Adapt Java code to Python refactoring #6
Description
The Java modules needs to be able to read the new annotation file and make use of this for shaping the PK molecule. 0.5 days used so far.
- Release current version as 1.1 (the one that works with the flagged python 0.1).
- Add ability to read additional verification field for sequence feature.
- Define in which section is the annotation data required within the Java code.
- Implement objects for CladeAnnotation
- Implement ability to skip clades if they are not verified, use highest ranking
- Update some of the tests to the new cladification annotation.
- Identify clades that produce stereo chemistry related exceptions with non-planar bonds.
- Move to newest CDK from 1.5.10, John suggests that this might fix this issue.