12/20/18 12:02 PM
||Added getType to both DefaultPhyDE2AlignmentModel and SingleReadContigAlignmentModel. Renamed some variables and methods that used the term document when in reality they referred to one of the PhyDE2AlignmentModels. Also renamed getPherogramModel to getPherogramReference as it returns the reference, not the model.
Labels of alignments are now written and can also be read. Worked on the pherogram-reading function (not yet finished) - added constants and a PherogramEventReader class.
Changed constructors of AlignmentModels - SingleReadContigAlignmentModel now also gets a CharSetModel and can be provided with a consensus model.
Added "Yes to all" and "No to all" options to HandleUnsavedChanges, although "Yes to all" has to be improved as it still refers to tabs/alignments, not to documents.
When loading a file, alignments will now be displayed in the FileContentTreeView.
Moved tabByAlignment from MainFrame to ClosableJTabbedPane. Added the enumerable AlignmentType (for now it only holds DEFAULT and SINGLE_READ_CONTIG) and the AlignmentTypeDataModel that implements DataModel in order to be used for reading (required when implementing AbstractDataModelEventReader, which is done in the new AlignmentTypeDataReader class that stores alignment types).