Version 2.9-1
Release 1.7.0
Internal Changes:
  + (r42536) parseXmlInteractorNodes uses 'parseXmlInteractorNode instead of indirect calling parseInteractor now
  + (r42537) refactor the parsing of interactors in parseComplex function. Till now only the parseComplex remains to be refactored
  + (r42538) add 'parseReleaseDate' function to avoid repeating codes in parsing interaction and complexes
  + (r42539) add 'parseXmlEntryInteractors' to allow one-call to parse interactors in one entry
Public Changes:
  + (r42541) remove function slots in psimi25source objects; rename 'complexMembers' to 'members' directly
  + (r42543) 'interactorRef' slot is added to 'psimi25Complex' object
  + (r42547) simi25Complex contains the virtual class attributesListBase now. 'comlexAttributes' function has been removed, instead user should use 'attributesList'
  + (r42589) 'psimi25Names' is not an abstract class any more
  + (r43055) 'translateID' fixes a bug and returns the real translted ID. TODO: if more than one translated IDs are returned, the original node (and its connections) should be duplicated.
  + (r43055) 'translateID' fixes: if a node is failed to be translated (NA), the default identifier (uniprotID) will be used.
  + 'translateID' fixes: if more than one nodes are translated into same identifier, only the first is left

Release 1.5.31 (Oct. 19, 2009)
Documentation:
  + (r42468) Modify the man page of psimi25InteractionEntry to reflect the current data structure of interactors. Thanks the report by Robert Gentleman.
API Changes:
  + (r42469) Add 'pubmedID' method for psimi25InteractionEntry object to return unique PubMed IDs of the papers reporting the interactions stored in the entry.

Release 1.5.30
  + A major refactoring of parsing functions

Release 1.5.27 (Oct. 13, 2009)
Internal Changes:
  + (r42344) 'parseXmlExperimentNodeSet' has been refactored, add 'getExperimentNodeSetPath' function
  + (r42344) 'parseXmlComplex' and 'parseXmlInteractor' renamed into 'parseXmlComplexNode' and 'parseXmlInteractorNode' respectively

Release 1.5.30 (Oct. 13, 2009)
Internal Changes:
  + (r42347) A major refactoring splitting the parseXmlInteractionNode, parseXmlEntryNode, etc. 
Test suite
  + Remove 'class_test.R', will be replaced by RUnit

Release 1.5.26 (Oct. 12, 2009)
Internal Changes:
  + (r42316) 'getMapped' is renamed as 'getValueByMatchingMatrixColumn' and moved out of the main function of 'parsePsimi25Interaction'
API Changes:
  + (r42347) 'interactions<-' and 'releaseDate<-' are exported

Release 1.5.25 (Oct. 08, 2009)
API Changes:
  + (r42265) The issue of conflicts between utils::head(tail) and hypergraph::head(tail) is solve by setting the method for ANY to the form in utils. However this solution is not perfect, since the conflict warning still appears.

Release 1.5.24 (Oct. 07, 2009)
API Changes:
  + The 'import' field is cleaned, only necessary methods are imported.
  + (r42214): 'sourceId' and 'sourceDb' are added to support any subclass inheriting 'sourceDbAndId'
  + (r42215): 'taxId' and 'organismName' are refactored to support any subclass inheriting 'organismTaxIdAndName'
  + (r42220): 'interactorListBase' abstract class is added as superclass for both psimi25Entry and psimi25GraphBase
  + (r42222): 'psimi25Experiment' now also inherits the 'sourceDbAndId' class. 'expSourceId' is treated as 'sourceId'
  + (r42223): Functions starting with '.' in their names were meant to be internal for XML parsing. Since they are confusing, these functions have been renamed as 'parseXML...'
  + (r42227): (nonNull)XMLvalueByPath and (nonNull)XMLattributeValueByPath refactored, reducing redundancy in the parsing codes
  + (r42230): bug fixed: 'shortLabel' is converted to 'NA' in case of 'NULL'

Release 1.5.23 (Oct. 07, 2009)
Internal Changes:
  + Add 'organismIdAndName', 'psimi25Entry' (abstract) and 'psimi25GraphBase' (abstact) classes to reduce redundancy in class definitions

Release 1.5.22 (Oct. 07, 2009)
Internal Changes:
  + Add 'sourceDbAndId' private class recoding pairs source database and ID
  + All new XML interfacing classes and methods have been temporally commented out. Their neccessity needs to be discussed
Package Structure Changes:
  + Remove the 'ChangeLog', subversion control log and NEWS take the reporting task.

Release 1.5.21 (Oct. 01, 2009)
API Changes:
  + Add 'psimi25Hypergraph2GraphNEL' function to convert a hypergraph to graphNEL object

Release 1.5.20 (Aug. 24, 2009)
Internal Changes:
  + All superfluos list-objects are removed to accelerate the parsing, which reduces the time by 25%.

Release 1.5.19 (Aug. 21, 2009)
API Changes:
  + 'typedList' is completely substituted by the 'list' data type, which reduces the parsing time by 33%.

Release 1.5.18 (Aug. 13, 2009)
Internal Changes:
  + ConfidenceType handler added. Profiling in progress

Release 1.5.17 (Aug. 13, 2009)
Internal Changes:
  + All elements of the PSI-MI 2.5 specifications have handlers, although some of them are not tested since
    no file has implemented them (in this situation these handlers will stop the program)

Release 1.5.16 (Aug. 12, 2009)
Internal Changes:
  + Filling most of the element handlers. Still some are missing. This will be finished in the next release.

Release 1.5.15 (Aug. 11, 2009)
API Changes:
  + Except for 'interactionList', all the other child elements of 'entry' have their handlers

Release 1.5.14 (Aug. 11, 2009)
API Changes:
  + 'psimi25ExperimentTypeHandler' almost fully implemented
  + 'psimi25EntrySet' and 'psimi25Entry' definition revised to reflect the data structure
  + source, availabilityList and experimentList elements of the entry can already be unmarshalled
  + global constant variables added to save memory and speed overhead in parsing. They follow the 
    naming convention of 'GC_mockClassName'. They will probably not be exported.
File Changes:
  + SAXhandler_test.R is removed temporarily from the test file sets, since it
    is mainly used internally.


Release 1.5.13 (Aug. 10, 2009)
API Changes:
  + DOM handlers added for several types, but not finished yet
  + Further modification of classes for easy use (no public API is affected)
  + Constructor of 'psimi25ExperimentType' added
File Changes:
  + 'null2na' function moved to 'SAXhandlers.R' file

Release 1.5.12
API Changes:
  + Constructors and accessors are added for most of the XML elements.

Release 1.5.11
API Changes:
  + 'psimi25Attribute' class is redefined to reflect the originial structure defined in the specification
  + constructors added for: 'typedList', 'psimi25NamesType', 'psimi25Attribute', 'psimi25AttributeListType',
    'psimi25DbReferenceType', 'psimi25XrefType' and 'psimi25AvailabilityType'
  + internal accessors added to organize the access of data slots, like 'name', 'nameAc', 'iValue' and 'id'
Documentation Changes:
  + Add 'psimi25Attribute-class.Rd' to accomodate the helps added recently. This is temporary.

Release 1.5.10
API Changes:
  + 'typedList' class and constructor method is exported, with documentation
File Changes:
  + 'handlers.R' is renamed as 'SAXhandler.R' to make the group clearer.
  + 'funcsAnnotation.R' is added to accomodate annotation functions
  + 'units' directory is added under 'tests' to accomodate RUnit scripts (not implemented yet)

Release 1.5.9
API Changes:
  + 'importClassesFrom' and 'importMethodsFrom' directives replace single 'import' in NAMESPACE for Biobase. Other imports will be fixed soon.
File Changes:
  + 'genericFunc.R' are renamed into 'AllGenerics.R' according to the convention
  + Add 'Makefile' to simplify check/install/distribution
Bug fix:
  + 'psimi25InferredInteractionAtomParticipantAtom' fixes wrong-spellt class name

Release 1.5.8
API Changes:
  + Classes supporting ALL features of PSI-MI 2.5 have been implemented, making preparation for a major update
File Changes:
  + 'classDefs.R' are renamed into 'AllClasses.R' according to the convention
Known Issues:
  + There warnings by checking, will be changed soon.