package compbio.controllers;
+import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
import java.util.regex.Pattern;
import compbio.beans.TotalByCounterBean;
import compbio.cassandra.readers.ReaderByCounter;
import compbio.cassandra.readers.SequenceReader;
-import compbio.statistic.CassandraRequester;
/**
* Spring controller for sequence queries. This version works in the servlet
model.put("njobs", 0);
model.put("prot", trimmedsequence);
model.put("searchtype", searchtype);
-
+ String csvline = "";
if (0 < trimmedsequence.length()) {
SequenceReader reader = new SequenceReader();
List<ProteinBean> result = reader.readProteins(trimmedsequence, searchtype);
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";
+ }
+ }
}
}
+ model.put("csvfile", csvline);
+
final long endTime = System.currentTimeMillis();
model.put("timeExecution", (endTime - startTime));
return "reportProteinSequences";
return "query/SequenceCounts";
}
- ReaderByCounter reader = new ReaderByCounter();
+ ReaderByCounter reader = new ReaderByCounter();
List<TotalByCounterBean> r = reader.readProteinByCounter(realcounter);
model.put("results", r);
model.put("njobs", 0);
+ String csvline = "";
if (null != r) {
model.put("njobs", r.size());
+ csvline = "\'Job%20 count\', \'Protein%20Sequence\'%0A";
}
+ // form line for CSV file
+
+ for (TotalByCounterBean b : r) {
+ if (b.getName().equals("")) {
+ csvline += "\'" + b.getTotaljobs() + "\',\'Alignment%20job\'%0A";
+ // fix problem with records without protein sequence (alignment
+ // jobs)
+ b.setName("Alignment job");
+ } else {
+ csvline += "\'" + b.getTotaljobs() + "\',\'" + b.getName() + "\'%0A";
+ }
+ }
+ model.put("csvfile", csvline);
+
+ model.put("results", r);
final long endTime = System.currentTimeMillis();
model.put("timeExecution", (endTime - startTime));
model.put("counter", realcounter);