A mathematical physicist and computer expert didn’t deprive a research firm of computer code for a program designed to measure brain waves.

The firm, Flint Hills Scientific LLC, Lawrence, had the code all along and didn’t realize it.

At least that’s the argument an attorney for Alexei Nikitin, 40, made during a hearing Friday in Douglas County District Court.

Nikitin, now a professor at Baker University, is charged with felony counts of theft and computer crime. The crimes allegedly took place when Nikitin worked for Flint Hills in 2000.

Nikitin is accused of deleting and copying computer program files he worked on or developed before leaving the firm in February 2000. One of the files was the source code for a percentile tracking filter, a device used to measure brain waves during an epileptic seizure.

Nikitin quit in a dispute over royalty fees for his work.

After he left the firm, an attorney for Nikitin sent Flint Hills a letter offering to license the computer programs for use.

Mark Frei, operating manager and technical director at Flint Hills, testified he then contacted the FBI and Lawrence Police.

Under questioning Friday from Nikitin’s attorney, Floyd Finch, Frei said his company had made backup files of its computer programs in December 1999 because of Y2K fears. The backup file wasn’t discovered until several months later.

Finch maintained the backup file had the tracking filter source code on it and thus Flint Hills had not been deprived of it.

During two days of hearings that began Thursday, Finch also raised questions about whether Nikitin had signed an employee agreement promising not to make copies of his work and try to profit from them if he left Flint Hills. Frei has insisted Nikitin did sign the agreement.

Judge Jack Murphy must decide whether there is enough evidence to try Nikitin on the charges. The hearing is scheduled to continue at 3:30 p.m. July 2.

Two civil lawsuits over the issue are pending in federal court.