Package edu.mssm.crover.tools.tissue

TissueInfo command line tools and classes.

See:
Description

Interface Summary

TissueInfo	Provides access to tissue information for sequences.
TIWeb	Provides access to tissue information for human mRNA.

Class Summary

CheckLibrary	Finds CuratedTissues for raw tissues, if they exist.
CuratedDevStage	Storage class for tissue information.
CuratedTissue	Storage class for tissue information.
DbestParser	Parses dbEST and extract tissue information.
DevStageCuration	Stores all the manual curation for every raw tissue string extracted from dbEST.
DumpNullsTissueInfo	Dumps information from the TissueInfo null table.
DumpTissueInfo	Dumps TissueInfo to files.
GetCuratedDevStage	Reads a file of raw tissues and checks whether a CuratedDevStage exists for that raw tissue.
GetCuratedTissue	Reads a file of raw tissues and checks whether a CuratedTissue exists for that raw tissue.
GetNulls	Checks whether the accession code exists in the table.
Hierarchy	This class determines the relationships between tissue classes.
HierarchyKeywords	Splits the hierarchy interface names up into keywords.
HSP	Storage class for information an HSP.
LibraryDivision	Gets the raw tissue library information for each accession number.
NullParser	Parses information for entries marked as null by DbestParser and passed through the Textractor program, and curates the tissue information.
NullTissueDetails	Storage class for details associated with ESTs which were originally marked as null, since we could not parse a tissue from their dbEST entry.
QueryTissueSummary	Processes the information about a query sequence and calculates a number of attributes for that query sequence.
ReplaceRawTissue	Replaces a raw tissue with the curated tissue, if it exists in the tissue curation table.
ReportParser	Parses report files from tiquery.
TIimport	Imports the information from the dbEST file to the database.
TImegablast	Converts megablast output type 3 (-D 3) to tiac format.
TIMegablastSql	Converts megablast output type 3 (-D 3) to a file with a series of SQL insert statements that can be easily uploaded to a database.
TINullImport	Imports the dbEST entries originally marked as null into the database.
TIQuery	Performs a series of analyses on the information in a tiac file.
TIQuerySql	Performs a series of analyses on the information in a tiac file.
TISearch	Blasts query sequences and parses the output.
TissueCuration	Stores all the manual curation for every raw tissue string extracted from dbEST.
TissueDetails	Storage class for details associated with ESTs.
TissueInfoCacheImpl	Cache TissueInfo in memory.
TissueInfoJDBCImpl	Provides access to tissue information for sequences.
TissueInfoMemoryImpl	Keeps TissueInfo in memory.
TissueInfoMemoryImpl2	Reads a file representation of TissueInfo and keeps the records in memory.
TissueInfoNullsJDBCImpl	Provides access to tissue information for sequences.
TissueSelection	Storage class for tissue information.
TissueSelectionHelper	Searches TissueCuration to return a CuratedTissue.
TissueSummary	Processes the information about a query sequence and calculates a number of attributes for that query sequence.
TIWebJDBCImpl	Provides access to human mRNA tissue information.

Exception Summary

ColumnIdentifierLengthException	Thrown when the column identifier is greater than 30 characters.
TissueInfoNotAvailableException	Thrown when the database is not available for some reason.

Package edu.mssm.crover.tools.tissue Description

TissueInfo command line tools and classes.

Package Specification

See the sub-packages for a list of available tools.

Related Documentation