- CassandraRequester cr = new CassandraRequester();
- List<DataBase> r = cr.readProteins(trimmedsequence, flag);
- model.put("results", r);
- if (null != r) {
- System.out.println("result size = " + r.size());
- model.put("njobs", r.size());
+ SequenceReader reader = new SequenceReader();
+ List<ProteinBean> result = reader.readProteins(trimmedsequence, searchtype);
+ model.put("results", result);
+ if (null != result) {
+ if (searchtype.equals("whole"))
+ model.put("njobs", result.get(0).getJobid().size());
+ else
+ model.put("njobs", result.size());
+ csvline = "\'Job\',\'Annotation\',\'Sequence\'%0A";
+ // form CSV file string
+ for (ProteinBean entry : result) {
+ List<String> jobs = entry.getJobid();
+ String protein = entry.getSequence();
+ LinkedHashMap<String, String> predictions = entry.getPredictions();
+ for (String job : jobs) {
+ csvline += "\'" + job + "\',\'Sequence\',\'" + protein + "\',\'%0A";
+ for (Map.Entry<String, String> pr : predictions.entrySet()) {
+ csvline += "\'\',\'" + pr.getKey() + "\',\'" + pr.getValue() + "\'%0A";
+ }
+ }
+ }