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

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
format.

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

Conflicts:¶

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

eu.etaxonomy.taxeditor/rcp.target¶

Merge branch 'develop' into LibrAlign

Conflicts:¶

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

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.

Updated version in pom / project files to taxeditor version : 4.4.0-SNAPSHOT and cdmlib version : 4.4.0-SNAPSHOT

fix #5759 remove all switches for remoting and standalone

Updated version in pom / project files to taxeditor version : 4.3.0-SNAPSHOT and cdmlib version : 4.3.0-SNAPSHOT

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.

Solved TODO removed.

Merge branch 'develop' into LibrAlign

Updated version in pom / project files to taxeditor version : 4.2.0-SNAPSHOT and cdmlib version : 4.2.0-SNAPSHOT

Merge branch 'develop' into LibrAlign

Updated version in pom / project files to taxeditor version : 4.1.0-SNAPSHOT and cdmlib version : 4.1.0-SNAPSHOT

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

Fix dependencies and model update

Initial version of ExportSingleReadAlignmentWizardPage added.

Merge branch 'develop' into LibrAlign

I18n

Updated version in pom / project files to taxeditor version : 4.0.0-SNAPSHOT and cdmlib version : 4.0.0-SNAPSHOT

Remove unused dependencies from MANIFEST.MF #5530

Refactor SingleReadContextMenu #5406

• split into separate commands, property testers and menu items
• adjusted molecular context menu entries to be grouped together with singler read entries

Structure derivative editor context menu (#5406)

• fixed context menu bug where some items would only show up every second time (menuManager.setRemoveAllWhenShown(true); //<- was the trick)

Updated version in pom / project files to taxeditor version : 3.13.0-SNAPSHOT and cdmlib version : 3.13.0-SNAPSHOT

Update eclipse compile / runtime to JavaSE-1.7

Conflicts:
eu.etaxonomy.taxeditor.application/.classpath

Revert "Updated version in pom / project files to taxeditor version : 3.13.0-SNAPSHOT and cdmlib version : 3.13.0-SNAPSHOT"

This reverts commit 9524fa3910c8335a6cbcb656f9aacaca01a3f5ca.

Updated version in pom / project files to taxeditor version : 3.13.0-SNAPSHOT and cdmlib version : 3.13.0-SNAPSHOT

#5300 Implement remoting in Alignment Editor

Fix versions

Revert project versions to 3.11.0-SNAPSHOT

Updated version in pom / project files to taxeditor version : 3.12.0-SNAPSHOT and cdmlib version : 3.12.0-SNAPSHOT

updating poms for 3.11.0-SNAPSHOT development

Revert project versions to 3.10.0-SNAPSHOT

Updated version in pom / project files to taxeditor version : 3.11.0-SNAPSHOT and cdmlib version : 3.11.0-SNAPSHOT

updating poms for 3.10.0-SNAPSHOT development

Revert project versions to 3.9.0-SNAPSHOT

Updated version in pom / project files to taxeditor version : 3.10.0-SNAPSHOT and cdmlib version : 3.10.0-SNAPSHOT

updating poms for 3.9.0-SNAPSHOT development

Revert project versions to 3.8.0-SNAPSHOT

Updated version in pom / project files to taxeditor version : 3.9.0-SNAPSHOT and cdmlib version : 3.9.0-SNAPSHOT

Revert "Updated version in pom / project files to taxeditor version : 3.9.0-SNAPSHOT and cdmlib version : 3.9.0-SNAPSHOT"

This reverts commit 7ed2ce1e9eca6a9dd72c740e72efdcd6ef1135c9.

Revert "Revert project versions to 3.8.0-SNAPSHOT"

This reverts commit e8268306693f047beef36ce53524adc00946cf74.

Revert project versions to 3.8.0-SNAPSHOT

Updated version in pom / project files to taxeditor version : 3.9.0-SNAPSHOT and cdmlib version : 3.9.0-SNAPSHOT

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.

Merge branch 'develop' into LibrAlign

Correct config for molecular plugin

Minor changes.

Fixed NPE when loading single reads without attached pherogram.

Added missing molecular plugin projects

Remove unused folder

Rename aggregator to lib

Integrate molecular plugins

Merge branch 'LibrAlign' into develop

Fixed NPE when saving an alignment with a read without attached pherogram.

Updated version due to trunk merge

Fix menu contributions

Dependency refactoring

Arranged classes and classpath in accordance to other taxeditor projects.

• added handler to exported packages

• moved "Add..." menu item to the bottom to avoid other items not to be drawn

• fixed dependencies

Missing LibrAlign BioJava1 dependency added to molecular plugin project.

Initial import of plugin files