LibrAlign subversion repository

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    Date Author Revision Message  
  2/4/21 4:01 PM VirginiaBoehm 1173 Changed the ShiftListObjectTranslator to work with Lists (Working with arrays caused bugs).
Added a system-out in AlignmentDataReader to investigate the bug in which the written shiftlist of saved Pherograms caused no alignment to be loaded.
  2/4/21 3:55 PM VirginiaBoehm 1172 Called the method revalidate() in afterTokenChange() in class AlignmentArea to fix problems with the GUI (for example problems with horizontal scroll).
Fixed a small problem in PherogramAreaModel which caused the editRecorder to always be null.
  1/28/21 1:43 PM BenStoever 1171 Bug fix in ShiftListObjectTranslator: Avoid consuming all future events after reading the metadata value. [more]
  1/7/21 3:33 PM VirginiaBoehm 1170 Moved PherogramEventReader from PhyDE2 to and named it PherogramEventReaderIO.
Added needed name spaces and predicates to PherogramIOConstants.
Added the class PherogramIOUtils which writes pherogram-related information.
Edited writeXMLRepresentation() in ShiftListObjectTranslator to convert the shift list into the needed array.
  1/7/21 3:25 PM VirginiaBoehm 1169 Added a constructor to PherogramAreaModel which has an additional shift change list parameter.
Added interface PherogramProviderByURL.
Moved PherogramReference from PhyDE2 to librAlign.core.
  1/7/21 3:22 PM VirginiaBoehm 1168 Relocated and renamed PherogramProviderByURL to BioJavaProviderByURL and put it in libralign.biojava1. [more]
  12/17/20 3:16 PM BenStoever 1167 Data type constant added to PherogramIOConstants. [more]
  12/17/20 3:04 PM BenStoever 1166 PherogramIOConstants and ShiftListObjectTranslator added. [more]
  12/16/20 12:35 PM VirginiaBoehm 1165 Added a new case for AMINO_ACID CharacterStateSetTypes in BioPolymerCharAlignmentModelFactory and changed the default case to create a Nucleotide tokenSet. DISCRETE and CONTINUOUS still need their own case too.
  11/25/20 10:22 AM VirginiaBoehm 1164 Added new AddSequence methods with an index parameter to AlignmentModel and implemented them in AbstractUndecoratedAlignmentModel and AbstractAlignmentModelDecorator.
Added the new AddSequence methods to SequenceAccessAlignmentModel as well and implemented them in AbstractUnmodifyableAlignmentModel.
Added the index parameter to SequenceChangeEvent.
Edited AlignmentModelAddSequenceEdit and AlignmentModelRemoveSequenceEdit to use the index parameter in the methods.
  11/25/20 10:10 AM VirginiaBoehm 1163 Added method createNewEmptySequence to BioJava3SequenceAlignmentModel. Method is still empty. [more]
  8/19/20 9:23 AM KatharinaSchulze 1162 TokenChangeEvent and AbstractListAlignmentModel were edited. Now the method setTokenAt() works properly. [more]
  8/7/20 10:44 AM VirginiaBoehm 1161 Added check if the listener is null in PherogramComponentModel.addModelListener(). If it is null then a NullPointerException is thrown.
Switched the order of creating the listener and setting the model in the ModelBasedDataArea() constructor to solve a bug.
  8/5/20 10:17 AM VirginiaBoehm 1160 Added the interface AlignmentModelEdit and renamed the abstract class AlignmentModelEdit to AbstractAlignmentModelEdit.
Made DataModelEdit interface inherit from AlignmentModelEdit.
Deleted DataModelListener as it was not needed anymore.
Added method hasUndoListener() to DataModel and implemented it in CharSetDataModel and PherogramAreaModel.
Added the field sequenceIDs to PherogramProviderChangeEvent and added a parameter to PherogramComponentModel.reverseComplement() and tofirePherogramProviderChanged().
Added a lot of fields and reverseComplement() to PherogramProviderChangeEdit.
Replaced UndoManager with AccessibleUndoManager in EditRecorder.

  8/3/20 11:03 AM VirginiaBoehm 1159 Added DataModelEdit as an interface and implemented it in AbstractDataModelEdit.
Made all CharSetEdits and DataModelEdits inherit from AbstractDataModelEdit.
Added EditRecorder field and getEditRecorder() to PherogramAreaModel.
  8/2/20 11:52 AM KatharinaSchulze 1158 Minor changes in AlignemntModelUtils.sequencesEqual(). [more]
  8/2/20 11:48 AM KatharinaSchulze 1157 Minor changes in AlignmentModelUtilsTest.test_sequencesEquals(). [more]
  7/31/20 10:35 AM VirginiaBoehm 1156 Made DataModel.ensureUndoListener() a default method and edited the implementations in CharSetDataModel and PherogramAreaModel.
Initialized the EditRecorder in the constructor of CharSetDataModel and PherogramAreaModel.
Initialized the UndoManager in the constructor of EditRecorder.
Added the possibility of deleted content being null to AlignmentModelREmoveSequenceEdit.
  7/29/20 12:59 PM VirginiaBoehm 1155 Modified createUndoListener(), removeUndoListener() and ensureUndoListener() in DataModel.
Removed implementation of createUndoListener(), removeUndoListener() and ensureUndoListener() in AbstractDataModel.
Modified the implementation of createUndoListener(), removeUndoListener() and ensureUndoListener() in PherogramAreaModel and CharSetDataModel and added the field undoListener.
Updated AlignmentModelUndoListener to work with these new changes.
Added DataModelListener and CharSetModelEdit now inherits from it.
All CharSetEdits had to be slightly modified due to that.
  7/27/20 2:16 PM VirginiaBoehm 1154 Added DataModelAddRemoveEdit.
Relocated DataModelAddEdit and DataModelRemoveEdit to libralign/model/undo/alignment/data.
DataModelAddEdit and DataModelRemoveEdit inherit now from DataModelAddRemoveEdit.
Removed DataModelEdit.addDataModel() and DataModelEdit.removeDataModel().
  7/27/20 2:08 PM VirginiaBoehm 1153 Added generic parameters to EditRecorder.addSubedit().
Modified CharSetDataModelUndoListener, AlignmentModelUndoListener and PherogramModelUndoListener to work with above changes.
  7/24/20 1:11 PM VirginiaBoehm 1152 Added DataModelAddEdit and DataModelRemoveEdit.
Added methods addDataModel() and removeDataModel() to DataModelEdit.
Implemented AlignmentModelUndoListener.afterDataModelChange().
Added PherogramModelProviderChangeEdit.
Implemented PherogramModelUndolistener.
Added the methods createUndoListener(), ensureUndoListener() and removeUndoListener() to DataModel.
Implemented these methods in AbstractDataModel, PherogramAreaModel and CharSetDataModel.
  7/23/20 1:54 PM VirginiaBoehm 1151 Reverted adding new properties to pherogram model classes. [more]
  7/23/20 12:47 PM KatharinaSchulze 1150 Added AlignemntModelUtils.sequencesEqual(). [more]
  7/23/20 12:45 PM KatharinaSchulze 1149 Added AlignmentModelUtilsTest.test_sequenceEquals().
Test classes adjusted to recent changes in core module.
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The development of LibrAlign was partly funded by the German Research Foundation (DFG) in this project.

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