SAN JOSE — First, his white roommates nicknamed him “Three-fifths,” referring to the way the government once counted blacks as just a fraction of a person. When he protested, they dubbed him “Fraction.”

Then they outfitted the four-bedroom dormitory suite they shared with a Confederate flag. They locked him in his room. They wrote the “N-word” on a dry-erase board in the living room. They fastened a bicycle lock around his neck and told him they lost the keys, then tried it again a few weeks later.

It may sound like something out of the civil rights struggles of the 1960s. But police reports indicate it happened last month in the Obama era to a black student at San Jose State University, a liberal campus boasting statues of Olympic athletes making a black power salute.

Late Wednesday, prosecutors filed misdemeanor hate-crime and battery charges against three of the student’s roommates over the alleged hazing, which has sparked anger in the community and on the diverse campus. The men are Logan Beaschler, 18, of Bakersfield; Joseph Bomgardner, 19, of Clovis; and Colin Warren, 18, of Woodacre (Marin County).

“This is outrageous,” said the Rev. Jethroe Moore II, president of the San Jose/Silicon Valley chapter of the NAACP. “This form of bullying cannot be tolerated.”

The students were not available for comment and it was unclear late Wednesday whether they had legal representation. They could face penalties ranging from probation to a year in jail if convicted, as well as university discipline.

University spokeswoman Pat Lopes Harris said the incident is still under investigation, and no decision has been made yet on whether the students will be sanctioned.

The alleged harassment began in late August when the freshman and seven other young white men — all assigned to live together — moved into the four-bedroom, on-campus suite. Eight weeks later, in mid-October, the freshman’s parents noticed a Confederate flag draped over a cardboard cutout of Elvis in the living room of the suite and a dry-erase board with the “N-word” scrawled on it, and reported it via housing officials to campus police. Two of the young men were immediately transferred to a different dorm.

But at least two residential assistants were aware before then that one of the roommates had tacked a Confederate flag to a bedroom window. They asked the young men to take it down “so it could not be seen by the general public,” but did not investigate any further, according to university police reports and campus-housing department memos.

The freshman, now 18, said in a brief telephone interview that he’s never experienced this kind of mistreatment, even though he was one of only a few black students at his high school in Santa Cruz. This newspaper is not naming him at his parents’ request because of the ongoing campus investigation.

“I’m still in shock,” he said, noting he tried not to spend much time in the suite and didn’t report the situation to campus police in hopes the conduct would stop. “I tried not to dwell on this. But my family is upset and I’m upset.”

He told university police he always locked his door at night because he was scared of most of the other students living in the four-bedroom suite. He also didn’t feel safe studying in his own room and believes his grades weren’t as good as they could be as a result.

The young men acknowledged during police interviews that they incessantly harassed the then-17-year-old, according to the reports. But they downplayed the incidents as mere “pranks” and “jokes,” denying their actions were racist.

University police, however, recommended that District Attorney Jeff Rosen file the case as a hate crime.

Prosecutor Erin West emphatically agreed, saying, “The District Attorney’s Office has no tolerance for those who criminally prey on others because they are different.”

Police reports, separate documents prepared by housing officials and photographs document the freshman’s ordeal. The events allegedly occurred after everyone in the suite attended a two-day orientation session this past summer that included sensitivity training.

After the nicknames, there followed a series of coercive incidents, including barring the freshman’s bedroom door with furniture several times to prevent him from coming out.

The first time they wrestled him to the ground, they succeeded in getting the metal bike lock around his neck, the suspects themselves told police. The second time, he managed to evade them, but he told police he got slightly banged up in the process.

One time, they removed the doorknob from inside a closet, and knowing that the freshman was claustrophobic, tried to induce him via a series of post-it messages around the suite to step inside it. One note referred to the closet as “the enrichment center,” and included a homophobic slur and the insult, “Eat —- and die.”

Investigators also found Nazi symbols in the apartment, including a picture of Adolf Hitler, the “SS” lightning bolt symbol and a swastika. They also discovered pictures of pentagrams, apparently intended to alarm the freshman, who is Christian.

After the freshman’s father talked to the roommates and reported the matter, the freshman received what police characterized as a “sarcastic apology note,” signed only “The Residents.” The note mentions “the Beloved Reverend Doctor Martin Luther King Jr.” and urges the freshman to let bygones be bygones. It also contains a warning of sorts in the postscript: “The Residents have welcomed you, it is not advised to ignore the call of The Residents.”

Contact Tracey Kaplan at 408-278-3482.

Follow her at Twitter.com/tkaplanreport.