EDIT

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.

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.
Typo correction.

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.

Merge branch 'develop' into LibrAlign

#5300 Implement remoting in Alignment Editor

Merge branch 'develop' into LibrAlign

Implementation of AlignmentEditorPasteHandler changed.

Paste action for AlignmentEditor added.

Shared functionality moved from AlignmentEditorCopyHandler to AlignmentModelUtils in LibrAlign.

JavaDoc extended.
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.)

AbstractFocusedAlignmentAreaHandler added.

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.
AlignmentEditorCopyHandler refactored.

Initial implementation of AlignmentCopyHandler finished.
Minor changes.

Add Copy functionality to AlignmentEditor

Test implementation of Copy action added to AlignmentEditor.

Minor changes.

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.

Dependency refactoring

Arranged classes and classpath in accordance to other taxeditor projects.