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See:
Description
| Class Summary | |
| BioSourceFactory | That class his hidding the logic which allow to get a valid biosource from a taxid. |
| Chrono | |
| Crc64 | Crc64 checksum computation. |
| DagNode | Auxiliary class to insert GO Dag nodes from a GO dag formatted flat file. |
| DocumentationIntegrityChecker | Allows to check if the IntAct documentation is ready to be generated by checking if a section is used several times. |
| GoaTools | |
| GoServerProxy | The proxy to the Go server. |
| GoServerProxy.GoResponse | |
| GoTools | Utilities to read and write files in GO format |
| HttpProxyManager | Setup the HTTP proxy setting in the current JVM. |
| InsertComplex | Insert complex data for Ho and Gavin publications. |
| InsertComplexGiot | Insert of the Giot data in IntAct |
| InsertComplexMerck | Insert binary iteraction data (customize to MERCK format). |
| InsertGo | Create GO crossreferences for Protein objects. |
| IntactStatistics | This class represents the Statistics table in the database. |
| InteractorComparator | This class provides a specific Comparator for 'hidden' Interactors, based on short label. |
| Key | This class provides a wrapper around a String object
for use with java Maps. |
| NewtServerProxy | The proxy to the Newt server. |
| NewtServerProxy.NewtResponse | |
| ObjectSet | Represents a set of IntAct objects |
| PropertyLoader | Allow to create a set of properties from a file. example : let's say the onfig/database.properties file contains : database.login=username --- |
| ProteinExport | |
| ProteinFastaDownload | This util class retrieves protein sequences from IntAct It downloads all IntAct sequences in fasta format into a file "proteinFastaDownload": * the fasta header contains the IntAct ac * the protein sequence follows (from the next line) like that: >ac seq........................... |
| SanityChecker | Utility class to perform some sanity checks on the DB. |
| SearchReplace | Managment of search replace with regular expression. |
| Serializer | Simple utility class for checking serialization for objects. |
| ShortLabelComparator | This class provides a specific Comparator for use with AnnotatedObjects. |
| StatisticsDataSet | |
| TestCaseHelper | Helper class for setting up/tearing down objects used for test cases. |
| UpdateProteins | Parse an URL and update the IntAct database. |
| UpdateProteinsI | Defines the functionality of protein import utilities. |
| Utilities | Various IntAct related utilities. |
| XmlBuilder | This utility class provides operations for generating XML, typically in the form of Document or Element objects. |
| Exception Summary | |
| GoServerProxy.GoIdNotFoundException | |
| HttpProxyManager.ProxyConfigurationNotFound | |
| NewtServerProxy.TaxIdNotFoundException | |
| UpdateProteinsI.UpdateException | |
Various utilities and auxiliary scripts.
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