~ronald-dekker/collatex/darmstadt : changes

~ronald-dekker/collatex/darmstadt » Changes from revision 1048

From Revision 1041 to 1022

Rev	Summary	Authors	Date
1041	moved graphviz server to separate module; housekeeping stuff moved graphviz server to separate module; housekeeping stuff	Gregor Middell	13 years ago
1040	[RHD] Updated ApiController to new CollateX Core API [RHD] Updated ApiController to new CollateX Core API	Ronald Haentjens Dek...	13 years ago
1039	[RHD] Updated alignment template to new CollateX Core API [RHD] Updated alignment template to new CollateX Core API	Ronald Haentjens Dek...	13 years ago
1038	[RHD] Made more transposition use cases work [RHD] Made more transposition use cases work	Ronald Haentjens Dek...	13 years ago
1037	[RHD] Reenabled previously broken example [RHD] Reenabled previously broken example	Ronald Haentjens Dek...	13 years ago
1036	[RHD] [RHD] - Fixed broken use case with transposition - Cleaned up Sequence class - Cleaned up Tranposition2 class - Renamed IRow.rowToString() method to just toString() - Cleaned up alignment unit tests; placed all the relevant tests in the same package and placed all the old tests in a separate package	Ronald Haentjens Dek...	13 years ago
1035	[RHD] Cleanup: removed IWitness.createPhrase method [RHD] Cleanup: removed IWitness.createPhrase method	Ronald Haentjens Dek...	13 years ago
1034	[RHD] Cleanup: removed addVertex method from IColumn interfa... [RHD] Cleanup: removed addVertex method from IColumn interface	Ronald Haentjens Dek...	13 years ago
1033	[RHD] [RHD] - Merged IColumn and IInternalColumn interfaces into one - Removed isMatch(base, witness) method from IColumn interface	Ronald Haentjens Dek...	13 years ago
1032	[RHD] Updated web examples to new API of the CollateX core [RHD] Updated web examples to new API of the CollateX core	Ronald Haentjens Dek...	13 years ago
1031	[RHD] [RHD] - Extracted interfaces IApparatus and IApparatusEntry - Moved ITokenIndex interface to nonpublic.alignment package - Moved joined graph interfaces to nonpublic.joined_graph package	Ronald Haentjens Dek...	13 years ago
1030	[RHD] [RHD] - More API cleanups: - Removed getPosition() method from ICell interface - Removed getPosition() method from IColumn interface - Removed getWitnessForSigil method from IVariantGraphVertex interface - Removed containsWitness(sigil) method from IVariantGraphVertex interface - Deleted IAlignmentTableVisitor interface... no references anymore - Deleted IInputPlugin interface... no references anymore	Ronald Haentjens Dek...	13 years ago
1029	[RHD] [RHD] - IVariantGraphVertex interface: added containsWitness(IWitness) method - IColumn: replaced containsWitness(sigil) method with containsWitness(witness) - IColumn: replaced getSigla() method with getWitnesses() method - BaseAlignmentTable: cleaned up class	Ronald Haentjens Dek...	13 years ago
1028	[RHD] [RHD] - Removed getRepeatedTokens() method from ITokenContainer interface - Moved implementation from VariantGraph2 and Witness classes to TokenIndexUtil class - Removed implementation from CyclicVariantGraph - Removed obsolete and empty IWitnessIndex interface - Moved getRepeatedTokens() method tests to specific container indexing tests	Ronald Haentjens Dek...	13 years ago
1027	[RHD] [RHD] - Removed method getTokenIndex from TokenContainer interface - Removed implementation from VariantGraph, Witness, CyclicVariantGraph - Removed duplicate VariantGraphIndexTest	Ronald Haentjens Dek...	13 years ago
1026	[RHD] Removed getPhrasesWithMultiples method from CollateXEn... [RHD] Removed getPhrasesWithMultiples method from CollateXEngine (Superseded by VariantGraphIndexer).	Ronald Haentjens Dek...	13 years ago
1025	[RHD] [RHD] - Cleanup: Remove method getTokensWithMultiples from CollateXEngine (Superseded by VariantGraph.getRepeatedTokens)	Ronald Haentjens Dek...	13 years ago
1024	[RHD] Removed obsolete methods from IColumn interface. [RHD] Removed obsolete methods from IColumn interface.	Ronald Haentjens Dek...	13 years ago
1023	[RHD] [RHD] - Removed duplication between VariantGraphIndex and WitnessIndex - Made WitnessIndex extends AbstractTokenIndex - Removed obsolete WitnessIndex0 class - Removed createWitnessIndex method from CollateXEngine (should not be public) - Reorganized indexing tests - Moved AlternativeTokenIndexMatcher and AlternativeWitnessIndex to todo package - Removed obsolete TokenColumn class	Ronald Haentjens Dek...	13 years ago
1022	[RHD] - Extracted AbstractTokenIndex class from VariantGraph... [RHD] - Extracted AbstractTokenIndex class from VariantGraphIndex class - Changed VariantGraphIndex factory method into standard constructor	Ronald Haentjens Dek...	13 years ago

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