- System.out.println();
- Elements tableRowElements = table.select(":not(thead) tr");
- for (int i = 0; i < tableRowElements.size(); i++)
- {
- Element row = tableRowElements.get(i);
- Elements rowItems = row.select("td");
- if (rowItems.size() > 11)
- {
- // for (int j = 0; j < rowItems.size(); j++)
- // {
- // System.out.println(">>> r:" + j + " = "
- // + rowItems.get(j).text());
- // }
-
- String c = rowItems.get(6).select("input").attr("onmouseover");
- String alignedRange = c.substring(c.indexOf("Residues ") + 9,
- c.indexOf(" of your sequence aligned "));
- String coverage = c.substring(c.lastIndexOf(" (") + 2,
- c.lastIndexOf(" coverage). Click to view detailed"));
- // System.out.println("coverage" + coverage);
- try
- {
- Phyre2SummaryPojo psp = new Phyre2SummaryPojo();
- String sn = rowItems.get(0).text();
- psp.setSerialNo(Integer.valueOf(sn));
- psp.setTemplateId(rowItems.get(1).text());
- psp.setCoverage(coverage);
- psp.setAlignedRange(alignedRange);
- psp.setConfidence(Double.valueOf(rowItems.get(8).text()));
- psp.setPid(Integer.valueOf(rowItems.get(9).text()));
- psp.setTemplateSummary(rowItems.get(10).text());
- // System.out.println("row >>>> " + psp.toString());
- // System.out.println();
- phyre2Results.add(psp);
- } catch (NumberFormatException e)
- {
- e.printStackTrace();
- } catch (IndexOutOfBoundsException e)
- {
- e.printStackTrace();
- } catch (Exception e)
- {
- e.printStackTrace();
- }
- }
- }
+ String[] lineData = line.split(" ");
+ Phyre2SummaryPojo psp = new Phyre2SummaryPojo();
+ psp.setSerialNo(Integer.valueOf(lineData[0]));
+ psp.setTemplateId(lineData[1]);
+ psp.setConfidence(100 * Double.valueOf(lineData[2]));
+ psp.setPid(Integer.valueOf(lineData[3]));
+ psp.setAlignedRange(lineData[4] + " - " + lineData[5]);
+ // psp.setCoverage(coverage);
+ // psp.setTemplateSummary(templateSummary);
+ phyre2Results.add(psp);