Fixing warning.
Merge branch 'development' of github.com:InformationIntegrationGroup/Web-Karma into development
Writing comments for methods in ontology/OntologyManager.java
Fixing the problem of fetching indirect subClasses and superClasses in OntologyManager.java
Changes to the semantic type assignment process

The domains of the properties are now saved in the CRF Model.
The semantic type window has been changed now.
Some interface changes are still required such as the background colors.
Add log4j.properties file to the project. You have to add the path (/config) to the project build path.
Change OntologyManager.java to improve the performance of Alignment algorithm.
Add OntologyCache.java which creates HashTable for what we need in building the graph.
test to see if GitHub shows my picture on commit or not
test
add log folder to .gitignore
Add log folder according to http://help.github.com/git-cheat-sheets/
Implementing new algorithm for generating the hierarchical headings for alignment and table headers
Removing some debug output statements
Fixing the problem of generating different Steiner trees in each alignment.
Added new API to handler ColumnFeatures such as column name.
Using the updated semantic typing API
Removing extra imports to remove warnings
Small bug fix
Adding the ability to Alignment.java to prefer links shown in UI in previous models for next modeling
Handling the preferred UI links in Alignment object rather than in UI side.