She had sexual intimacy on 16 , 25 May and 4 June. She has done urine pregnancy tests on 25 and 30 May. The rest of the story is irrelevant.
Now she should do a urine
pregnancy test on 25 June if she doesn't get her periods by that time. Since her periods are irregular it is difficult to wait for the period and all that.
A safe method is urine test on 25 June.
She should consult with a Gynaecologist on Practo with the report.