NAME¶

SWISS::TextFunc

DESCRIPTION¶

This module is designed to be a repository of functions that are repeatedly used during parsing and formatting of SWISS-PROT/TREMBL lines. If more than two line types need to do aproximately the same thing then it is probably in here.

All functions expect to be called as package->function(param list)

listFromText

Takes a piece of text, a seperator regex and a seperator that may appear at the end. Returns an array of items that were seperated in the text by that seperator. Takes care of null items (looses them for you).

textFromList

Takes an array of items, a separator, a terminating string, and a line width. Returns an array of strings, each ending with the separator or the terminator with a width less than or equal to the width specified.

Seems to do the wrong thing for references - not sure why. Don't use it for that.

wrapText

Takes a string and a length. Returns an array of strings which are shorter or equal in length to length, spliting the string on white space.

wrapOn ($firstLinePrefix, $linePrefix, $colums, $text[, @separators])

Wraps $text into lines with at most $colums colums. Prepends the prefixes to the lines. @separators is a list of expressions on which to wrap. The expression itself is part of the upper line.

If no @separators are provided, the $text is wrapped at whitespace except in EC/TC numbers or at dashes that separate words.

First tries to wrap on the first item of @separators, then the next etc. If no wrap on any element of @separators or whitespaces is possible, wraps into lines of exactly length $colums.

A special case is that the first item of @separators may be a reference to an array. This is used internally for wrapping FT VARIANT-like lines.

Example:

 wrapOn('DE ', 'DE ', 40, 
        '14-3-3 PROTEIN BETA/ALPHA (PROTEIN KINASE C INHIBITOR PROTEIN-1)', 
        '\s+') 
 returns ['14-3-3 PROTEIN BETA/ALPHA (PROTEIN ', 
          'KINASE C INHIBITOR PROTEIN-1)']
 wrapOn('DE ', 'DE ', 40, 
        '14-3-3 PROTEIN BETA/ALPHA (PROTEIN KINASE C INHIBITOR PROTEIN-1)', 
        ' (?=\()', '\s+')
 returns ['14-3-3 PROTEIN BETA/ALPHA ', 
          '(PROTEIN KINASE C INHIBITOR PROTEIN-1)']
    

cleanLine

Remove the leading line Identifier and three blanks and trailing spaces from an SP line.

joinWith ($text, $with, $noAddAfter, @list)

Concatenates $text and @list into one string. Adds $with between the original elements, unless the postfix of the current string is $noAddAfter. This is used to avoid inserting blanks after hyphens during concatenation. So unpleasant strings like 'CALMODULIN- DEPENDENT' are avoided. Unfortunately a correct reassembly of strings like 'CARBON-DIOXIDE' is not done.

insertLineGroup ($textRef, $text, $pattern)

Inserts text block $text into the text referred to by $textRef. $text will replace the text block in $textRef matched by $pattern.

uniqueList (@list)

Returns a list in which all duplicates from @list have been removed.

currentSpDate

returns the current date in SWISS-PROT format

toMixedCase($text, @regexps)

Convert a text to mixed case, according to one or more regular expressions. In scalar context, returns the new text; in array context, also returns the regexp with which the change was performed, or undef on failure. See corresponding item in SWISS::GN for more details.