src/jalview/io/HtmlFile.java

   1 package jalview.io;
   2
   3 import jalview.datamodel.Sequence;
   4
   5 import java.io.IOException;
   6 import java.util.Iterator;
   7
   8 import org.json.simple.JSONArray;
   9 import org.json.simple.JSONObject;
  10 import org.json.simple.parser.JSONParser;
  11 import org.jsoup.Jsoup;
  12 import org.jsoup.nodes.Document;
  13 import org.jsoup.nodes.Element;
  14
  15 public class HtmlFile extends AlignFile {
  16         public static final String FILE_EXT = "html";
  17
  18         public static final String FILE_DESC = "HTML";
  19
  20         public HtmlFile() {
  21                 super();
  22         }
  23
  24         public HtmlFile(FileParse source) throws IOException {
  25                 super(source);
  26         }
  27
  28         public HtmlFile(String inFile, String type) throws IOException {
  29                 super(inFile, type);
  30         }
  31
  32         @SuppressWarnings("unchecked")
  33         @Override
  34         public void parse() throws IOException {
  35                 try {
  36                         StringBuilder htmlData = new StringBuilder();
  37                         String currentLine;
  38                         while ((currentLine = nextLine()) != null) {
  39                                 htmlData.append(currentLine);
  40                         }
  41
  42                         Document doc = Jsoup.parse(htmlData.toString());
  43                         Element content = doc.getElementById("seqData");
  44
  45                         String alignmentJsonString = "{\"seqs\":" + content.val() + "}";
  46                         JSONParser jsonParser = new JSONParser();
  47                         JSONObject alignmentJsonObj = (JSONObject) jsonParser.parse(alignmentJsonString);
  48                         JSONArray seqJsonArray = (JSONArray) alignmentJsonObj.get("seqs");
  49
  50                         for (Iterator<JSONObject> sequenceIter = seqJsonArray.iterator(); sequenceIter.hasNext();) {
  51                                 JSONObject sequence = sequenceIter.next();
  52                                 System.out.println(sequence.get("id").toString() + " " + sequence.get("name"));
  53                                 String sequcenceString = sequence.get("seq").toString();
  54                                 Sequence seq = new Sequence(sequence.get("name").toString(), sequcenceString, 0, sequcenceString.length());
  55                                 seqs.add(seq);
  56
  57                         }
  58                 } catch (Exception e) {
  59                         e.printStackTrace();
  60                 }
  61         }
  62
  63         @Override
  64         public String print() {
  65                 throw new UnsupportedOperationException("Print method of HtmlFile not yet supported!");
  66         }
  67
  68 }