To programatically modify a search query, you can use the API on RAMAssetQueryBuilder. As shown in the Simple search example you can use the RAMSession.createAssetQuery(String) to create a RAMAssetQueryBuilder.
SearchQuery query = session.createAssetQuery("Rational Asset Manager javadoc");
RAMAssetQueryBuilder queryBuilder = (RAMAssetQueryBuilder)query;
There is also a constructor you can use where you pass in your session object.
queryBuilder = new RAMAssetQueryBuilder(session);