As far as I know, ther shouldn't be a method to perform re-indexes. When you re-index your JIRA, the instance would be unaccessible, so I think that to avoid any sudden accessibility problems, you might want to reconsider doing so programatically.
However, in JIRA 5.2, there iss the option to perform a background re-index, where you can re-index AND still use your instance.
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