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.
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.
CDMSequenceMatrixAdapter now exports sequence metadata.
Bug fix: CDMSequenceMatrixAdapter now does not create CharacterSetIntervalEvents if the alignment has no columns.
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.
Exported packages of molecular plugin updated. Basic export functionality for direct export of consensus sequence alignments implemented (untested).