How to build SPARQL queries in java?

You can build queries programmatically in Jena using two methods: syntax or algebra. There's an introduction in the jena wiki.

Using the algebra you'd do something like:

Op op;
BasicPattern pat = new BasicPattern();                 // Make a pattern
pat.add(pattern);                                      // Add our pattern match
op = new OpBGP(pat);                                   // Make a BGP from this pattern
op = OpFilter.filter(e, op);                           // Filter that pattern with our expression
op = new OpProject(op, Arrays.asList(Var.alloc("s"))); // Reduce to just ?s
Query q = OpAsQuery.asQuery(op);                       // Convert to a query
q.setQuerySelectType();                                // Make is a select query

(taken from the wiki page)

It's not CriteriaBuilder (nor was it intended to be), but is some of the way there. You OpJoin rather than AND, OpUnion when you want to OR, etc. The pain points are expressions in my experience: you probably want to parse them from a string.

I implemented SPARQL Java - a kind of DSL for writing SPARQL queries in Java.

It solves the problem with IDE's auto formatting of concatenated SPARQL query strings and things like that.

As for example:

String shortQuery = Q.prefix("books", "http://example.org/books#")
            .select("?book ?authorName", new where() {
                {
                    $("?book books:author ?author");
                    $("?author books:authorName ?authorName");
                }
            }).get();

The recent versions of Jena have added a StringBuilder style API for building query/update strings and parameterizing them if desired.

This class is called ParameterizedSparqlString, here's an example of using it to create a query:

ParameterizedSparqlString queryStr = new ParameterizedSparqlString();
queryStr.setNSPrefix("sw", "http://skunkworks.example.com/redacted#");
queryStr.append("SELECT ?a ?b ?c ?d");
queryStr.append("{");
queryStr.append("   ?rawHit sw:key");
queryStr.appendNode(someKey);
queryStr.append(".");
queryStr.append("  ?rawHit sw:a ?a .");
queryStr.append("  ?rawHit sw:b ?b .");
queryStr.append("  ?rawHit sw:c ?c . ");
queryStr.append("  ?rawHit sw:d ?d .");
queryStr.append("} ORDER BY DESC(d)");

Query q = queryStr.asQuery();

Disclaimer - I'm the developer who contributed this functionality to Jena

See What's the best way to parametize SPARQL queries? for more discussion on doing this across various APIs.