Package edu.mssm.crover.webapps.dimlib.util

Class Summary
AddRbdgXML Adds the mapping information for GIF images for Mutant and WildType proteins to the database.
AlnValidator Used to ensure that all sequences in an alignment that is being imported are present in the database.
ExportAln A number of different ways in which an alignment can be exported to a file.
ExportXML Exports the database as a series of XML files, which can be used to re-submit the data.
HTMLFormatter Formats ArcadiaAlignments (Multiple Sequence Alignments) into HTML.
ImportAln This is a command line interface only and should only be used for administrative purposes.
ImportFHExcel This is a command line interface only.
ImportWTP Imports the sequences from a SwissProt formatted sequence file into the database.
ImportXML Parses an XML file for an Arcadia submission.
LitRefSorter Comparison class to sort LiteratureReference.
MailAlert Used to send e-mail alerts to users of the Arcadia database.
MPSorter Sorts MutantProteins based on a number of different methods.
MutantQueryManager Retrieves MutantProteins from the database.
MutationParser Used to parse mutation information from a String.
MutationSorter Sorts Mutations.
MutationValidator Checks whether a mutation is valid.
RbdgXMLGenerator Generates the XML file used as input for rbdg.
Setup Sets up all the different things that are needed by the application, such as organism lists, GPCRDB colours, etc.
SNPSorter SNP sorter.
SNPValidator Validates the SNP inputted by the user.
TMValidator Checks if the given TM segment is valid.
WTPQueryManager Used to retrieve WildTypeProteins from the database.
WTPSorter Wildtype protein sorter.
XMLValidator XML Document Validator.
 

Exception Summary
InvalidMutationException Constructs a message detailing why a mutation is invalid.
InvalidResidueException Constructs a message detailing why a Residue is invalid.
InvalidSNPException Constructs a message detailing why a SNP is invalid.
InvalidSubmissionException Constructs a message detailing why a submission is invalid.
InvalidTMException Constructs a message detailing why a TM domain is invalid.
 



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