- StringBuilder htmlData = new StringBuilder();
- String currentLine;
- while ((currentLine = nextLine()) != null)
- {
- htmlData.append(currentLine);
- }
-
- Document doc = Jsoup.parse(htmlData.toString());
- Element content = doc.getElementById("seqData");
-
- String alignmentJsonString = content.val();
- JSONParser jsonParser = new JSONParser();
- JSONObject alignmentJsonObj = (JSONObject) jsonParser
- .parse(alignmentJsonString);
- JSONArray seqJsonArray = (JSONArray) alignmentJsonObj.get("seqs");
- String bioJsColourScheme = (String) alignmentJsonObj
- .get("globalColorScheme");
- cs = getJalviewColorScheme(bioJsColourScheme);
-
- for (Iterator<JSONObject> sequenceIter = seqJsonArray.iterator(); sequenceIter
- .hasNext();)
- {
- JSONObject sequence = sequenceIter.next();
- String sequcenceString = sequence.get("seq").toString();
- Sequence seq = new Sequence(sequence.get("name").toString(),
- sequcenceString, Integer.valueOf(sequence.get("start")
- .toString()), Integer.valueOf(sequence.get("end")
- .toString()));
-
- JSONArray jsonSeqArray = (JSONArray) sequence.get("features");
- SequenceFeature[] retrievedSeqFeatures = getJalviewSequenceFeatures(
- jsonSeqArray, seq);
- if (retrievedSeqFeatures != null)
- {
- seq.setSequenceFeatures(retrievedSeqFeatures);
- }
- seqs.add(seq);
-
+ Element content = null;
+ Document doc = null;
+ try {
+ StringBuilder htmlData = new StringBuilder();
+ String currentLine;
+ while ((currentLine = nextLine()) != null)
+ {
+ htmlData.append(currentLine);
+ }
+
+ doc = Jsoup.parse(htmlData.toString());
+ } catch (OutOfMemoryError oom) {
+ errormessage = "Not enough memory to process HTML document";
+ throw new IOException(errormessage);