iPE::Instance(3)

NAME
iPE::Instance - an instance of parameter estimation, defined by the iPE_instance XML file.

DESCRIPTION
Each running instance of iPE defines a set of options, sequences, annotations, feature maps, null definitions, and a gHMM. The most basic type of instance is the run instance which runs all the sequences and annotations on a single processor.

A thread or job instance defines a set of sequences and annotations which will be split up to be run on separate threads or nodes in a queue. If a job instance is submitted to iPE, it will be divided up into files and output paths, and a jobfile is created. The user will then have to manually submit the job to a queue. A thread instance will run on separate threads on the same machine, splitting up the sequences and annotations as in the job instance.

Both thread and job instances will have a special running instance called a gather instance, which will gather the files from the subinstances and add all the counts together and convert all the numbers into scores.

These are defined in XML files. This class inherits from the iPE::XML::DocObject class.

FUNCTIONS

run ()
    After new ()ing and parse_file ()ing an instance file, you can call this function to run the estimator based on the instance created. At this point, all sanity checks have been performed on the instance.

SEE ALSO
iPE::XML::DocObject

AUTHOR
Bob Zimmermann (rpz@cse.wustl.edu)