ApplyTransactionsTable of Contents

Apply TransactionsIntroductionMethodsAddAddFeatureChangeDeleteFixSubsystemsnewSetupSetupGenomeTeardownGenomeApply TransactionsIntroductionThis is a TransactionProcessor subclass that applies the transaction changes t the FIG data store.

Methodsnewmy $xprc = ApplyTransactions->new(\%options, $command, $directory, $idFile);

Construct a new ApplyTransactions object.

optionsReference to a hash table containing the command-line options.

commandCommand specified on the TransactFeatures command line. This command determine which TransactionProcessor subclass is active.

directoryDirectory containing the transaction files.

idFileName of the ID file (if needed).

Setup$xprc->Setup();

Set up to apply the transactions. This includes reading the ID file.

SetupGenome$xprc->SetupGenome();

Set up for processing this genome.

TeardownGenome$xprc->TeardownGenome();

Clean up after processing this genome. This involves optionally committing any updates.

Add$xprc->Add($newID, $locations, $translation);

Add a new feature to the data store.

newIDID to give to the new feature.

locationsLocation of the new feature, in the form of a comma-separated list of locatio strings in SEED format.

translation (optional)Protein translation string for the new feature. If this field is omitted an the feature is a peg, the translation will be generated by normal means.

Change$xprc->Change($fid, $newID, $locations, $aliases, $translation);

Replace a feature to the data store. The feature will be marked for deletion an a new feature will be put in its place.

This is a much more complicated process than adding a feature. In addition t the add, we have to create new aliases (or copy over the old ones) and transfe across the assignment, subsystem linkages, and the annotations.

fidID of the feature being changed.

newIDNew ID to give to the feature.

locationsNew location to give to the feature, in the form of a comma-separated list of locatio strings in SEED format.

aliases (optional)A new list of alias names for the feature.

translation (optional)New protein translation string for the feature. If this field is omitted an the feature is a peg, the translation will be generated by normal means.

Delete$xprc->Delete($fid);

Delete a feature from the data store. The feature will be marked as deleted which will remove it from consideration by most FIG methods. A garbag collection job will be run later to permanently delete the feature.

fidID of the feature to delete.

FixSubsystems$sfx->FixSubsystems($fid, $newID);

Remove the specified feature from all subsystems. If the feature is being replace by a new feature, the specified new feature will be added in the old feature's place.

fidID of the feature to be deleted.

newID (optional)ID of the new feature replacing the old one, if any. This should be a real ID, not pseudo-ID.

AddFeaturemy $realID = $self->AddFeature($ordinal, $key, $ftype, $locations, $aliases, $translation);

Add the specified feature to the FIG data store. This involves generating the new feature' ID, creating the translation (if needed), and adding the feature to the data store. Th generated ID will be returned to the caller.

ordinalZero-based ordinal number of the proposed feature in the ID space. This is added to th base ID number to get the real ID number.

keyKey to use for getting the base ID number from the ID hash.

ftypeProposed feature type (peg, rna, etc.)

locationsLocation of the new feature, in the form of a comma-separated list of locatio strings in SEED format.

aliases (optional)A new list of alias names for the feature.

translation (optional)Protein translation string for the new feature. If this field is omitted an the feature is a peg, the translation will be generated by normal means.