eclarke

        postParams.add(new BasicNameValuePair("longestOnly","false"));
        postParams.add(new BasicNameValuePair("wholeWordOnly","true"));
        postParams.add(new BasicNameValuePair("filterNumber", "true"));
        postParams.add(new BasicNameValuePair("stopWords","protein,gene,disease,disorder,cell,syndrome,CAN"));
        postParams.add(new BasicNameValuePair("withDefaultStopWords","true"));
        postParams.add(new BasicNameValuePair("isTopWordsCaseSensitive","false"));
        postParams.add(new BasicNameValuePair("mintermSize","3"));
        postParams.add(new BasicNameValuePair("scored", "true"));
        postParams.add(new BasicNameValuePair("withSynonyms","true")); 
        postParams.add(new BasicNameValuePair("ontologiesToExpand", ""));

eclarke

public static String fixLinks(String src, Wiki target) {
    
    // add a marker to all the links so we can iterate through them (except the ones that point to wikipedia)
    String src2 = src.replaceAll("\\[\\[(?!(wikipedia))", "[[%");
    
    try {
        while (src2.contains("[[%")) {
            
            // extract the link text
            int a = src2.indexOf("[[%")+3;  // left inner bound