/**
 *
 * @author James Gosling
 */
import java.io.*;
import java.util.*;
import java.util.ArrayList;
import java.util.regex.*;

public class BibReorder {
  String[] parts;
  DocumentFragment[] documentBody, bibliography;
  static Pattern bibRefPattern = Pattern.compile("\\[([0-9]+)\\]");
  public static void main(String[] args) {
    try {
      BibReorder doc = new BibReorder();
      boolean byFirstOccurrance = false;
      boolean processed = false;
      for(String s:args)
        if("-f".equals(s)) byFirstOccurrance = true;
        else {
          processed = true;
          doc.load(new FileInputStream(s));
          doc.reorder(byFirstOccurrance);
          doc.dumpDocument();
        }
      if(!processed) {
        doc.load(BibReorder.class.getResource("sample. Data").openStream());
        doc.reorder(byFirstOccurrance);
        doc.dumpDocument();
      }
    } catch (IOException ex) {
      System.err.println("Error reading file: "+ex);
    }
  }
  void load(InputStream in) throws IOException {
    Reader inc = new BufferedReader(new InputStreamReader(new BufferedInputStream(in)));
    StringBuilder sb = new StringBuilder();
    int c;
    while((c=inc.read())>=0) sb.append((char)c);
    parts = sb.toString().split("@footnote:");
    if(parts.length!=2) throw new IOException("Must have exactly 2 parts");
    documentBody = parseDocumentPart(parts[0]);
    bibliography = parseDocumentPart(parts[1]);
    in.close();
  }
  void reorder(boolean byFirstOccurrance) {
    int slot = 0;
    if(byFirstOccurrance) {
      for(DocumentFragment p:documentBody)
        if(p.tag!=null && p.tag.sequenceNumber==0) p.tag.sequenceNumber = ++slot;
      Arrays.sort(bibliography, new Comparator<DocumentFragment>(){
        public int compare(DocumentFragment o1, DocumentFragment o2) {
          return (o1.tag==null ? 0 : o1.tag.sequenceNumber)-(o2.tag==null ? 0 : o2.tag.sequenceNumber);
        }
      });
    } else
      for(DocumentFragment p:bibliography)
        if(p.tag!=null) p.tag.sequenceNumber = ++slot;
  }
  void dumpDocument() {
    dumpDocumentPart(documentBody, parts[0]);
    System.out.append("@footnote:");
    dumpDocumentPart(bibliography, parts[1]);
  }
  DocumentFragment[] parseDocumentPart(String s) {
    Matcher m = bibRefPattern.matcher(s);
    DocumentFragment prev = new DocumentFragment(0,null);
    ArrayList<DocumentFragment> pieces = new ArrayList<DocumentFragment>();
    pieces.add(prev);
    while(m.find()) {
      prev.end = m.start(0);
      String tlabel = s.substring(m.start(1),m.end(1));
      BibliographyTag t = tags.get(tlabel);
      if(t==null) { t = new BibliographyTag();
             tags.put(tlabel, t); }
      prev = new DocumentFragment(m.end(0),t);
      pieces.add(prev);
    }
    prev.end = s.length();
    return pieces.toArray(new DocumentFragment[pieces.size()]);
  }
  void dumpDocumentPart(DocumentFragment[] pieces, String part) {
    for(DocumentFragment p:pieces) {
      if(p.tag!=null) System.out.print("["+p.tag.sequenceNumber+"]");
      System.out.append(part,p.start,p.end);
    }
  }
  class DocumentFragment {
    int start, end;
    BibliographyTag tag;
    DocumentFragment(int st, BibliographyTag t) { start = st; tag = t; }
  }
  class BibliographyTag { int sequenceNumber; }
  HashMap<String,BibliographyTag> tags = new HashMap<String, BibliographyTag>();
}