FudgeTransactionsTable of Contents

Fudge TransactionsIntroductionMethodsAddChangenewSetupSetupGenomeTeardownTeardownGenomeFudge TransactionsIntroductionThis is a TransactionProcessor subclass that creates test data from transaction that have already been applied. Each ADD is converted into an ADD and a DELETE and each CHANGE is updated to use the new ID. Note that the ID file will need t be modified before the transactions can be applied.

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

Construct a new FudgeTransactions 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.

Teardown$xprc->Teardown();

Update the ID table with high numbers to avoid duplication.

SetupGenome$xprc->SetupGenome();

Set up for processing this genome. This opens the output file.

TeardownGenome$xprc->TeardownGenome();

Clean up after processing this genome. This involves closing the output file an doing a rename.

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

Add a new feature to the data store. The Add is transmitted unmodified to th output file and then a delete is created for the ID added the last time.

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.

We change this so that it replaces the original real ID.

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.