] eigenValues)
       native int setStateFrequencies (int instance, int stateFrequenciesIndex, final double[] stateFrequencies)
       native int setCategoryWeights (int instance, int categoryWeightsIndex, final double[] categoryWeights)
       native int setCategoryRates (int instance, final double[] inCategoryRates)
       native int setTransitionMatrix (int instance, int matrixIndex, final double[] inMatrix, double paddedValue)
       native int getTransitionMatrix (int instance, int matrixIndex, final double[] outMatrix)
       native int updateTransitionMatrices (int instance, int eigenIndex, final int[] probabilityIndices, final int[] firstDerivativeIndices,
	   final int[] secondDervativeIndices, final double[] edgeLengths, int count)
       native int updatePartials (final int instance, final int[] operations, int operationCount, int cumulativeScalingIndex)
       native int waitForPartials (final int instance, final int[] destinationPartials, int destinationPartialsCount)
       native int accumulateScaleFactors (final int instance, final int[] scaleIndices, final int count, final int cumulativeScalingIndex)
       native int removeScaleFactors (final int instance, final int[] scaleIndices, final int count, final int cumulativeScalingIndex)
       native int resetScaleFactors (final int instance, final int cumulativeScalingIndex)
       native int copyScaleFactors (final int instance, final int destScalingIndex, final int srcScalingIndex)
       native int calculateRootLogLikelihoods (int instance, final int[] bufferIndices, final int[] categoryWeightsIndices, final int[]
	   stateFrequenciesIndices, final int[] cumulativeScaleIndices, int count, final double[] outSumLogLikelihood)
       native int calculateEdgeLogLikelihoods (int instance, final int[] parentBufferIndices, final int[] childBufferIndices, final int[]
	   probabilityIndices, final int[] firstDerivativeIndices, final int[] secondDerivativeIndices, final int[] categoryWeightsIndices, final
	   int[] stateFrequenciesIndices, final int[] scalingFactorsIndices, int count, final double[] outSumLogLikelihood, final double[]
	   outSumFirstDerivative, final double[] outSumSecondDerivative)
       native int getSiteLogLikelihoods (final int instance, final double[] outLogLikelihoods)

   Static Public Member Functions
       static void loadBeagleLibrary ()  throws UnsatisfiedLinkError

   Static Public Attributes
       static final String LIBRARY_NAME = getPlatformSpecificLibraryName()
       static BeagleJNIWrapper INSTANCE

Author
       Generated automatically by Doxygen for HMSBEAGLE from the source code.

Version 1.0.0							  Fri May 25 2012					beagle.BeagleJNIWrapper(3)

Check Out this Related Man Page

BIO_f_cipher(3) 						      OpenSSL							   BIO_f_cipher(3)

NAME

       BIO_f_cipher, BIO_set_cipher, BIO_get_cipher_status, BIO_get_cipher_ctx - cipher BIO filter

SYNOPSIS

	#include <openssl/bio.h>
	#include <openssl/evp.h>

	BIO_METHOD *   BIO_f_cipher(void);
	void BIO_set_cipher(BIO *b,const EVP_CIPHER *cipher,
		       unsigned char *key, unsigned char *iv, int enc);
	int BIO_get_cipher_status(BIO *b)
	int BIO_get_cipher_ctx(BIO *b, EVP_CIPHER_CTX **pctx)

DESCRIPTION

       BIO_f_cipher() returns the cipher BIO method. This is a filter BIO that encrypts any data written through it, and decrypts any data read
       from it. It is a BIO wrapper for the cipher routines EVP_CipherInit(), EVP_CipherUpdate() and EVP_CipherFinal().

       Cipher BIOs do not support BIO_gets() or BIO_puts().

       BIO_flush() on an encryption BIO that is being written through is used to signal that no more data is to be encrypted: this is used to
       flush and possibly pad the final block through the BIO.

       BIO_set_cipher() sets the cipher of BIO b to cipher using key key and IV iv. enc should be set to 1 for encryption and zero for decryption.

       When reading from an encryption BIO the final block is automatically decrypted and checked when EOF is detected. BIO_get_cipher_status() is
       a BIO_ctrl() macro which can be called to determine whether the decryption operation was successful.

       BIO_get_cipher_ctx() is a BIO_ctrl() macro which retrieves the internal BIO cipher context. The retrieved context can be used in
       conjunction with the standard cipher routines to set it up. This is useful when BIO_set_cipher() is not flexible enough for the
       applications needs.

NOTES

       When encrypting BIO_flush() must be called to flush the final block through the BIO. If it is not then the final block will fail a
       subsequent decrypt.

       When decrypting an error on the final block is signalled by a zero return value from the read operation. A successful decrypt followed by
       EOF will also return zero for the final read. BIO_get_cipher_status() should be called to determine if the decrypt was successful.

       As always, if BIO_gets() or BIO_puts() support is needed then it can be achieved by preceding the cipher BIO with a buffering BIO.

RETURN VALUES

       BIO_f_cipher() returns the cipher BIO method.

       BIO_set_cipher() does not return a value.

       BIO_get_cipher_status() returns 1 for a successful decrypt and 0 for failure.

       BIO_get_cipher_ctx() currently always returns 1.

EXAMPLES

       TBA

SEE ALSO

       TBA

1.0.1e								    2013-02-11							   BIO_f_cipher(3)
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