RefSouceOnlyMain.java Source code

Java tutorial

Introduction

Here is the source code for RefSouceOnlyMain.java

Source

import java.io.BufferedInputStream;
import java.io.BufferedWriter;

import java.io.File;

import java.io.FileInputStream;

import java.io.FileWriter;

import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.Reader;
import java.io.UnsupportedEncodingException;

import java.io.Writer;
import java.lang.Character.UnicodeBlock;
import java.nio.charset.Charset;
import java.nio.charset.CharsetDecoder;
import java.nio.charset.CodingErrorAction;

import java.util.*;

import java.util.logging.Level;

import java.util.logging.Logger;

import java.util.regex.Matcher;

import java.util.regex.Pattern;

import javax.swing.JOptionPane;
import org.apache.poi.hpsf.DocumentSummaryInformation;

import org.apache.poi.hwpf.*;

import org.apache.poi.hwpf.extractor.WordExtractor;

import org.apache.poi.hwpf.usermodel.*;

import org.apache.poi.poifs.filesystem.*;

import org.w3c.dom.*;

import javax.xml.parsers.*;

import javax.xml.transform.*;

import javax.xml.transform.stream.*;

import javax.xml.transform.dom.*;
import org.apache.poi.hssf.usermodel.HSSFCell;
import org.apache.poi.hssf.usermodel.HSSFRow;
import org.apache.poi.hssf.usermodel.HSSFSheet;
import org.apache.poi.hssf.usermodel.HSSFWorkbook;
import org.apache.poi.ss.usermodel.Cell;
import org.apache.poi.ss.usermodel.DataFormatter;
import org.apache.poi.ss.util.CellReference;

public class RefSouceOnlyMain {

    public static javax.swing.JTextArea ta;
    public static String title = "";
    public static ArrayList<String> refs = new ArrayList<String>();
    public static String shortTitle = "";
    public static String doi = "";
    public static String ppub = "";
    public static String epub = "";
    public static String volume = "";
    public static String issue = "";
    public static String fpage = "";
    public static String lpage = "";
    public static String manuscriptDateAccepted = "";
    public static String dateAccepted = "";
    public static String copyrightStat = "";
    public static String copyrightYear = "";
    public static String isOriginal = "";
    public static ArrayList<String> abstractArr = new ArrayList<String>();
    public static ArrayList<String> keywordArr = new ArrayList<String>();
    public static ArrayList<String> discussion = new ArrayList<String>();
    public static ArrayList<String> acknowledgement = new ArrayList<String>();
    public static ArrayList<String> disclosure = new ArrayList<String>();
    public static ArrayList<String> figAlready = new ArrayList<String>();
    public static ArrayList<String> tableAlready = new ArrayList<String>();
    public static HashMap<String, String> articleType = new HashMap<String, String>();
    public static ArrayList table = new ArrayList();
    public static ArrayList figure = new ArrayList();
    public static ArrayList<String> authors = new ArrayList<String>();
    public static ArrayList<String> references = new ArrayList<String>();
    public static DocSegment aDoc;
    //Matcher matcher =
    //       pattern.matcher(console.readLine("Enter input string to search: "));
    public static DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
    public static Document doc;
    public static String journalTitle = "";
    public static boolean isValidBoday;
    public static boolean isValidBack;
    public static boolean isValidRefs;
    public static String magzineTitle;
    public static String magzineShortTitle;
    public static String issn_ppub;
    public static String issn_epub;

    public static void cleanArrs() {

        if (ta != null) {
            ta.setText("");
            ta.append("cleaning arrays \n");
        }

        isValidBoday = false;
        isValidBack = false;
        isValidRefs = false;

        if (refs != null)
            refs.clear();
        if (figAlready != null)
            figAlready.clear();
        if (abstractArr != null)
            abstractArr.clear();
        if (keywordArr != null)
            keywordArr.clear();

        if (discussion != null)
            discussion.clear();

        if (acknowledgement != null)
            acknowledgement.clear();
        if (disclosure != null)
            disclosure.clear();
        if (table != null)
            table.clear();
        if (figure != null)
            figure.clear();
        if (authors != null)
            authors.clear();
        if (references != null)
            references.clear();
        if (articleType != null)
            articleType.clear();

    }

    public static void init(String fileName) {

        ta.append("reading doc......\n");

        RefSouceOnlyMain.readMyDocument(fileName);

        articleType.put("Original Article", "research-article");
        articleType.put("Case Report", "case-report");
        articleType.put("Review", "review-article");
        articleType.put("Letter to the Editor", "letter");
        articleType.put("Short Communication", "rapid-communication");
        articleType.put("Meeting Report", "meeting-report");
        articleType.put("News", "news");
        articleType.put("Editorial", "editorial");
        articleType.put("Book Review", "book-review");
        articleType.put("Abstract", "abstract");
        articleType.put("Announcement", "announcement");
        articleType.put("Addendum", "addendum");
        articleType.put("Article Commentary", "article-commentary");
        articleType.put("Brief Report", "brief-report");
        articleType.put("Calendar", "calendar");
        articleType.put("Discussion", "discussion");
        articleType.put("In Brief", "in-brief");
        articleType.put("Introduction", "Introduction");
        articleType.put("Partial Retraction", "partial-retraction");
        articleType.put("Product Review", "product-review");
        articleType.put("Retraction", "retraction");
        articleType.put("Retraction", "retraction");
        articleType.put("Translation", "translation");
        articleType.put("Reprint", "reprint");
        articleType.put("Oration", "oration");
        articleType.put("Correction", "correction");
        articleType.put("Obituary", "obituary");
        articleType.put("Books Received", "books-received");
        articleType.put("Collection", "collection");
        articleType.put("Translation", "translation");
        articleType.put("Dissertation", "dissertation");
        articleType.put("Reply", "reply");

        ta.append("trim the array elements....\n");

        abstractArr = RefSouceOnlyMain.arrayCleaner(abstractArr);
        if (abstractArr.size() > 0) {
            abstractArr.remove(0);
        }

        keywordArr = RefSouceOnlyMain.arrayCleaner(keywordArr);
        if (keywordArr.size() > 0) {
            keywordArr.remove(0);
        }

        discussion = RefSouceOnlyMain.arrayCleaner(discussion);
        if (discussion.size() > 0) {
            discussion.remove(0);
        }

        acknowledgement = RefSouceOnlyMain.arrayCleaner(acknowledgement);

        disclosure = RefSouceOnlyMain.arrayCleaner(disclosure);
        if (disclosure.size() > 0) {
            disclosure.remove(0);
        }

        //  table = RefSouceOnlyMain.arrayCleaner(table);

        //figure = RefSouceOnlyMain.arrayCleaner(figure);

        authors = RefSouceOnlyMain.arrayCleaner(authors);
        //  authors.remove(0);

        references = RefSouceOnlyMain.arrayCleaner(references);

        DocumentBuilder db = null;

        try {

            db = dbf.newDocumentBuilder();

        } catch (ParserConfigurationException ex) {

            ta.append("\nerrors happen:\n");
            ta.append(ex.getMessage() + "\n");

        }

        doc = db.newDocument();

        Element root = doc.createElement("article");

        root.setAttribute("xmlns:mml", "http://www.w3.org/1998/Math/MathML");

        root.setAttribute("xmlns:xlink", "http://www.w3.org/1999/xlink");

        if (articleType.get(RefSouceOnlyMain.isOriginal) == null) {

            root.setAttribute("article-type", RefSouceOnlyMain.isOriginal);
        } else {
            root.setAttribute("article-type", articleType.get(RefSouceOnlyMain.isOriginal));
        }

        root.appendChild(generateFront());

        root.appendChild(generateBody());

        root.appendChild(generateBack());

        doc.appendChild(root);

        DOMSource domSource = new DOMSource(doc);

        TransformerFactory tf = TransformerFactory.newInstance();

        Transformer transformer = null;

        try {

            transformer = tf.newTransformer();
            transformer.setOutputProperty(OutputKeys.METHOD, "xml");
            transformer.setOutputProperty(OutputKeys.ENCODING, "UTF-8");
            transformer.setOutputProperty(OutputKeys.INDENT, "yes");
            transformer.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "no");
            transformer.setOutputProperty(OutputKeys.DOCTYPE_PUBLIC,
                    "-//NLM//DTD Journal Publishing DTD v3.0 20080202//EN");
            transformer.setOutputProperty(OutputKeys.DOCTYPE_SYSTEM, "journalpublishing3.dtd");

        } catch (TransformerConfigurationException ex) {

            ta.append("\nerrors happen:\n");
            ta.append(ex.getMessage() + "\n");

        }

        java.io.StringWriter sw = new java.io.StringWriter();

        StreamResult sr = new StreamResult(sw);

        try {

            transformer.transform(domSource, sr);

        } catch (TransformerException ex) {

            ta.append("\nerrors happen:\n");
            ta.append(ex.getMessage() + "\n");

        }

        String xml = sw.toString();

        //xml = xml.replace("<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"no\"?>", "");

        ta.append("\n" + xml);
        // finalXMLString = "<!DOCTYPE article PUBLIC \"-//NLM//DTD Journal Publishing DTD v3.0 20080202//EN\" \"http://dtd.nlm.nih.gov/publishing/3.0/journalpublishing3.dtd\">";
        finalXMLString += xml;

    }

    private static Element appendChilds(Element a, ArrayList<Element> b) {

        a.appendChild(b.get(b.size() - 1));

        for (int i = 0; i < b.size() - 1; i++) {

            a.appendChild(b.get(i));

        }

        return a;

    }

    public static Element generateBack() {

        Element back = doc.createElement("back");
        if (RefSouceOnlyMain.acknowledgement.size() > 0) {

            Element ack = doc.createElement("ack");

            back.appendChild(ack);

            for (String aString : acknowledgement) {

                aDoc = new DocSegment();
                aDoc.setDoc(doc);
                aDoc.setList(RefSouceOnlyMain.acknowledgement);
                ack = RefSouceOnlyMain.appendChilds(ack, aDoc.addTableFigure(aString));

            }
        }

        aDoc = new DocSegment();
        aDoc.setDoc(doc);
        aDoc.setList(RefSouceOnlyMain.disclosure);
        List<Element> tempString = aDoc.getGeneral(disclosure, "[s]", "isBack");
        for (Element a : tempString) {
            back.appendChild(a);
        }

        Element refList = doc.createElement("ref-list");

        back.appendChild(refList);

        Element refListTitle = doc.createElement("title");

        refListTitle.appendChild(doc.createTextNode("References"));

        refList.appendChild(refListTitle);

        //Humphris G, Blinkhorn A, Freeman R, Gorter R, Hoad-Reddick G, Murtomaa H, O'Sullivan R, et al. Psychological stress in undergraduate dental students: baseline results from seven European dental schools. Eur J Dent Educ. 2002;6(1):22-29. 11872070
        //
        for (int i = 0; i < references.size(); i++) {

            String temp = references.get(i).trim();

            ta.append("\n" + "dealing with the " + i + " ref:" + temp);

            System.out.println("\n" + "dealing with the " + i + " ref:" + temp);

            Element tempOneRef = doRefs(temp, i);

            if (tempOneRef != null) {

                refList.appendChild(tempOneRef);

            }

        }

        return back;

    }

    public static Element doRefs(String refs, int i) {

        String[] newRefs = refs.split("httphttp");

        refs = newRefs[0];

        String souceString = newRefs[0].trim();

        String sourcePattern = "\\d{1,}\\s*[\\.,]\\s*";
        souceString = souceString.replaceFirst(sourcePattern, "");

        System.out.println("souceString;" + souceString);

        refs = refs.trim();
        //  refs = refs.replaceFirst("^[0-9]+\\.", "");

        System.out.println("what is before:" + refs);
        refs = refs.replaceAll("\\.,", ",");

        refs = refs.replaceAll("\\?", ".");

        System.out.println("what is before:" + refs);

        String[] refInfo = refs.split("\\.");

        System.out.println("refingo length:" + refInfo.length);

        if (refInfo.length < 2) {

            // return null;

        }

        if (refInfo.length < 5) {

            //   ta.append("\ncurrent ref format is not correct, please check it.");

            //  return null;

        }

        //    System.out.println("1,"+refInfo[0]+" 2,"+refInfo[1]+" 3,"+refInfo[2]+" 4,"+refInfo[3]+" 5,"+refInfo[4]);

        if (refInfo.length > 4) {
            String[] refInfoTemp = new String[4];
            refInfoTemp[3] = refInfo[refInfo.length - 1];
            refInfoTemp[2] = refInfo[refInfo.length - 2];
            //refInfoTemp[1] = refInfo[refInfo.length - 3];
            refInfoTemp[0] = refInfo[1];
            String titleTemp = refInfo[2];
            ;
            for (int x = 2; x < refInfo.length - 2; x++) {
                titleTemp = titleTemp + "." + refInfo[x];
            }
            refInfoTemp[1] = titleTemp;
            refInfo = refInfoTemp;
        }

        Element e1 = doc.createElement("ref");

        Element refLabel = doc.createElement("label");

        Element e200 = doc.createElement("element-citation");

        e200.setAttribute("publication-type", "journal");

        Element e2 = doc.createElement("source");

        e200.appendChild(e2);

        String idString = (i + 1) + "";

        e1.appendChild(refLabel);

        refLabel.appendChild(doc.createTextNode(idString));

        e1.appendChild(e200);

        if (i < 9) {

            idString = "0" + (i + 1);

        }

        e1.setAttribute("id", "R" + idString);

        System.out.println(i + " idstring is " + idString);

        //e2.setAttribute("publication-type", "journal");

        e2.appendChild(doc.createTextNode(souceString));
        /**
                String[] names = refInfo[0].split(",");
            
            
                for (int j = 0; j < names.length; j++) {
            
        names[j] = names[j].trim();
            
        System.out.println("one ref name:"+names[j]);
            
        if (j == (names.length - 1) && (names[j].equals("et al") || names[j].equals("etal"))) {
            Element e3 = doc.createElement("etal");
            e3.appendChild(doc.createTextNode("et al"));
           // e2.appendChild(e3);
        } else {
            
            String surname = "";
            
            String givenName = "";
            
            if (names[j].contains(" ")) {
            
                String[] name = names[j].split(" ");
            
                surname = name[0];
                givenName = name[1];
                    
                if(name.length>2) {
                    for(int iii=2; iii< name.length;iii++) {
            
                       givenName += " "+name[iii];
                    }
                }
            
            } else {
            
                surname = names[j];
            
            }
            
            Element e3 = doc.createElement("name");
            
            Element e4 = doc.createElement("surname");
            
            Element e5 = doc.createElement("given-names");
            
            e4.appendChild(doc.createTextNode(surname.trim()));
            
            e5.appendChild(doc.createTextNode(givenName.trim()));
            
            e3.appendChild(e4);
            
            e3.appendChild(e5);
            
           // e2.appendChild(e3);
        }
            
                }
            
            
            
                System.out.println("done with name ");
            
                Element e6 = doc.createElement("article-title");
            
                e6.appendChild(doc.createTextNode(refInfo[1].trim()));
            
                //e2.appendChild(e6);
            
            
            
                System.out.println("done with title ");
            
                Element e7 = doc.createElement("source");
            
                String source = "";
            
                String supply = "";
            
                // 2005;43(3):235-243
            
                if (refInfo[2].contains("(")) {
            
        String[] sourceSupply = refInfo[2].split("\\(");
            
        source = sourceSupply[0];
            
        supply = sourceSupply[1].replace(")", "");
            
        e7.appendChild(doc.createTextNode(source.trim()));
            
                   // e2.appendChild(e7);
            
        Element e8 = doc.createElement("supplement");
            
        e8.appendChild(doc.createTextNode(supply.trim()));
            
                   // e2.appendChild(e8);
            
                } else {
            
        source = refInfo[2];
            
        e7.appendChild(doc.createTextNode(source.trim()));
            
                  //  e2.appendChild(e7);
            
                }
            
            
            
                System.out.println("done with source ");
            
                Pattern pattern = Pattern.compile("[0-9]{4};");
            
                Matcher matcher = pattern.matcher(refInfo[3]);
            
                while (matcher.find()) {
            
        String yearInfo = matcher.group();
            
        yearInfo = yearInfo.replace(";", "");
            
            
            
        Element e9 = doc.createElement("year");
            
        e9.appendChild(doc.createTextNode(yearInfo.trim()));
            
                  //  e2.appendChild(e9);
            
                }
            
            
            
                System.out.println("done with year ");
            
                pattern = Pattern.compile(";[0-9]{1,}");
            
                matcher = pattern.matcher(refInfo[3]);
            
                while (matcher.find()) {
            
        String volume = matcher.group();
            
        volume = volume.replace(";", "");
            
            
            
        Element e10 = doc.createElement("volume");
            
        e10.appendChild(doc.createTextNode(volume.trim()));
            
                  //  e2.appendChild(e10);
            
                }
            
            
            
                System.out.println("done with volume ");
            
            
            
                pattern = Pattern.compile(";[0-9]{1,}\\(([0-9]{1,}(-[0-9]{1,}){0,1}|suppl\\s[0-9]{1,})\\)");
            
                matcher = pattern.matcher(refInfo[3]);
            
                while (matcher.find()) {
            
        String issue = matcher.group();
            
        String[] issueArray = issue.split("\\(");
            
        issue = issueArray[1].replace(")", "");
            
        Element e11 = doc.createElement("issue");
            
        e11.appendChild(doc.createTextNode(issue.trim()));
            
                  //  e2.appendChild(e11);
            
                }
            
            
            
                System.out.println("done with issue ");
            
            
            
                pattern = Pattern.compile(":[0-9a-zA-Z]{0,}-[0-9a-zA-Z]{0,}");
            
                matcher = pattern.matcher(refInfo[3]);
            
                while (matcher.find()) {
            
        String pageInfo = matcher.group();
            
        pageInfo = pageInfo.replace(":", "");
            
        String[] pageInfoArr = pageInfo.split("-");
            
        String fpage = pageInfoArr[0];
            
        String lpage = pageInfoArr[1];
            
            
        if (!fpage.equals("000")) {
            
            Element e12 = doc.createElement("fpage");
            
            e12.appendChild(doc.createTextNode(fpage.trim()));
            
          //  e2.appendChild(e12);
        }
            
            
            
        if (!lpage.equals("000")) {
            Element e13 = doc.createElement("lpage");
            
            e13.appendChild(doc.createTextNode(lpage.trim()));
            
          //  e2.appendChild(e13);
        }
            
                }
            
                pattern = Pattern.compile("discussion\\s[0-9]{1,}");
            
                matcher = pattern.matcher(refInfo[3]);
            
                while (matcher.find()) {
        String pageInfo = matcher.group();
        Element e13 = doc.createElement("comment");
        e13.appendChild(doc.createTextNode(pageInfo.trim()));
                 //   e2.appendChild(e13);
                }
            
            
            
                System.out.println("done with lpage ");
                    
                **/

        if (newRefs.length > 1 && newRefs[1] != null && !newRefs[1].trim().equals("000")) {

            String result = newRefs[1].trim();
            System.out.println(result);

            String doiString = "";
            String pmidString = "";

            Pattern pattern = Pattern.compile("aaaaapmid(.{1,})(aaaaa.{1,}){0,1}");

            Matcher matcher = pattern.matcher(result);
            while (matcher.find()) {
                //doiString = matcher.group(1);
                pmidString = matcher.group(1);
                if (doiString.contains("aaaaadoi")) {
                    String[] pmidStringArr = doiString.split("aaaaadoi");
                    pmidString = pmidStringArr[0];
                }
                // pmidString=pmidString.replaceAll("aaaaapmid", "");
                System.out.println("find pmid match:" + pmidString);
            }

            pattern = Pattern.compile("aaaaadoi(.{1,})(aaaaa.{1,}){0,1}");

            matcher = pattern.matcher(result);

            while (matcher.find()) {
                doiString = matcher.group(1);
                if (doiString.contains("aaaaapmid")) {
                    String[] doiStringArr = doiString.split("aaaaapmid");
                    doiString = doiStringArr[0];
                }
                //doiString=doiString.replaceAll("aaaaadoi", "");
                System.out.println("find doi match:" + doiString);
                // pmidString = matcher.group(3);

            }

            System.out.println("doi and pmid:" + doiString + " " + pmidString);

            if (!doiString.trim().equals("")) {
                Element e14 = doc.createElement("pub-id");

                e14.appendChild(doc.createTextNode(doiString));

                e200.appendChild(e14);

                e14.setAttribute("pub-id-type", "doi");
            }

            if (!pmidString.trim().equals("")) {
                Element e14 = doc.createElement("pub-id");

                e14.appendChild(doc.createTextNode(pmidString));

                e200.appendChild(e14);

                e14.setAttribute("pub-id-type", "pmid");
            }

        }

        System.out.println("done with pmid ");

        return e1;

    }

    public static Element generateBody() {

        Element body = doc.createElement("body");

        aDoc = new DocSegment();
        aDoc.setDoc(doc);
        aDoc.setList(RefSouceOnlyMain.discussion);
        List<Element> tempString = aDoc.getGeneral(discussion, "[s]", "isBody");
        for (Element a : tempString) {
            body.appendChild(a);
        }

        return body;

    }

    public static Element generateFront() {

        Element front = doc.createElement("front");

        Element journalMeta = doc.createElement("journal-meta");

        Element journalTa = doc.createElement("journal-id");

        journalTa.setAttribute("journal-id-type", "nlm-ta");

        journalTa.appendChild(doc.createTextNode(RefSouceOnlyMain.magzineShortTitle));

        journalMeta.appendChild(journalTa);

        Element journalId = doc.createElement("journal-id");

        journalId.setAttribute("journal-id-type", "publisher-id");

        journalId.appendChild(doc.createTextNode("Elmer Press"));

        journalMeta.appendChild(journalId);

        Element journalTitleGroup = doc.createElement("journal-title-group");

        journalMeta.appendChild(journalTitleGroup);

        Element journalTitle = doc.createElement("journal-title");

        journalTitle.appendChild(doc.createTextNode(RefSouceOnlyMain.magzineTitle));

        journalTitleGroup.appendChild(journalTitle);

        Element issnP = doc.createElement("issn");

        issnP.setAttribute("pub-type", "ppub");

        issnP.appendChild(doc.createTextNode(RefSouceOnlyMain.issn_ppub));

        Element issnE = doc.createElement("issn");

        issnE.setAttribute("pub-type", "epub");

        issnE.appendChild(doc.createTextNode(RefSouceOnlyMain.issn_epub));

        journalMeta.appendChild(issnP);

        journalMeta.appendChild(issnE);

        Element publisher = doc.createElement("publisher");

        Element publisherName = doc.createElement("publisher-name");

        journalMeta.appendChild(publisher);

        publisher.appendChild(publisherName);

        publisherName.appendChild(doc.createTextNode("Elmer Press"));

        Element articleMeta = doc.createElement("article-meta");

        Element articleId = doc.createElement("article-id");

        articleId.setAttribute("pub-id-type", "doi");

        articleId.appendChild(doc.createTextNode(RefSouceOnlyMain.doi.trim()));

        articleMeta.appendChild(articleId);

        Element articleCategories = doc.createElement("article-categories");

        articleMeta.appendChild(articleCategories);

        Element subjGroup = doc.createElement("subj-group");

        subjGroup.setAttribute("subj-group-type", "heading");

        articleCategories.appendChild(subjGroup);

        Element subject = doc.createElement("subject");

        subjGroup.appendChild(subject);

        subject.appendChild(doc.createTextNode(RefSouceOnlyMain.isOriginal.trim()));

        Element titleGroup = doc.createElement("title-group");

        articleMeta.appendChild(titleGroup);

        Element articleTitle = doc.createElement("article-title");

        titleGroup.appendChild(articleTitle);

        articleTitle.appendChild(doc.createTextNode(RefSouceOnlyMain.title.trim()));

        if (RefSouceOnlyMain.shortTitle != null) {

            Element altTitle = doc.createElement("alt-title");

            titleGroup.appendChild(altTitle);

            altTitle.appendChild(doc.createTextNode(RefSouceOnlyMain.shortTitle.trim()));

            altTitle.setAttribute("alt-title-type", "short");

        }

        //Element contribGroup = doc.createElement("contrib-group");

        // Element contrib = doc.createElement("contrib");

        articleMeta = doAuthor(articleMeta, authors);

        String[] ppubArr = RefSouceOnlyMain.ppub.split("/");

        String[] epubArr = RefSouceOnlyMain.epub.split("/");

        Element pubDatePP = doc.createElement("pub-date");

        pubDatePP.setAttribute("pub-type", "ppub");

        Element pubDatePP_month = doc.createElement("month");

        pubDatePP_month.appendChild(doc.createTextNode(ppubArr[0].trim()));

        Element pubDatePP_year = doc.createElement("year");

        pubDatePP_year.appendChild(doc.createTextNode(ppubArr[1].trim()));

        articleMeta.appendChild(pubDatePP);

        pubDatePP.appendChild(pubDatePP_month);

        pubDatePP.appendChild(pubDatePP_year);

        Element pubDateEP = doc.createElement("pub-date");

        pubDateEP.setAttribute("pub-type", "epub");

        Element pubDateEP_day = doc.createElement("day");

        pubDateEP_day.appendChild(doc.createTextNode(epubArr[0].trim()));

        Element pubDateEP_month = doc.createElement("month");

        pubDateEP_month.appendChild(doc.createTextNode(epubArr[1].trim()));

        Element pubDateEP_year = doc.createElement("year");

        pubDateEP_year.appendChild(doc.createTextNode(epubArr[2].trim()));

        articleMeta.appendChild(pubDateEP);

        pubDateEP.appendChild(pubDateEP_day);

        pubDateEP.appendChild(pubDateEP_month);

        pubDateEP.appendChild(pubDateEP_year);

        Element volume = doc.createElement("volume");

        volume.appendChild(
                doc.createTextNode(RefSouceOnlyMain.volume == null ? "" : RefSouceOnlyMain.volume.trim()));

        articleMeta.appendChild(volume);

        Element issue = doc.createElement("issue");

        issue.appendChild(doc.createTextNode(RefSouceOnlyMain.issue == null ? "" : RefSouceOnlyMain.issue.trim()));

        articleMeta.appendChild(issue);

        Element fpage = doc.createElement("fpage");

        fpage.appendChild(doc.createTextNode(RefSouceOnlyMain.fpage == null ? "" : RefSouceOnlyMain.fpage.trim()));

        articleMeta.appendChild(fpage);

        Element lpage = doc.createElement("lpage");

        lpage.appendChild(doc.createTextNode(RefSouceOnlyMain.lpage == null ? "" : RefSouceOnlyMain.lpage.trim()));

        articleMeta.appendChild(lpage);

        Element history = doc.createElement("history");

        Element historyDate = doc.createElement("date");

        historyDate.setAttribute("date-type", "accepted");

        String[] historyDateArr = RefSouceOnlyMain.manuscriptDateAccepted.split("/");

        Element history_day = doc.createElement("day");

        history_day.appendChild(doc.createTextNode(historyDateArr[0].trim()));

        Element history_month = doc.createElement("month");

        history_month.appendChild(doc.createTextNode(historyDateArr[1].trim()));

        Element history_year = doc.createElement("year");

        history_year.appendChild(doc.createTextNode(historyDateArr[2].trim()));

        historyDate.appendChild(history_day);

        historyDate.appendChild(history_month);

        historyDate.appendChild(history_year);

        history.appendChild(historyDate);

        articleMeta.appendChild(history);

        Element permissions = doc.createElement("permissions");

        articleMeta.appendChild(permissions);

        Element copyright_statement = doc.createElement("copyright-statement");
        copyright_statement.appendChild(doc.createTextNode(RefSouceOnlyMain.copyrightStat.trim()));

        Element copyright_year = doc.createElement("copyright-year");
        copyright_year.appendChild(doc.createTextNode(RefSouceOnlyMain.copyrightYear.trim()));

        Element license = doc.createElement("license");

        license.setAttribute("license-type", "open access");

        license.setAttribute("xlink:href", "http://creativecommons.org/licenses/by-nc/4.0/");

        Element license_p = doc.createElement("license-p");

        license_p.appendChild(doc.createTextNode(Main.textNote));

        license.appendChild(license_p);

        permissions.appendChild(copyright_statement);

        permissions.appendChild(copyright_year);

        permissions.appendChild(license);

        aDoc = new DocSegment();
        aDoc.setDoc(doc);

        if (abstractArr.size() > 0) {
            Element abstractElem = doc.createElement("abstract");
            articleMeta.appendChild(abstractElem);
            List<Element> tempString = aDoc.getAbstract(abstractArr);
            for (Element a : tempString) {
                abstractElem.appendChild(a);
            }

        }

        if (keywordArr.size() > 0) {
            Element keywordElem = doc.createElement("kwd-group");
            keywordElem.setAttribute("kwd-group-type", "author");
            articleMeta.appendChild(keywordElem);
            for (String aKeywordLine : keywordArr) {
                if (!aKeywordLine.startsWith("[s1]")) {
                    if (aKeywordLine.contains(";")) {
                        for (String aKeyword : aKeywordLine.split(";")) {
                            Element aKeywordElem = doc.createElement("kwd");
                            keywordElem.appendChild(aKeywordElem);
                            aKeywordElem.appendChild(doc.createTextNode(aKeyword.trim()));
                        }
                    }
                }
            }
        }

        front.appendChild(journalMeta);

        front.appendChild(articleMeta);

        return front;

    }

    public static ArrayList<String> arrayCleaner(ArrayList<String> a) {

        ArrayList<String> temp = new ArrayList<String>();

        for (String aString : a) {

            aString = aString.trim();

            if (aString != null && !aString.equals("")) {

                temp.add(aString);

            }

        }

        return temp;

    }

    public static Element doAuthor(Element e0, ArrayList<String> refs) {

        String[] authors = refs.get(1).split(",");

        List<String> authorsInitList = new ArrayList<String>();

        for (String aAuthString : authors) {
            if (aAuthString.trim().length() == 1) {
                authorsInitList.add(aAuthString.trim());
            }
        }

        Collections.sort(authorsInitList);

        Element e3 = doc.createElement("contrib-group");

        Element e11 = null;

        e0.appendChild(e3);

        for (int i = 0; i < authors.length; i++) {

            authors[i] = authors[i].trim();

            System.out.println("author name:" + authors[i]);

            if (authors[i] == null || authors[i].equals("")) {

                continue;

            }

            if (authors[i].trim().length() == 1) {
                NodeList contribArr = e3.getElementsByTagName("contrib");

                Node lastContrib = contribArr.item(contribArr.getLength() - 1);
                Element e10 = doc.createElement("xref");

                lastContrib.appendChild(e10);
                if (authors[i].trim().equalsIgnoreCase(authorsInitList.get(authorsInitList.size() - 1).trim())) {

                    e10.setAttribute("ref-type", "corresp");

                    e10.setAttribute("rid", "COR" + authors[i]);

                    e10.appendChild(doc.createTextNode(authors[i].trim()));

                } else {
                    e10.setAttribute("ref-type", "aff");

                    e10.setAttribute("rid", "A" + authors[i].trim());

                    e10.appendChild(doc.createTextNode(authors[i].trim()));
                }

                continue;
            }

            String authorName = authors[i].substring(0, authors[i].length() - 1);

            String[] authorNameArr = authorName.split(" ");

            String surname = authorNameArr[authorNameArr.length - 1];

            String given_names = authorNameArr[0];

            int j = 1;

            while (j < (authorNameArr.length - 1)) {

                given_names += " " + authorNameArr[j];

                j++;

            }

            String refIndex = authors[i].substring(authors[i].length() - 1);

            Element e4 = doc.createElement("contrib");

            e3.appendChild(e4);

            e4.setAttribute("contrib-type", "author");

            Element e5 = doc.createElement("name");

            e4.appendChild(e5);

            Element e6 = doc.createElement("surname");

            Element e7 = doc.createElement("given-names");

            e5.appendChild(e6);

            e5.appendChild(e7);

            e6.appendChild(doc.createTextNode(surname.trim()));

            e7.appendChild(doc.createTextNode(given_names.trim()));

            Element e8 = doc.createElement("xref");

            e4.appendChild(e8);

            e8.setAttribute("ref-type", "aff");

            e8.setAttribute("rid", "A" + refIndex);

            e8.appendChild(doc.createTextNode(refIndex.trim()));

        }

        ArrayList<String> authorNotes = new ArrayList<String>();

        for (int x = 2; x < refs.size(); x++) {

            char index = refs.get(x).charAt(0);

            String context = refs.get(x).substring(1);

            if (context.startsWith("Corresponding")) {

                authorNotes.add(refs.get(x));

                continue;

            }

            e11 = doc.createElement("aff");

            Element e12 = doc.createElement("label");

            e11.appendChild(e12);

            e0.appendChild(e11);

            e11.setAttribute("id", "A" + index);

            e12.appendChild(doc.createTextNode("" + index));

            e11.appendChild(doc.createTextNode(context));

        }

        if (authorNotes.size() > 0) {

            Element e13 = doc.createElement("author-notes");

            e0.appendChild(e13);

            for (int x = 0; x < authorNotes.size(); x++) {

                char index = authorNotes.get(x).charAt(0);

                String context = authorNotes.get(x).substring(1);

                Element e14 = doc.createElement("corresp");

                Element e15 = doc.createElement("label");

                e13.appendChild(e14);

                e14.appendChild(e15);

                e14.setAttribute("id", "COR" + index);

                e15.appendChild(doc.createTextNode(index + ""));

                if (context.contains("Email:")) {
                    String[] aaa = context.split("Email:");
                    e14.appendChild(doc.createTextNode(aaa[0].trim() + " Email: "));
                    Element e20 = doc.createElement("email");
                    e14.appendChild(e20);
                    aaa[1] = aaa[1] == null ? "" : aaa[1].trim();
                    e20.appendChild(doc.createTextNode(aaa[1]));
                } else {
                    context = context == null ? "" : context.trim();
                    e14.appendChild(doc.createTextNode(context));
                }

            }

        }

        return e0;

    }

    public static Element getTable(String name) {
        DataFormatter formatter = new DataFormatter(Locale.US);
        if (name == null) {
            DocumentBuilder db = null;
            try {
                db = dbf.newDocumentBuilder();
            } catch (ParserConfigurationException ex) {
                ta.append("\nerrors happen:\n");
                ta.append(ex.getMessage() + "\n");
            }
            doc = db.newDocument();
        }

        if (name == null) {
            name = "C:\\Users\\DLiu1\\Documents\\NetBeansProjects\\Simon\\dist\\Table 1";
        }
        String fileName = name + ".xls";

        File aaa = new File(fileName);
        if (!aaa.exists()) {
            RefSouceOnlyMain
                    .error(fileName + " doesn't exist, please copy the " + fileName + " into the same folder!");
            return null;
        }
        Element tableFrame = null;
        try {

            tableFrame = doc.createElement("table");

            tableFrame.setAttribute("frame", "hsides");

            tableFrame.setAttribute("rules", "groups");
            Element thead = doc.createElement("thead");
            Element tbody = doc.createElement("tbody");
            tableFrame.appendChild(thead);
            tableFrame.appendChild(tbody);
            /** Creating Input Stream**/
            //InputStream myInput= ReadExcelFile.class.getResourceAsStream( fileName );
            FileInputStream myInput = new FileInputStream(aaa);

            /** Create a POIFSFileSystem object**/
            POIFSFileSystem myFileSystem = new POIFSFileSystem(myInput);

            /** Create a workbook using the File System**/
            HSSFWorkbook myWorkBook = new HSSFWorkbook(myFileSystem);

            /** Get the first sheet from workbook**/
            HSSFSheet mySheet = myWorkBook.getSheetAt(0);

            /** We now need something to iterate through the cells.**/
            Iterator rowIter = mySheet.rowIterator();

            int theRow = 0;
            int theadRows = 1;
            while (rowIter.hasNext()) {
                theRow++;
                HSSFRow myRow = (HSSFRow) rowIter.next();
                Iterator cellIter = myRow.cellIterator();
                //Vector cellStoreVector=new Vector();
                System.out.println("\nprinting " + theRow);
                Element tr = doc.createElement("tr");

                System.out.println("\nprinting " + theRow);
                while (cellIter.hasNext()) {
                    HSSFCell myCell = (HSSFCell) cellIter.next();
                    CellProperties cp = new CellProperties(myCell);

                    Element td = null;
                    int colspan = cp.getColspan();
                    int rowspan = cp.getRowspan();
                    CellReference ref = new CellReference(myCell);
                    System.out.println(
                            "The value of " + ref.formatAsString() + " is " + formatter.formatCellValue(myCell));
                    // String myCellValue = myCell.toString();
                    //  myCell.setCellType(Cell.CELL_TYPE_STRING);
                    // String myCellValue = myCell.getRichStringCellValue().toString();
                    String myCellValue = formatter.formatCellValue(myCell);
                    if (myCellValue != null && myCellValue.trim().endsWith(".0")) {
                        System.out.println(myCellValue + " have 0");
                        myCellValue = myCellValue.replace(".0", "");
                    }
                    System.out
                            .println(myCellValue + ": colspan:" + cp.getColspan() + " rowspan:" + cp.getRowspan());
                    if (rowspan > 1) {
                        if (theRow == 1) {
                            theadRows = rowspan;
                        }
                    }
                    if (theRow <= theadRows) {
                        td = doc.createElement("th");
                        td.setAttribute("align", "left");
                    } else {
                        td = doc.createElement("td");
                        td.setAttribute("align", "left");
                        td.setAttribute("valign", "top");
                    }
                    if (colspan > 1) {
                        td.setAttribute("colspan", colspan + "");
                    }
                    if (rowspan > 1) {
                        td.setAttribute("rowspan", rowspan + "");
                    }
                    if ((colspan > 1 || rowspan > 1) && myCellValue.trim().equals("")) {
                        continue;
                    }

                    Element bold = doc.createElement("bold");

                    tr.appendChild(td);

                    td.appendChild(doc.createTextNode(myCellValue.trim()));

                    //  cellStoreVector.addElement(myCell);
                }

                if (theRow <= theadRows) {
                    thead.appendChild(tr);
                } else {
                    tbody.appendChild(tr);
                }
                // cellVectorHolder.addElement(cellStoreVector);
            }
        } catch (Exception e) {
            ta.append("\nerrors happen:\n");
            ta.append(e.getMessage() + "\n");
        }

        return tableFrame;
    }

    public static void readMyDocument(String fileName) {

        POIFSFileSystem fs = null;

        try {

            fs = new POIFSFileSystem(new FileInputStream(fileName));

            HWPFDocument doc = new HWPFDocument(fs);

            /** Read the content **/
            Main.readParagraphs(doc, RefSouceOnlyMain.ta, RefSouceOnlyMain.refs);

            int realIndex = 0;

            try {

                for (int i = 0; i < refs.size(); i++) {

                    String temp = refs.get(i).trim();

                    System.out.println(i + ":" + temp);

                    refs.set(i, temp);

                    if (temp == null || temp.length() < 3) {

                        continue;

                    }

                    realIndex++;

                    ta.append("\n" + "dealing with the " + i + " ref:" + refs.get(i));

                    if (realIndex == 1) {
                        RefSouceOnlyMain.isOriginal = temp;
                        continue;
                    }

                    if (realIndex == 2) {

                        title = (temp == null ? "Unknown Title" : temp);
                        continue;
                    }

                    if (temp.startsWith("[a]")) {
                        if (realIndex < 3) {
                            RefSouceOnlyMain.error("author tag is located at wrong place.");
                        }
                        if (temp.equals("[a]")) {

                            int j = i;

                            while (!refs.get(j).equals("[/a]")) {

                                temp = refs.get(j).trim();
                                refs.set(j, temp);

                                if (temp == null || temp.length() < 3) {
                                    j++;

                                    continue;

                                }

                                authors.add(refs.get(j));

                                j++;

                            }

                            i = j;
                            continue;

                        } else {
                            RefSouceOnlyMain.error("[a] must not be followed by anything.\n" + temp);
                        }
                    }

                    Pattern p = Pattern.compile("^\\s{0,}\\d+/\\d+/\\d+\\s{0,}$");

                    if (temp.startsWith("Manuscript accepted")) {
                        manuscriptDateAccepted = temp.replace("Manuscript accepted:", "");
                        Matcher m = p.matcher(manuscriptDateAccepted);
                        if (m.find()) {
                            continue;
                        } else {
                            RefSouceOnlyMain.error(
                                    "manuscriptDateAccepted must follow by data format:dd/dd/dddd.\n" + temp);
                        }

                    }

                    if (temp.startsWith("Short title")) {

                        shortTitle = temp.replace("Short title:", "");
                        continue;
                    }

                    if (temp.startsWith("doi:")) {

                        doi = temp.replace("doi:", "");
                        continue;
                    }

                    if (temp.startsWith("ppub:")) {

                        ppub = temp.replace("ppub:", "");
                        Pattern ppub_p = Pattern.compile("^\\s{0,}\\d+/\\d+\\s{0,}$");
                        Matcher m = ppub_p.matcher(ppub);
                        if (m.find()) {
                            continue;
                        } else {
                            RefSouceOnlyMain.error("ppub data format must be:dd/dd/dddd.\n" + temp);
                        }
                    }

                    if (temp.startsWith("epub:")) {

                        epub = temp.replace("epub:", "");
                        Matcher m = p.matcher(epub);
                        if (m.find()) {
                            continue;
                        } else {
                            RefSouceOnlyMain.error("epub data format must be:dd/dd/dddd.\n" + temp);
                        }
                    }

                    if (temp.startsWith("volume:")) {

                        volume = temp.replace("volume:", "");
                        Pattern pc = Pattern.compile("^\\s{0,}\\d+\\s{0,}$");
                        Matcher m = pc.matcher(volume);
                        if (m.find()) {
                            continue;
                        } else {
                            RefSouceOnlyMain.error("must only be digit number:\n" + temp);
                        }
                    }

                    if (temp.startsWith("issue")) {

                        issue = temp.replace("issue:", "");
                        Pattern pc = Pattern.compile("^\\s{0,}\\d+\\s{0,}$");
                        Matcher m = pc.matcher(issue);
                        if (m.find()) {
                            continue;
                        } else {
                            RefSouceOnlyMain.error("must only be digit number:\n" + temp);
                        }
                    }

                    if (temp.startsWith("fpage")) {

                        fpage = temp.replace("fpage:", "");
                        Pattern pc = Pattern.compile("^\\s{0,}\\d+\\s{0,}$");
                        Matcher m = pc.matcher(fpage);
                        if (m.find()) {
                            continue;
                        } else {
                            RefSouceOnlyMain.error("must only be digit number:\n" + temp);
                        }
                    }

                    if (temp.startsWith("lpage")) {

                        lpage = temp.replace("lpage:", "");
                        Pattern pc = Pattern.compile("^\\s{0,}\\d+\\s{0,}$");
                        Matcher m = pc.matcher(lpage);
                        if (m.find()) {
                            continue;
                        } else {
                            RefSouceOnlyMain.error("must only be digit number:\n" + temp);
                        }
                    }

                    if (temp.startsWith("date accepted")) {

                        dateAccepted = temp.replace("date accepted:", "");
                        Matcher m = p.matcher(dateAccepted);
                        if (m.find()) {
                            continue;
                        } else {
                            RefSouceOnlyMain.error("data format must be:dd/dd/dddd.\n" + temp);
                        }
                    }

                    if (temp.startsWith("copyright-statement")) {

                        copyrightStat = temp.replace("copyright-statement:", "");
                        continue;
                    }

                    if (temp.startsWith("copyright-year")) {

                        copyrightYear = temp.replace("copyright-year:", "");
                        Pattern pc = Pattern.compile("^\\s{0,}\\d{4}\\s{0,}$");
                        Matcher m = pc.matcher(copyrightYear);
                        if (m.find()) {
                            continue;
                        } else {
                            RefSouceOnlyMain.error("must only be 4 digit numbers:\n" + temp);
                        }
                    }

                    if (temp.equalsIgnoreCase("Abstract")) {
                        int j = i;
                        while (!refs.get(j).trim().equals("[s1]Keywords")) {

                            ta.append("try find out introduction " + refs.get(j) + "\n");

                            temp = refs.get(j).trim();
                            refs.set(j, temp);

                            if (temp == null || temp.length() < 3) {
                                j++;

                                continue;

                            }

                            abstractArr.add(refs.get(j));

                            j++;

                        }

                        i = j - 1;
                        continue;
                    }

                    if (temp.trim().equalsIgnoreCase("[s1]Keywords")) {
                        int j = i;
                        while (!refs.get(j).trim().equals("[body]")) {

                            ta.append("try find out introduction " + refs.get(j) + "\n");

                            temp = refs.get(j).trim();
                            refs.set(j, temp);

                            if (temp == null || temp.length() < 3) {
                                j++;

                                continue;

                            }

                            keywordArr.add(refs.get(j));

                            j++;

                        }

                        i = j - 1;
                        continue;
                    }

                    if (temp.equals("[body]")) {
                        RefSouceOnlyMain.isValidBoday = true;
                        int j = i;
                        while (!refs.get(j).equals("Acknowledgement") && !refs.get(j).equals("[back]")) {

                            ta.append("try find out introduction " + refs.get(j) + "\n");

                            temp = refs.get(j).trim();
                            refs.set(j, temp);

                            if (temp == null || temp.length() < 3) {
                                j++;

                                continue;

                            }

                            RefSouceOnlyMain.discussion.add(refs.get(j));

                            j++;

                        }

                        i = j - 1;
                        continue;
                    }

                    if (temp.equals("Acknowledgement")) {

                        int j = i + 1;

                        while (!refs.get(j).equals("[back]")) {

                            temp = refs.get(j).trim();
                            refs.set(j, temp);

                            if (temp == null || temp.length() < 3) {
                                j++;

                                continue;

                            }

                            RefSouceOnlyMain.acknowledgement.add(refs.get(j));

                            j++;

                        }

                        i = j - 1;
                        continue;
                    }

                    if (temp.equals("[back]")) {
                        RefSouceOnlyMain.isValidBack = true;

                        int j = i;

                        while (!refs.get(j).equals("Table") && !refs.get(j).equals("Figure legends")
                                && !refs.get(j).equals("References")) {

                            temp = refs.get(j).trim();
                            refs.set(j, temp);

                            if (temp == null || temp.length() < 3) {
                                j++;

                                continue;

                            }

                            RefSouceOnlyMain.disclosure.add(refs.get(j));

                            j++;

                        }

                        i = j - 1;

                        continue;

                    }

                    if (temp.equalsIgnoreCase("Table")) {

                        int j = i + 1;

                        while (!refs.get(j).startsWith("Figure legends") && !refs.get(j).equals("References")) {

                            List<String> aTable = new ArrayList<String>();

                            refs.set(j, refs.get(j).trim());

                            String tempTemp = refs.get(j).trim();
                            System.out.println("setup table:" + tempTemp);

                            if (refs.get(j) == null || tempTemp.length() < 3) {
                                j++;

                                continue;

                            }

                            if (!tempTemp.contains("[title]")) {
                                RefSouceOnlyMain.error("problem happened around " + tempTemp);
                                //System.exit(-1);
                            }

                            String[] a = refs.get(j).split("\\[title\\]");

                            aTable.add(a[0]);

                            String[] b = new String[2];

                            if (a[1].contains("footnotes")) {
                                b = a[1].split("\\[footnotes\\]");
                                j++;
                                while (!refs.get(j).startsWith("Figure legends")
                                        && !refs.get(j).equals("References") && !refs.get(j).startsWith("Table")) {
                                    b[1] += "aaaaa" + refs.get(j);
                                    j++;
                                }
                                j--;
                            } else {
                                b[0] = a[1];
                                b[1] = "";
                            }

                            aTable.add(b[0]);

                            aTable.add(b[1]);

                            RefSouceOnlyMain.table.add(aTable);

                            j++;

                        }

                        i = j - 1;
                        continue;
                    }

                    if (temp.equals("Figure legends")) {

                        int j = i + 1;

                        while (!refs.get(j).startsWith("References")) {

                            List<String> aTable = new ArrayList<String>();

                            refs.set(j, refs.get(j).trim());

                            String tempTemp = refs.get(j).trim();

                            if (tempTemp == null || tempTemp.length() < 3) {
                                j++;

                                continue;

                            }

                            if (!tempTemp.contains("[legend]")) {
                                RefSouceOnlyMain.error("problem happened around " + tempTemp);
                                // System.exit(-1);
                            }

                            String[] a = refs.get(j).split("\\[legend\\]");

                            aTable.add(a[0]);

                            String[] b = a[1].split("\\[file\\]");

                            aTable.add(b[0]);

                            aTable.add(b[1]);

                            RefSouceOnlyMain.figure.add(aTable);

                            j++;
                        }

                        i = j - 1;
                        continue;
                    }

                    if (temp.equals("References")) {
                        RefSouceOnlyMain.isValidRefs = true;

                        i++;

                        while (i < refs.size()) {

                            System.out.println("adding reference:" + refs.get(i));
                            String result = refs.get(i);
                            result += "httphttp";

                            String secondString = null;
                            if (i + 1 < refs.size()) {
                                secondString = refs.get(i + 1);
                            }

                            System.out.println("new string 1:" + secondString);
                            String thirdString = null;
                            if (i + 2 < refs.size()) {
                                thirdString = refs.get(i + 2);
                            }

                            if (secondString != null && (secondString.trim().startsWith("http://")
                                    || secondString.trim().startsWith("Http://"))) {
                                result += secondString.trim();
                                i++;

                                if (thirdString != null && (thirdString.trim().startsWith("http://")
                                        || thirdString.trim().startsWith("Http://"))) {
                                    result += thirdString.trim();
                                    i++;
                                }
                            }

                            result = result.replaceAll("http://dx.doi.org/", "aaaaadoi");
                            result = result.replaceAll("Http://dx.doi.org/", "aaaaadoi");
                            result = result.replaceAll("http://www.ncbi.nlm.nih.gov/pubmed/", "aaaaapmid");
                            result = result.replaceAll("Http://www.ncbi.nlm.nih.gov/pubmed/", "aaaaapmid");

                            RefSouceOnlyMain.references.add(result);

                            i++;

                        }

                    }

                    //doit(refs.get(i), i);

                }

            } catch (Exception e) {

                // TODO Auto-generated catch block

                ta.append("\nerrors happen:\n");
                ta.append(e.getMessage() + "\n");

            }

            int pageNumber = 1;

            /** We will try reading the header for page 1**/
            //readHeader(doc, pageNumber);
            /** Let's try reading the footer for page 1**/
            //readFooter(doc, pageNumber);
            /** Read the document summary**/
            //readDocumentSummary(doc);
        } catch (Exception e) {

            ta.append(e.getMessage());

        }

    }

    public static void readHeader(HWPFDocument doc, int pageNumber) {

        HeaderStories headerStore = new HeaderStories(doc);

        String header = headerStore.getHeader(pageNumber);

        ta.append("\n" + "Header Is: " + header);

    }

    public static void readFooter(HWPFDocument doc, int pageNumber) {

        HeaderStories headerStore = new HeaderStories(doc);

        String footer = headerStore.getFooter(pageNumber);

        ta.append("\n" + "Footer Is: " + footer);

    }

    public static void readDocumentSummary(HWPFDocument doc) {

        DocumentSummaryInformation summaryInfo = doc.getDocumentSummaryInformation();

        String category = summaryInfo.getCategory();

        String company = summaryInfo.getCompany();

        int lineCount = summaryInfo.getLineCount();

        int sectionCount = summaryInfo.getSectionCount();

        int slideCount = summaryInfo.getSlideCount();

        ta.append("\n" + "---------------------------");

        ta.append("\n" + "Category: " + category);

        ta.append("\n" + "Company: " + company);

        ta.append("\n" + "Line Count: " + lineCount);

        ta.append("\n" + "Section Count: " + sectionCount);

        ta.append("\n" + "Slide Count: " + slideCount);

    }

    public final static String prefixFileName = "c:\\";

    private static void replaceChar(String[] aaa) {
    }

    public static void generateXML(String theString, String fileName) throws IOException {

        Writer output = null;

        String prefix = "out/";

        File file = new File("out");

        if (!file.exists()) {
            file.mkdir();
        }

        file = new File(prefix + fileName);

        output = new BufferedWriter(new FileWriter(file));

        theString = theString.replaceAll("", "&#8216;").replaceAll("", "&#8217;").replaceAll("?", "&#8221;")
                .replaceAll("", "&#8220;").replaceAll("", "&#8805;").replaceAll("", "&#8804;")
                .replace("", "&#8226;");
        //theString = theString.replaceAll("","'").replaceAll("","'").replaceAll("?", "\"").replaceAll("", "\"");
        String[] aaaaa = theString.split("\n");
        Main.fixEncoding(aaaaa, RefSouceOnlyMain.ta, output);

        output.close();

        ta.append("\n" + "the final xml file has been written to " + file.getAbsolutePath());

    }

    public static void error(String a) {

        JOptionPane.showMessageDialog(null, a, "Error happening", JOptionPane.ERROR_MESSAGE);
    }

    public static void info(String a) {

        JOptionPane.showMessageDialog(null, a, "Important info", JOptionPane.INFORMATION_MESSAGE);
    }

    public static String finalXMLString = "";

    public static void main(String[] args) {
        RefSouceOnlyMain.getTable(null);
    }
}