PhyDE2 subversion repository

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    Date Author Revision Message  
  2/5/21 12:19 PM VirginiaBoehm 157 Removed edit classes which are now obsolete after LibrAlign was updated to have the edits instead. [more]
  2/4/21 4:06 PM VirginiaBoehm 156 Edited the way consensus sequences were loaded in OpenAction as it caused many bugs. This solution is not optimal but it works.
Made a small bug fix in ReverseComplementWithPherogramAction.
  1/7/21 3:45 PM VirginiaBoehm 155 Added an Editrecorder.endEdit() and Editrecorder.startEdit() to every action so that user edits can be undone or redone.
Moved PherogramProviderByURL, PherogramEventReader and PherogramReference to LibrAlign.
Updated references to the moved classes.
Removed pherogram-related name spaces and predicates from IOConstants and ReadWriteParameterConstants.
  12/17/20 3:17 PM BenStoever 154 TODO added to PherogramEventReader.
New pherogram shift list translator from LibrAlign used in AbstractFileAction.
  12/10/20 3:08 PM VirginiaBoehm 153 Solved a bug in OpenAction where a saved alignment with a pherogram would lose the pherogram once it's loaded again. (By adding the alignment id to the sequence id)
Changed the position of endEdit() in AddSequenceAction so that no possible edits are made during the loading of a pherogram.
  12/2/20 2:45 PM VirginiaBoehm 152 Fixed Pherogram loading bug in AddSequenceAction by creating the PherogramReference after adding all tokens to the alignment model. [more]
  8/19/20 11:08 AM KatharinaSchulze 151 RefreshConsensusSequenceAction was deleted because it is no longer needed. RefreshAll- and RefreshSelectedConsnesusSequences were edited. [more]
  8/19/20 10:30 AM KatharinaSchulze 150 In DefaultPhyde2AlignemntModel the method AddConsensus() has been renamed to AddContigReference().
Temporary workaround in AlignmentTypeDataModel.
For reading and writing consensus sequences and contig references the PhyDEAlignmentDataAdapter has been converted to AbstractPhyde2AlignmentDataAdapter. Furthermore, SingleReadContigAlignmentDataAdapter, DefaultAlignmentDataAdapter and ConsensusAlignmentDataAdapter have been added.
ConsensusSequenceDataModel and ContigReferenceDataModel were created. ConsensusSequenceDataReader and ContigReferenceDataReader were created and added to PhyDEAlignmentDataReader. In PhyDEDocumentDataAdapter it was ensured that contig models are written first, because they can be referenced by the default model. PREDICATE_HAS_CONTIG_REFERENCE was added to IOConstants and ReadWriteParameterConstants. OpenAction was edited. For reading the sequenceIDs must be passed correctly, this is not yet done in (revision_1146 AlignmentModelEventReader line 337).
  8/19/20 9:32 AM KatharinaSchulze 149 info.bioinfweb.phyde2.test was created.
ExtendGereratedCosenusSequenceEditTest and GenerateConsensusSequenceEditTest were added.
  8/7/20 10:46 AM VirginiaBoehm 148 Removed everything to do with the consensus model in ReverseComplementWithPherogramAction since it is not needed. [more]
  8/7/20 10:30 AM KatharinaSchulze 147 PhyDEDocumentDataAdapter now writes contig alignments before default alignments. [more]
  8/5/20 2:11 PM VirginiaBoehm 146 Modified RefreshAllConsensusSequenceAction and RefreshConsensusSequenceAction to do what their Edit did and added the use of the EditRecorder to start and end Edits. [more]
  8/5/20 2:05 PM VirginiaBoehm 145 Modified all SequenceActions and PherogramActions (except RefreshActions) to do the same as their respective Edits and to use the EditRecorder to start and end Edits. [more]
  8/5/20 1:28 PM KatharinaSchulze 144 Added ConsensusSequenceModel to the SingleReadContigAlignmentModel constructor. Added ConsensusSequenceModel and its corresponding DataModel to ContigTab.
Added ExtendGeneratedConsensusSequenceEdit/-Action, GenerateConsensusSequenceEdit/-Action.
Added the menu option for ExtendGeneratedConsensusSequenceAction and GenerateConsensusSequenceAction in ActionManagment and MainFrame.
Bug fix (370) in RefreshConsensusSequenceEdit.
RefreshConsensusSequenceAction was renamed to RefreshSelectedConsensusSequenceAction; Minor changes in RefressAll- and RefreshSelectedConsensusSequenceAction
  8/5/20 11:01 AM VirginiaBoehm 143 Modified all CharSetActions to do what their respective Edits were doing.
Added the usage of the EditRecorder for all of them.
  8/5/20 10:53 AM VirginiaBoehm 142 Removed the SwingUndoAlignmentModel from PhyDE2AlignmentModel and removed all uses of getUnderlyingModel() from it.
Added the EditRecorder to PhyDE2AlignmentModel and added with it the UndoAlignmentListener in setAlignment().
  7/21/20 12:36 PM KatharinaSchulze 141 RefreshAllConsensusSequencesAktion was added. Therefore, it is possible to refresh all sequences that are linked to a consensus sequence at the same time. RefreshAllConsensusSequencesAktion uses the same Edit as RefreshConsensusSequencesAktion -> RefreshConsensusSequencesEdit.
Changed name "Refresh consensus sequence" to "Refresh selected consensus sequences" in RefreshConsensusSequenceAction
Added the menu option for RefreshAllConsensusSequencesAktion in ActionManagment and MainFrame.
  7/17/20 1:16 PM VirginiaBoehm 140 Modified CharacterStateSetChooserAction to take conflicting Tokens into account and to replace them.
Added method to CharacterStateSetChooserAction which creates a new alignment with the new tokenSet. Not finished.
  7/15/20 12:33 PM KatharinaSchulze 139 Changed design of AddContigAlignment16 and AddContigAlignment22 ToolBar buttons [more]
  7/14/20 2:07 PM KatharinaSchulze 138 Linked AddContigAlignmentAction, AddDefaultPhyDE2AlignmentAction and DeleteAlignmentAction to TooBarPanel and added respective icon images. [more]
  7/6/20 3:32 PM VirginiaBoehm 137 Added implementation for CharacterStateSetChooser (PhyDE2CharacterStateSetChooser).
Added CharacterStateSetChooserDialog for choosing a new CharacterStateSet.
Added CharacterStateSetChooserAction for changing the CharacterStateSet after loading the alignment (it does not work yet).
Added the menu option for CharacterStateSetChooserAction in ActionManagment and MainFrame.
  1/16/20 4:41 PM BenStoever 136 Adjustments to new bound parameter for token edits in LibrAlign.
Removed unused imports.
  1/7/20 4:22 PM BenStoever 135 pherogramModelMap removed from SingleReadContigAlignmentModel. New data structure for data models from LibrAlign is now used.
Bug fix: Creation of data area factory moved from ContigTab to Tab to be available when setting the initial model.
Debug outputs removed from PhyDE2DataAreaFactory.
  1/7/20 8:46 AM BenStoever 134 PhyDE2DataAreaFactory added that replaced pherogram area creation in application code. (Model adjustments to links between alignment and data models still ongoing.)
AddSequenceEdit now allows sequences without attached pherograms.
Minor changes and simplifications.
  12/20/19 1:28 PM BenStoever 133 Bug fix: AddSequenceEdit now created PherogramReference after the sequenceID is known.
Minor changes.
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