PhyDE2 subversion repository

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    Date Author Revision Message  
  12/20/18 3:54 PM BenStoever 128 Minor changes. [more]
  12/20/18 3:00 PM SarahvanGroen 127 ContigReferenceChangeEvent, SequenceReferenceChangeEvent, DeleteSequencesEdit, ContigReferenceTreeNode, PherogramReferenceTreeNode added.
The FileContentTreeView can now handle changes on sequences, so that the nodes are displayed/deleted when adding/removing a sequence that has a pherogram or a contig as reference. PherogramReferenceTreeNode, ContigReferenceTreeNode, SequenceReferenceChangeEvent and ContigReferenceChangeEvent have been implemented therefore.
The AbstractAddDeleteSequenceEdit has been deleted, because it is not useful anymore, that DeleteSequenceEdit and AddSequenceEdit use the same parent class. The DeleteSequencesEdit has to be implemented during further development.
Minor changes.
[more]
  12/20/18 2:01 PM LaraKoesters 126 Added necessary methods to PhyDE2AlignmentDataAdapter for adding the consensus sequence. Added comments to cases where handleUnsavedChanges is used (reference to ticket ID). [more]
  12/20/18 1:55 PM LaraKoesters 125 Now canceling the handleUnsavedChanges-dialog when exiting the program works as well as not saving an alignment. [more]
  12/20/18 12:02 PM LaraKoesters 124 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).
[more]
  12/19/18 4:42 PM SarahvanGroen 123 CutLeftAction and CutRightAction moved to package info.bioinfweb.phyde2.gui.actions.edit.
CutLeftEdit and CutRightEdit implemented.
Minor changes.
[more]
  12/17/18 5:05 PM SarahvanGroen 122 Reverse complement is now possible for sequences with pherograms attached (special cases still produce errors).
Minor changes.
[more]
  12/17/18 10:25 AM LaraKoesters 121 [more]
  12/16/18 3:23 PM LaraKoesters 120 The treeView in the ExportDialog now only shows rows up to the level of the alignments (pherograms, etc. are not visible anymore). Furthermore, the treeView-class was renamed to SelectForExportTreeView. When exiting the program, selecting cancel in the handleUnsavedChanged-dialog now cancels the entire exiting process. [more]
  12/16/18 1:52 PM LaraKoesters 119 Added a cancel button to handleUnsavedChanges. Added a ClosableJTabbedPane class, which contains methods for adding close buttons to tabs and also for getting the tab at a certain position (instead of the component).
Additionally, written files will now include metadata for contigs such as information about pherograms. Minor changes (i.e. renaming one of the dialogs, putting the dialogs in front of their owner) were included.
[more]
  12/14/18 4:21 PM SarahvanGroen 118 It is now possible to refresh the sequence that has a reference to a contig. [more]
  12/13/18 7:26 PM SarahvanGroen 117 RefreshConsensusSequenceAction and RefreshConsensusSequenceEdit have been implemented to give the user the possibility to refresh those sequences that have been created from the consensus sequence of a contig. Implementation not finished. [more]
  12/13/18 2:02 PM SarahvanGroen 116 AddSequenceDialog and SelectContigView created. The SelectContigView creates a tree, where all Documents are shown, that contain a contig alignment (the contigs are displayed as well). The AddSequenceDialog contains an instance of the SelectContigView, so that the user optional can select a contig in the tree . The consensus sequence of the contig is then used to build the new sequence in the alignment. [more]
  12/12/18 1:20 PM SarahvanGroen 115 New property consensusSequenceID added to SingleReadContigAlignmentModel.
[more]
  12/12/18 1:17 PM LaraKoesters 114 Bug fix: Couldn't load pherograms from local files before. PhyDE now generates correct URL for local files. [more]
  12/11/18 4:36 PM LaraKoesters 113 Export function now creates a PhyDEDocumentDataAdapter that holds AlignmentAdapters for each of the selected alignments. Also changed the name of the document in the FileContentTreeView to the last part of the path. [more]
  12/11/18 4:29 PM SarahvanGroen 112 Minor changes. [more]
  12/11/18 4:15 PM SarahvanGroen 111 Minor changes.
Double click on pherogram in tree view now also opens the tab (contig) where the pherogram belongs to.
[more]
  12/11/18 2:54 PM LaraKoesters 110 Eliminated error when using the text field in ExportDialog instead of the JFileChooser. [more]
  12/11/18 2:24 PM SarahvanGroen 109 A new class PherogramProviderByURL has been implemented. When adding a pherogram to a sequence the class checks if there is already a PherogramProvider for the specific used URL and returns that. If there is no PherogramProvider for that specific URL the PherogramProvider is created and returned. The returned PherogramProvider is now used in AddSequenceAction to create the PherogramModel.
Minor changes.
[more]
  12/11/18 12:50 PM SarahvanGroen 108 When creating a PhyDE2AlignmentModel it is now necessary to pass the Document the PhyDE2AlignmentModel belongs to. So The PhyDE2AlignmentModel now has a Document as property.
FileContentTreeView now has a ChangeListener of the DocumentList, so that it registers changes in the DocumentList. When a new Document is added to the List, it gets a Node in the TreeView.
The getNewDocument() method in MainFrame has been removed. Instead of that a method getSelectedDocument() has been implemented, that gives the selected Document in the FileContentTreeView, when the Documents itself or any child of it is selected.
[more]
  12/11/18 12:17 PM LaraKoesters 107 Updated the layout of ExportDialog. JFileChooser is now always on top and the JTree fills up the center of the dialog window. Also added the constants for the upcoming read/write function that will include contigs. [more]
  12/10/18 12:58 PM SarahvanGroen 106 PherogramReference added. It contains the PherogramAreaModel and the URL. SingleReadContigAlignmentModel now contains a list with SequenceID and PherogramReference (instead of PherogramAreaModel). All classes that have been using the list before have been adapted.
The documentList in MainFrame is now a ObservableList, where ListChangeListeners can be registered. The FileContentTreeView registers a ListChangeListener, to get informed about changes in the list.
[more]
  12/9/18 6:19 PM LaraKoesters 105 When exporting a file, a new export dialog will show up, with an extra file chooser that can be opened. Format choice influences the number of alignments one can choose to export. Alignments are chosen by ticking alignments in a tree similar to the FileContentTreeView in the main window. [more]
  12/9/18 1:00 PM SarahvanGroen 104 When adding a pherogram to a contig this will now be shown in the tree. When double clicking on the pherogram component in the tree the original pherogram will be displayed. [more]
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