Download version 0.6.0 of LibrAlign

You are downloading an older version (0.6.0-1011 beta) of LibrAlign which was released on Feb 13, 2018 12:15:00 PM The latest version can be found here.

License

GNU Lesser General Public License, version 3

LibrAlign is distributed under GNU Lesser General Public License. Copyright (C) 2014-2018 by Ben Stöver. This program is distributed in the hope that it will be useful, but without any warranty; without even the implied warranty of merchantability or fitness for a particular purpose. See the GNU Lesser General Public License for more details.

By downloading LibrAlign you agree with the License. Please read it carefully.

Note that the releases 0.3.0 and earlier were distributed under GNU General Public License instead.

Downloads

Complete download

The complete download contains the classes of all components associated with this release.

Complete binary, sources, docs Download icon LibrAlign complete-0.6.0.zip
Complete binary only Download icon LibrAlign complete-0.6.0-bin.zip

[Browse source codes]    [Browse JavaDoc]

Single component downloads

The following components are associated with version 0.6.0. Components that were updated in this version are shown in bold.

Component Module binary JAR Module sources
Core Download icon core-0.6.0.jar Download icon core-0.6.0-source.zip
Swing Download icon swing-0.5.0.jar Download icon swing-0.5.0-source.zip
SWT Download icon swt-0.6.0.jar Download icon swt-0.6.0-source.zip
IO Download icon io-0.6.0.jar Download icon io-0.6.0-source.zip
BioJava1 Download icon biojava1-0.4.0.jar Download icon biojava1-0.4.0-source.zip

Subversion

Developers can also check out the source codes directly from the subversion repository under https://secure.bioinfweb.info/Code/svn/LibrAlign/trunk/main/.

Maven

Developers can use the following code to add dependencies for the modules of LibrAlign to their Maven project.

Dependencies

<dependency>
    <groupId>info.bioinfweb.libralign</groupId>
    <artifactId>libralign-core</artifactId>
    <version>0.6.0</version>
</dependency>

<dependency>
    <groupId>info.bioinfweb.libralign</groupId>
    <artifactId>libralign-swing</artifactId>
    <version>0.5.0</version>
</dependency>

<dependency>
    <groupId>info.bioinfweb.libralign</groupId>
    <artifactId>libralign-swt</artifactId>
    <version>0.6.0</version>
</dependency>

<dependency>
    <groupId>info.bioinfweb.libralign</groupId>
    <artifactId>libralign-io</artifactId>
    <version>0.6.0</version>
</dependency>

<dependency>
    <groupId>info.bioinfweb.libralign</groupId>
    <artifactId>libralign-biojava1</artifactId>
    <version>0.4.0</version>
</dependency>

Repository

<repository>
    <id>bioinfweb-maven-repo</id>
    <name>bioinfweb repository</name>
    <url>http://bioinfweb.info/MavenRepository/</url>
</repository>

Changes in this version

  • New version of core.
  • New version of io.
  • New version of swt.
  • Dependencies to bioinfweb.commons core, bio and swing updated to version 3.0.0.
  • Dependency to TIC core updated to version 3.0.1.
  • Dependency to JPhyloIO core updated to version 0.5.1.

Core

  • CharSetArea now allows to select character sets with the mouse and programmatically.
  • CharSetDataModel now fires change events and offers listeners.
  • CharSetArea.setModel() added.
  • Overloaded method AlignmentModel.addSequence() added to allow to specify a certain sequence ID.
  • ID property added to AlignmentModel and AbstractAlignmentModel.
  • SequenceIDManager refactored to allow multiple sequence with the same name and sequences without names.
  • TokenPainterList now allows to specify different token painters depending on the actual token set using the new class TokenPainterMap.
  • Property reuseSequenceIDs added to AbstractUndecoratedAlignmentModel.
  • Names in swing undo alignment model implementations adjusted to current standards.
  • AbstractAlignmentModelFactory now optionally uses a default token to replace unknown tokens.
  • BioPolymerCharAlignmentModelFactory now allows to optionally convert lower case tokens.
  • CharacterTokenSet now optionally supports alternative lower case tokens.
  • SequenceArea and TextLabelArea now use fractional text metrics to avoid cutting off texts.
  • AlignmentModelChangeEvent and inherited classes now support cloning (with and without a new source).
  • SequentialAccessIndexTranslator removed from trunk due to bugs. (It may come back in later releases. Use RandomAccessIndexTranslator until then.)
  • AlignmentArea.revalidate() now recalculates label area widths.
  • AlignmentModelChangeListener.afterProviderChanged() renamed to AlignmentModelChangeListener.afterModelChanged().
  • DelegatedAlignmentModelView added.
  • AbstractAlignmentModelAdapter renamed to AbstractBasicAlignmentModelView.
  • Bug fix: SwingInsertRemoveTokensEdit now calculates correct length.
  • Bug fix: SwingUndoAlignmentModel now fires events with itself as the source.
  • Bug fix in SwingRenameSequenceEdit: Undoing sequence renaming now works.
  • Bug fix: Missing implementation for AbstractTokenSet.isMissingInformationToken() added.
  • Bug fix: Correct enumeration type now used in TokenDefinition.
  • Bug fix in AlignmentArea and CharSetArea: New model is now also set, if the contents of the new and old model are equal.

SWT

  • Bug fix: SWTAlignmentLabelArea now resizes its subcomponents correctly.

IO

  • IOTools added.
  • AlignmentModelDataAdapter now also allows empty strings as ID prefixes.
  • CharSetDataAdapter added for writing character set model data.
  • Support for reading and writing characater set colors as metadata added.
  • Convenience constructors added to AlignmentDataReader.
  • AlignmentDataReader.processNextEvent() made protected.
  • AbstractDataModelEventReader refactored to use maps for multiple loading models and for the completed models.
  • AlignmentModelEventReader refactored to consider linked alignment ID of character sets.
  • AlignmentModelEventReader now loads alignment ID.
  • Invalid error output in CharSetEventReader removed.
  • Bug fix: AlignmentModelEventReader now makes use of token set definition.
  • Bug fix: TokenSetAdapter now writes all atomic token before uncertain token, so that uncertain tokens can reference atomic tokens in file formats where necessary.
  • Bug fix in AlignmentModelDataAdapter: Writing sequences with the length 0 is now possible.
  • Bug fix in AlignmentModelDataAdapter: Missing token is now written after atomic tokens.
  • Bug fix: CharSetEventReader.getCurrentCharSet() now returns null if no character set is currently loaded.
  • Bug fix in TokenSetAdapter: No empty character set interval events created anymore.

Other versions

The following links lead you to lists of all releases of the different components.

bioinfweb RSS feed LibrAlign on ResearchGate bioinfweb on twitter  on GitHub

DFG logo

The development of LibrAlign was partly funded by the German Research Foundation (DFG) in this project.

bioinfweb - Biology & Informatics Website