Dim3Int(3) HMSBEAGLE Dim3Int(3)NAME
Dim3Int -
SYNOPSIS
Public Attributes
unsigned int x
unsigned int y
unsigned int z
Author
Generated automatically by Doxygen for HMSBEAGLE from the source code.
Version 1.0.0 Fri May 25 2012 Dim3Int(3)
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beagle::BeagleImpl(3) HMSBEAGLE beagle::BeagleImpl(3)NAME
beagle::BeagleImpl -
SYNOPSIS
Inherited by beagle::cpu::BeagleCPUImpl, and beagle::gpu::BeagleGPUImpl.
Public Member Functions
virtual int createInstance (int tipCount, int partialsBufferCount, int compactBufferCount, int stateCount, int patternCount, int
eigenBufferCount, int matrixBufferCount, int categoryCount, int scaleBufferCount, int resourceNumber, long preferenceFlags, long
requirementFlags)=0
virtual int getInstanceDetails (BeagleInstanceDetails *returnInfo)=0
virtual int setTipStates (int tipIndex, const int *inStates)=0
virtual int setTipPartials (int tipIndex, const double *inPartials)=0
virtual int setPartials (int bufferIndex, const double *inPartials)=0
virtual int getPartials (int bufferIndex, int scaleIndex, double *outPartials)=0
virtual int setEigenDecomposition (int eigenIndex, const double *inEigenVectors, const double *inInverseEigenVectors, const double
*inEigenValues)=0
virtual int setStateFrequencies (int stateFrequenciesIndex, const double *inStateFrequencies)=0
virtual int setCategoryWeights (int categoryWeightsIndex, const double *inCategoryWeights)=0
virtual int setPatternWeights (const double *inPatternWeights)=0
virtual int setCategoryRates (const double *inCategoryRates)=0
virtual int setTransitionMatrix (int matrixIndex, const double *inMatrix, double paddedValue)=0
virtual int setTransitionMatrices (const int *matrixIndices, const double *inMatrices, const double *paddedValues, int count)=0
virtual int getTransitionMatrix (int matrixIndex, double *outMatrix)=0
virtual int updateTransitionMatrices (int eigenIndex, const int *probabilityIndices, const int *firstDerivativeIndices, const int
*secondDerivativeIndices, const double *edgeLengths, int count)=0
virtual int updatePartials (const int *operations, int operationCount, int cumulativeScalingIndex)=0
virtual int waitForPartials (const int *destinationPartials, int destinationPartialsCount)=0
virtual int accumulateScaleFactors (const int *scalingIndices, int count, int cumulativeScalingIndex)=0
virtual int removeScaleFactors (const int *scalingIndices, int count, int cumulativeScalingIndex)=0
virtual int resetScaleFactors (int cumulativeScalingIndex)=0
virtual int copyScaleFactors (int destScalingIndex, int srcScalingIndex)=0
virtual int calculateRootLogLikelihoods (const int *bufferIndices, const int *categoryWeightsIndices, const int *stateFrequenciesIndices,
const int *scalingFactorsIndices, int count, double *outSumLogLikelihood)=0
virtual int calculateEdgeLogLikelihoods (const int *parentBufferIndices, const int *childBufferIndices, const int *probabilityIndices,
const int *firstDerivativeIndices, const int *secondDerivativeIndices, const int *categoryWeightsIndices, const int
*stateFrequenciesIndices, const int *scalingFactorsIndices, int count, double *outSumLogLikelihood, double *outSumFirstDerivative,
double *outSumSecondDerivative)=0
virtual int getSiteLogLikelihoods (double *outLogLikelihoods)=0
virtual int getSiteDerivatives (double *outFirstDerivatives, double *outSecondDerivatives)=0
Public Attributes
int resourceNumber
Author
Generated automatically by Doxygen for HMSBEAGLE from the source code.
Version 1.0.0 Fri May 25 2012 beagle::BeagleImpl(3)
I have a huge matrix file containing some 1.5 million rows and 6000 columns. The matrix looks something like this:
1 2 3
4 5 6
7 8 9
3 4 5
I want to add all the numbers in the columns of this matrix and display the result to my stdout. This means that the numbers in the first column are:
... (2 Replies)
Hi,
Just trying to get to grips with sed and awk for some reporting for work and I need some assistance:
I have a file that lists policy names on the first line and then on the second line whether the policy is active or not.
Policy Name: Policy1
Active: yes
Policy... (8 Replies)
version info :
vi availabe with RHEL 5.4
I have a text file with 10,000 lines. I want to copy lines from 5000th line to 7000th and redirect to a file. Any idea how I can do this?
Note:
The above scenario is just an example. In my actual requirement, the file has 14 million lines and I want... (9 Replies)
Hi everyone,
I know the following questions are noobish questions but I am asking them because I am confused about the basics of history behind UNIX and LINUX.
Ok onto business, my questions are-:
Was/Is UNIX ever an open source operating system ?
If UNIX was... (21 Replies)
Hello,
I couldn't find an actual introduction thread, so I decided to just put this here.
I go by d0wngrade online. I have been programming in multiple languages for about 15+ years. I started with standard web design languages like HTML and CSS, but I then advanced from design to development... (2 Replies)
Hi guys...
The first active code line in AudioScope.sh is set -u .
This causes a complete exit if a variable is used/found but has not been allocated at the start of the program.
However, apart from writing code to do the task, is there a switch to to check which variables have been... (17 Replies)
Hi.
In thread https://www.unix.com/shell-programming-and-scripting/267833-grouping-counting.html rovf and I had a mini-discussion on grep and awk.
Here is a demo script that compares the awk and grep approaches for this single problem:
#!/usr/bin/env bash
# @(#) s2 Demonstrate group... (1 Reply)
Hello,
I have to fish out some specific columns from a file based on the header value. I have the list of columns I need in a different file. I thought I could read in the list of headers I need,
# file with header names of required columns in required order
headers_file=$2
# read contents... (11 Replies)
For those interested in installing dash shell on OSX Lion to help test POSIX compliancy of shell scripts, it is quite easy. I did it like this:
If you don't have gcc on your system:
0. Download and install the Command Line Tools for Xcode package from Sign In - Apple *
1. Download the dash... (2 Replies)
Hello and thanks in advance for any help anyone can offer me
I'm trying to learn the find command and thought I was understanding it... Apparently I was wrong. I was doing compound searches and I started getting weird results with the -size test. I was trying to do a search on a 1G file owned by... (14 Replies)
I have data of an excel files as given below,
file1
org1_1 1 1 2.5 100
org1_2 1 2 5.5 98
org1_3 1 3 7.2 88
file2
org2_1 1 1 2.5 100
org2_2 1 2 5.5 56
org2_3 1 3 7.2 70
I have multiple excel files as above shown.
I have to copy column 1, column 4 and paste into a new excel file as... (26 Replies)
Dear All,
Taking a break from Vue.js coding for the site, SEO and YT videos; and hopefully addressing some well deserved criticism from some here that I have been too focused on the visual aspects of the forums versus the substance and the community....
While the "current generation... (9 Replies)
Hi all...
Well guys and gals, I jumped in at the deep end and found things that PERL cannot do by default.
Many tricky terminal escape codes are not catered for so I had to create workarounds.
One thing I searched for was this:
Passing perl variable to shell command
AND, @Neo this was... (15 Replies)