Can I programmatically set the hibernate.cfg.xml file configuration in Java?

hibernate.cfg.xml is old school - I haven't used it for years. Use the javax.persistance annotations and annotate your classes - hibernate does the rest.

Here's a very basic example:

import javax.persistence.*;

@Entity
@Table(name = "my_table")
public class MyTable {

    private Integer id;
    private String someColumn;

    @Id
    @GeneratedValue
    @Column(name = "my_table_id", unique = true, nullable = false)
    public Integer getId() {
        return id;
    }

    public void setId(Integer id) {
        this.id = id;
    }

    @Column(name = "some_column")
    public String getSomeValue() {
        return someColumn;
    }

    public void setSomeColumn(String someColumn) {
        this.someColumn = someColumn;
    }    
}

See this documentation for an explanation of all hibernate annotations.