ref #6913 Remove pherogram view
ref #6913 Remove alignment editor
fix #7009 Replace part descriptor IDs in open handler with constants
ref #6925 Set conversation and cdmEntitySession to null for dispose
ref #6913 Remove IEditorInput dependency from alignment editor input
ref #6925 Rename utility getter methods
ref #6925 Migrate getActivePart()
ref #6902 migrate alignment editor and pherogram view
Bug fix in reverse complementing uncut read sequences.
Change FileDialog to directoy dialog
ref #6597 Re-enable molecular handlers
ref #6902 migrate remaining context menu items for molecular module
ref #6902 Migrate sequence editing menu item
ref #6596 Refactored selection handling to support e3 and e4 parts
ref #4611 Fix Messages.java bundle path
ref #4611 Fix l10n property path
ref #4611 Restructure string externalization for taxeditor.molecular
ref #4611 i18n for molecular plugin
Saving files before refreshing line endings
Merge branch 'develop' into LibrAlign
ref #6190 removing svn property place holder in first line of code - java files
Additional strings externalized in molecular plugin.
Wizard for exporting single read alignments now warns and prompts if files are overwritten.
Bug fix: Changes in the format selection in the wizard now trigger validation again.
ExportSingleReadAlignmentWizardModel uses format list instead of map again.
Support for parameters to export only single reads or only consensus implemented.
Missing files from last commit added.
Export single read alignment wizard separated into two pages.
Option to elongate sequences added.
Application information parameters of JPhyloIO set.
Exported single read sequences are now filled up with gaps. (Will be dependent on a parameter in the future.)
Texts in ExportSequenceToFileHandler extzernalized and translated.
Strings in ExportSingleReadAlignmentWizardPage externalized and translated.
Fixes in ExportSingleReadAlignmentWizardPage layout.
Default values added to ExportSingleReadAlignmentWizardModel.
Updating values after model binding in ExportSingleReadAlignmentWizardPage implemented.
Export single read alignment wizard validation refactored and extended.
Some German translations in molecular plug-in added.
Intermediate commit in implementing wizard validation (before moving to MultiValidator).
Plug-in dependencies added to molecular.
ExportSingleReadAlignmentWizard now exposes whole format info object.
FileDialog added to ExportSingleReadAlignmentWizardPage.
Missing dependency Apache commons.lang added to molecular.lib.
Single read alignment export feature now makes use of wizard. (Selecting which sequences to export is not yet supported.)
New JPhyloIO package now exported by molecular.lib.
SingleReadAlignmentPredicates renamed to SingleReadAlignmentRDFXMLConstants.
Pherogram alignment shifts are now written to single read export unsing a custom ObjectTranslator implementation.
ExportSingleReadAlignmentWizardPage now allows to select output file and
CDMSequenceMatrixAdapter now exports sequence metadata.
Bug fix: CDMSequenceMatrixAdapter now does not create CharacterSetIntervalEvents if the alignment has no columns.
Merge branch 'LibrAlign' of https://dev.e-taxonomy.eu/git/taxeditor into LibrAlign
Plugin molecular.lib refactored to use direct project dependencies. This should not be merged into trunk, since this is only for development state. (Currently the trunk is anyway already using different Maven dependencies.)
Adjustments to recent changes in JPhyloIO.
fix #5759 remove all switches for remoting and standalone
Bug fix: CDMSequenceMatrixAdapter now defines valid columns for its character set.
Draft for ExportSingleReadAlignmentWizard added.
Molecular plugin adjusted to recent changes in JPhyloIO.
Debug outputs removed.
Token set added to CDMSequenceMatrixAdapter.
Debug output added to ExportSequenceToFileHandler.
Bug fix in CDMSequenceMatrixAdapter.
Test case for SequenceIDIterator added.
Context menu entry for exporting alignment files added.
ExportSingleReadAlignmentHandler renamed to ExportSequenceToFileHandler.
Exported packages of molecular plugin updated.
Basic export functionality for direct export of consensus sequence alignments implemented (untested).
Fix dependencies and model update
Initial version of ExportSingleReadAlignmentWizardPage added.
#5300 Implement remoting in Alignment Editor
Implementation of AlignmentEditorPasteHandler changed.
Paste action for AlignmentEditor added.
Shared functionality moved from AlignmentEditorCopyHandler to AlignmentModelUtils in LibrAlign.
Different LibrAlign model action used in AlignmentEditorCutHandler.
Cut action for AlignmentEditor implemented.
Shared clipboard added to AlignmentEditor. (Should be moved to a global EDITor class in the future.)
Some general methods moved from AlignmentEditor to SWTUtils in bioinfweb.commons.
AlignmentEditorCopyHandler now sets current action status.
Move property tester to editor plugin
AlignmentEditorCopyHandler now offers copying functionality as a static method.
Copying not performed, if no nucleotides are selected.
Moved functionality to be shared from AlignmentEditorCopyHandler to AlignmentEditor.
Initial implementation of AlignmentCopyHandler finished.
Add Copy functionality to AlignmentEditor
Test implementation of Copy action added to AlignmentEditor.
Fixed NPE when loading single reads without attached pherogram.
Merge branch 'LibrAlign' into develop
Fixed NPE when saving an alignment with a read without attached pherogram.
Arranged classes and classpath in accordance to other taxeditor projects.