| |
|
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.
|
[more] |
| |
|
| |
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. |
[more] |
| |
|
| |
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 LibrAlign.io 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. |
[more] |
| |
|
| |
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. |
[more] |
| |
|
| |
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.
|
[more] |
| |
|
| |
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. |
[more] |
| |
|
| |
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. |
[more] |
| |
|
| |
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.
|
[more] |
| |
|
| |
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. |
[more] |
| |
|
| |
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. |
[more] |
| |
|
| |
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. |
[more] |
| |
|
| |
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(). |
[more] |
| |
|
| |
7/27/20 2:08 PM
|
VirginiaBoehm |
1153 |
Added generic parameters to EditRecorder.addSubedit().
Modified CharSetDataModelUndoListener, AlignmentModelUndoListener and PherogramModelUndoListener to work with above changes.
|
[more] |
| |
|
| |
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. |
[more] |
| |
|
| |
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. |
[more] |
| |
|
|
Next 25
|
|
|
|
