BadCallTable of Contents

Bad Call UtilitiesIntroductionPublic MethodsLocationListnewOverlapsOverlapStringsBad Call UtilitiesIntroductionThis module contains utility methods for finding and analyzing bad gene calls. Th default constructor uses a FIG object; however, any other object that mimics th FIG object signatures can be used. By convention, all calls to FIG object method will use the variable name $fig, so that the FIG methods used can be easil identified.

Most Location objects manipulated by this package are augmented locations. A augmented location contains two additional fields-- the feature ID ($loc-{fid}> and the location's index in the feature's location list ($loc-{index}). A augmented location enables us to relate the location back to the feature of interest.

Public Methodsnewmy $bc = BadCall->new($figLikeObject);

Construct a new, blank BadCall object.

figLikeObjectAn object that mimics the FIG object, which will be used to access genetic information If no parameter is specified, a vanilla FIG object will be used.

RETURNReturns an object that can be used to locate and analyze bad gene calls.

LocationListmy @locs = $bc->LocationList($genomeID);

Return a sorted list of the augmented locations for the features of the specified genome.

genomeIDID of the genome whose features should be put into the list.

RETURNReturns a list of augmented locations for all the feature segments on the genome's contigs sorted in the order they appear on the contigs, so that overlapping segments will be nex to each other.

Overlapsmy %overlaps = $bc->Overlaps($genomeID);

Find the overlapping features in a genome.

This method processes the sorted segment list for a genome's features amd produce a hash describing which features overlap other features. Each feature ID maps t a list of overlap objects describing the overlaps. Each overlap will appea in two lists of the hash-- one for each participating feature.

genomeIDID of the genome whose overlaps are desired.

RETURNReturns a hash of lists, keyed by feature ID. Each list will contain overlap object describing the overlaps involving the specified feature.

OverlapStringsmy %overlaps = $bc->OverlapStrings($genomeID);

Return a hash of all the overlaps in a genome. Unlike Overlaps, which returns a has of lists of overlap objects, this method returns a hash of lists of strings. This makes i easier to format the overlaps for display.

genomeIDID of the genome whose overlaps are desired.

RETURNReturns a hash of lists, keyed by feature ID. Each list will contain overlap string describing the overlaps involving the specified feature.