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.\" ========================================================================
.\"
.IX Title "PMP::Array 3"
.TH PMP::Array 3 "2009-02-28" "perl v5.10.1" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
PMParray \- convenience functions for controlling multiple PMP pipes.
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
See the synopsis in the \s-1PMP\s0 documentation for an illustration of how
to use PMParray.
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
PMParray contains a series of convenience functions for dealing with
multiple pipelines. The definition of a pipeline in the \s-1PMP\s0 context
relates to all the stages for an individual subject. In most cases,
however, a program will execute all stages for multiple
subjects. This is where PMParray comes in, as it provides facilities
for doing just that.
.SH "OVERVIEW"
.IX Header "OVERVIEW"
The basic usage of PMParray is the following: PMParray is initialized
with a call to PMParray\->\fInew()\fR. Then the individual \s-1PMP\s0 pipelines are
created. Once each pipeline is created it is added to PMParray with
the PMParray\->addPipe method. Then PMParray is used to call the same
method on all its component pipelines \- such as running them all to
completion.
.SH "METHODS"
.IX Header "METHODS"
.SS "new"
.IX Subsection "new"
Initialises the pipeline \- has to be the first method called.
.SS "maxQueued"
.IX Subsection "maxQueued"
Set the maximum number of running jobs in queue.
.SS "setGranularity"
.IX Subsection "setGranularity"
Set the granularity level for the scheduling of the stages. An argument 
value of 0 will submit each stage to the queue whereas a value of 1 will
lump together all stages for a given subject and submit them in one job 
to the queue (one queue submission per subject).
.SS "addPipe"
.IX Subsection "addPipe"
Takes a \s-1PMP\s0 object as its argument and adds it to the PMParray.
.SS "run"
.IX Subsection "run"
Runs all the pipelines that have been added until nothing is left to
be done in any of them.
.SS "updateFromFiles"
.IX Subsection "updateFromFiles"
Sets the status of all stages in all pipelines based on their inputs
and outputs. In other words, calls the \s-1PMP\s0 method statusFromFiles on
all pipelines.
.SS "printUnfinished"
.IX Subsection "printUnfinished"
Prints the unfinished stages for each pipeline.
.SS "resetFromStage"
.IX Subsection "resetFromStage"
Takes a stage name as an argument, and resets all stages from that
one onwards in each pipeline (uses a method of the same name in \s-1PMP\s0).
.SS "resetAfterStage"
.IX Subsection "resetAfterStage"
Takes a stage name as an argument, and resets all stages after that
one onwards in each pipeline (uses a method of the same name in \s-1PMP\s0).
.SS "resetAll"
.IX Subsection "resetAll"
Resets all stages in all pipelines.
.SS "printStages"
.IX Subsection "printStages"
Prints the stages of the first pipeline in the array (i.e. it assumes
that this information will be the same for all pipelines).
.SS "createDotGraph"
.IX Subsection "createDotGraph"
Takes a filename as an argument, and creates a dot graph description
therein. One can then use the command line program dot to actually
generate the graph.
.SS "createFilenameDotGraph"
.IX Subsection "createFilenameDotGraph"
Takes a filename as an argument, and a substring as an optional second
argument. Then creates a dot graph description in the filename; this
graph contains each stage along with its output files. The substring,
if provided, is removed from each filename (so the best use of it is
to provide the base directory of all the files). Uses the first
pipeline in the array to generate this graph.
.SS "printPipelineStatus"
.IX Subsection "printPipelineStatus"
Takes a filename as an optional argument. If provided, prints the
status of all pipelines in the Array to that file, otherwise to
stout.
.SS "registerPrograms"
.IX Subsection "registerPrograms"
Registers the programs of the first pipeline in the array, exiting if
any program cannot be found in the current path.
.SS "subsetToStage"
.IX Subsection "subsetToStage"
Takes a stagename as an argument, and subsets each pipeline to run
from the first stage until the stagename provided as the argument.
.SS "printStatusReport"
.IX Subsection "printStatusReport"
Takes a filename as an argument and prints a \s-1CSV\s0 separated status
report therein.
.SS "sleepTime"
.IX Subsection "sleepTime"
Gets or sets the number of seconds to sleep between pipeline
executions.