X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=server%2Fcompbio%2Fcontrollers%2FSequenceController.java;h=738e2d8924e45174639f860dc9def02350ca4a9a;hb=8256bed38c0abeefe003adf6d9f126113f9cc5b3;hp=df4c98720e03b1936a2a2653aa919a50ccb354e1;hpb=025c55d49c191f24d0e06c5cbb69a9894c50af22;p=proteocache.git

diff --git a/server/compbio/controllers/SequenceController.java b/server/compbio/controllers/SequenceController.java
index df4c987..738e2d8 100644
--- a/server/compbio/controllers/SequenceController.java
+++ b/server/compbio/controllers/SequenceController.java
@@ -1,5 +1,6 @@
 package compbio.controllers;
 
+import java.util.LinkedHashMap;
 import java.util.List;
 import java.util.Map;
 import java.util.regex.Pattern;
@@ -9,7 +10,9 @@ import org.springframework.web.bind.annotation.RequestMapping;
 import org.springframework.web.bind.annotation.RequestMethod;
 import org.springframework.web.bind.annotation.RequestParam;
 
+import compbio.cassandra.DataBase;
 import compbio.cassandra.ProteinBean;
+import compbio.cassandra.Total;
 import compbio.cassandra.TotalByCounterBean;
 import compbio.statistic.CassandraRequester;
 
@@ -68,7 +71,7 @@ public class SequenceController extends BasicController {
 		model.put("njobs", 0);
 		model.put("prot", trimmedsequence);
 		model.put("searchtype", searchtype);
-
+		String csvline = "";
 		if (0 < trimmedsequence.length()) {
 			CassandraRequester cr = new CassandraRequester();
 			List<ProteinBean> r = cr.readProteins(trimmedsequence, searchtype);
@@ -78,8 +81,23 @@ public class SequenceController extends BasicController {
 					model.put("njobs", r.get(0).getJobid().size());
 				else
 					model.put("njobs", r.size());
+				csvline = "\'Job\',\'Annotation\',\'Sequence\'%0A";
+			}
+			// form CSV file string
+			for (ProteinBean entry : r) {
+				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";
@@ -113,11 +131,27 @@ public class SequenceController extends BasicController {
 
 		CassandraRequester cr = new CassandraRequester();
 		List<TotalByCounterBean> r = cr.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);