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Asked: 2026-05-15T13:26:14+00:00

I am trying to use regular expressions to determine what format the user have

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I am trying to use regular expressions to determine what format the user have applied when entering input in a textbox.
The regular expressions are as follows:

(\\s?[" + alphabet + "]{9,9})+

To determine whether the input is one or more strings of length 9 in a given alphabet, possibly separated by whitespace.

(>[\\w\\s]+\\n[" + alphabet + "\\s]+)+

To check if the input is in FASTA format

The regular expressions run terribly slow when matching with inputString.matches(regexString). Why is this?

I figured this may be due to Java storing all potential matches (which I don’t need at this point), but adding ?: in every parenthesis breaks the regex. How should this be done?

Thank you,

Martin

Edit 1: I was unable to reproduce this issue – it only happens on one computer. This could suggest something wrong with that particular VM setup.
We need something more robust, and so we will be implementing this differently. I have picked Joel’s answer as the right one, since I believe that some special case in Pattern may be the cause.

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1 Answer

  1. Editorial Team

    If you have a number of different regular expression patterns that are being matched against the same input to try to categorize the input, then you are likely to be better off using a lexical analyzer generator like JFlex.

    Other Java-based lexical analyzer and parsing tools that are typically used in compiler construction can be found listed here.

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