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.

Messages edited.
Support for parameters to export only single reads or only consensus implemented.
JavaDoc extended.

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.

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.

Merge branch 'LibrAlign' of https://dev.e-taxonomy.eu/git/taxeditor into LibrAlign

Conflicts:¶

eu.etaxonomy.taxeditor.molecular.lib/.classpath¶

eu.etaxonomy.taxeditor/rcp.target¶

Debug outputs removed.
Token set added to CDMSequenceMatrixAdapter.

Debug output added to ExportSequenceToFileHandler.
Bug fix in CDMSequenceMatrixAdapter.
Typo correction.

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

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.

AbstractFocusedAlignmentAreaHandler added.

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

Merge branch 'LibrAlign' into develop

Dependency refactoring

Arranged classes and classpath in accordance to other taxeditor projects.