~gregor-middell/collatex/1.0development

From Revision 1030 to 1011

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Rev		Summary	Authors	Date	Diff	Files
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 [RHD] Removed getPhrasesWithMultiples method from CollateXEngine (Superseded by VariantGraphIndexer).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1025		[RHD] [RHD] - Cleanup: Remove method getTokensWithMultiples from CollateXEngine (Superseded by VariantGraph.getRepeatedTokens)	Ronald Haentjens Dek...	13 years ago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
1021		[RHD] Removed IToken.getSigil() [RHD] Removed IToken.getSigil()	Ronald Haentjens Dek...	13 years ago
1020		[RHD] Fixed test [RHD] Fixed test	Ronald Haentjens Dek...	13 years ago
1019		[RHD] [RHD] Changes to adapt to changes in the CollateX core	Ronald Haentjens Dek...	13 years ago
1018		[RHD] [RHD] - Reverted API change ITokenNormalizer; With previous version it is easier to stack function on top of eachother. - Reintroduced a simple NormalizedToken class in input package	Ronald Haentjens Dek...	13 years ago
1017		[RHD] [RHD] - Removed sigil parameter in constructor of NullToken class - Removed IPhrase.getSigil() method	Ronald Haentjens Dek...	13 years ago
1016		[RHD] [RHD] - Removed getPosition() from INormalizedToken interface - Moved NormalizedToken class from input to container.witness package - Renamed NormalizedToken class to WitnessToken - Renamed NormalizedWitness class to Witness - Moved NullToken class from legacy to input package	Ronald Haentjens Dek...	13 years ago
1015		[RHD] [RHD] - Refactoring: one step closer to removing getPosition() method - Refactoring: pushed getPosition() method down from IToken to INormalizedToken interface - Refactoring: ITokenNormalizer function now return the Normalized String instead of the NormalizedToken making it easier for WitnessBuilders to customize the buildprocess while reusing TokenNormalizers. - Refactoring: use the WitnessBuilder class in the CollateXEngine	Ronald Haentjens Dek...	13 years ago
1014		[RHD] [RHD] - Moved getLongestPath() method from VariantGraph2 class to VariantGraphUtil class. - Refactored: Changed return type of getPath(Witness) to edges instead of vertices - Refactored: used graph.getTokens(IWitness) instead of graph.getPath(IWitness) in VariantGraphIndex; General cleanup of VariantGraphIndex class.	Ronald Haentjens Dek...	13 years ago
1013		[RHD] [RHD] - Cleaned up: VariantGraph2 and VariantGraphAligner class;  - Removed obsolete factory method in VariantGraph2 class; - Moved remarked optimalisation code from VariantGraph2 to VariantGraphAligner class	Ronald Haentjens Dek...	13 years ago
1012		[RHD] [RHD] - Refactoring: Extracted Analyzer class from VariantGraphAligner and CollateXEngine classes. - Refactoring: Added getGraph() and getWitness() methods to IAlignment2 interface. - Refactoring: Made constructor on SequenceDetection2 class work with just an IAlignment2 object.	Ronald Haentjens Dek...	13 years ago
1011		[RHD] [RHD] - Refactoring: VariantGraphAligner: Inlined VariantGraph2Creator class into the VariantGraphAligner class. - VariantGraph2 class: Removed factory method and removed addNewVertex and addNewEdge methods. - CollateXEngine: Removed dependency on VG2Creator class, used createAligner() method instead	Ronald Haentjens Dek...	13 years ago

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