iPE::Globals(3)

NAME
iPE::Globals - Package containing global variables and routines for iPE.

DESCRIPTION
This package contains the functions to access and set global variables used in iPE. In using iPE as a set of modules, you will need to create a front end to parse the commandline to create the iPE::Estimator, and to parse options such as verbosity level, debug level, and output files.

GLOBALS

greeting ()
    Returns the standard greeting for launching iPE.

seqtypes ()
    Return a reference to an array of sequence types. These are all in iPE format. To translate to zoe or class format see zoe_seqtype () and seqclass ()

seqtype_exists ()
    Return 1 if the sequence type is in the seqtypes array.

zoe_seqtype (iPE_seqtype)
    Translates the iPE seqtype into the corresponding zoe sequence type. First looks to see if any zoeIrregularSeqtype has been defined for the passed iPE seqtype (e.g. dna => DNA, not DNASEQ), and if none is present, returns the uppercased sequence type followed by SEQ. For example, if you passed "bob", you would get zoe_seqtype would return BOBSEQ.

seqclass (iPE_seqtype)
    Returns the sequence class that defines the sequence type passed. This is usually just the capitalized name preceeded by iPE::Sequence:: (e.g. cons => iPE::Sequence::Cons). Looks for irregular sequence classes in the global irregularSeqclasses hash, and if none is there, translates as described.

sr_prefix (type)
    Return the sequence reader prefix for a type of sequence reader. At time of writing this is only 'load' or 'noload'

seqreader (filename-extension)
    Return the sequence reader that handles the filename-extension given.

gHMM ()
    Returns the global iPE::gHMM object if it has been defined. If it has not, any access to this function will cause the script to die. The iPE::Estimator object constructs this object as its first object.

bntree ()
    Returns the global iPE::Model::BNTree object. This is only defined if the nscanModel and nscanTopology options are defined, and someone instantiates it (usually the iPE::Estimator object).

state (stateName)
    Return the state in the gHMM object whose name is stateName.

states
    Return a hash reference to the states in the gHMM, keyed by state name.

ssSeqNames
    Return a hash reference to the sequence names for the significant statistics files (for n-scan estimation).

options
    Return the iPE::Options object. You may use this to check for any defined option by calling the name of the option, for example,
        $g->options->allowPartialTranscripts returns 1 if partial transcripts are allowed, 0 otherwise.

levels
    Return the global iPE::Levels object. This includes the levels of the current sequence (which may be a bad idea to use) and the cumulative levels of all sequences input.

FUNCTIONS

msg (message), Msg (message), Warn (message)
    Alert the user of an event or warn about an error. Warnings can be plentiful, and are optionally left in a file. The Msg function should be reserved for progress events and not used for errors. All Msg calls are broadcast to all filehandles.

SEE ALSO
iPE::gHMM, iPE::Options, iPE::Estimator

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