retrieve a matched pattern in a context with javascript

Question

[jamedong]

Hi, I am trying to retrieve a pattern in a context, that is, 30 amino acids before and after the pattern ( the matched pattern presented as uppercase, while the unmatched part of 60 amino acids was displayed as lowercase), how to rewrite the code of "protein_pattern.js" in Sequence manipulation suite (sms)? Here is the original code of "protein_pattern.js":

//Written by Paul Stothard, University of Alberta, Canada
 function proteinPattern (theDocument) {    
var newProtein = "";
var maxInput = 500000000;

if (testScript() == false) {
    return false;
}

var re;
var matches = new Array();

if ((checkFormElement (theDocument.forms[0].elements[0]) == false) || (checkSequenceLength(theDocument.forms[0].elements[0].value, maxInput) == false) || (checkFormElement (theDocument.forms[0].elements[1]) == false))   {
    return false;
}

var re = "/" + theDocument.forms[0].elements[1].value.replace(/\//g,"") + "/gi";
re = removeWhiteSpace(re);
try {
    re = eval(re);
    var testString = "teststring";
    testString = testString.replace(re, "");
}
catch(e) {
    alert ("The regular expression is not formatted correctly.");
    return false;
}

openWindow("Protein Pattern Find");
openPre();
var arrayOfFasta = getArrayOfFasta (theDocument.forms[0].elements[0].value);


for (var i = 0; i < arrayOfFasta.length; i++)   {

    newProtein = getSequenceFromFasta (arrayOfFasta[i]);
    title = getTitleFromFasta (arrayOfFasta[i]);
    newProtein = removeNonProteinStrict(newProtein);

    outputWindow.document.write(getInfoFromTitleAndSequence(title, newProtein));

    writeProteinPattern(newProtein, re);

    outputWindow.document.write ('\n\n');
}

closePre();
closeWindow();
return true;
}

 function writeProteinPattern (proteinSequence, re) {
var matchArray;
var matchPosition;
var matchCount = 0;
var simplePattern = re.toString();
simplePattern = simplePattern.replace(/\/gi$|\/ig$|^\//gi, "");

while (matchArray = re.exec(proteinSequence)) {
    matchCount++;

            var match_end = re.lastIndex;
            var match_start = match_end - RegExp.lastMatch.length + 1;

    outputWindow.document.write ("&gt;match number " + matchCount + " to \"" + simplePattern + "\" start=" + match_start + " end=" + match_end + "\n" + addReturns(matchArray[0]) + "\n\n");

    re.lastIndex = re.lastIndex - RegExp.lastMatch.length + 1;

}
if (!(matchCount > 0)) {
    outputWindow.document.write ("no matches found for this sequence.\n\n");
}
}

Any suggestions? Thanks a lot!