GAF parser review and enhancement

[KeywanHP]

The GAF file format (v2.2) seems to have evolved since I last looked at it. Especially the information in qualifier-column-4 looks very useful. This column is populated with relations from the Relations Ontology that indicate the intended meaning, or interpretation, of a gene product-to-GO term association. Allowed values are listed in the table below; for negation, “NOT” may be prepended to a relation with a pipe. http://geneontology.org/docs/go-annotation-file-gaf-format-2.2/#qualifier-column-4

Our GAF parser needs to be reviewed and potentially improved/simplified to use gene-go relation types as specified in column 4. This is the code that sets the relation type:

knetbuilder/ondex-knet-builder/modules/go/src/main/java/net/sourceforge/ondex/parser/gaf/transformer/GAFTransformer.java

Line 364 in 95d880d

private String getRelationType(String ontology, String qualifier) {