Merge branch 'DAO'

[proteocache.git] / server / compbio / controllers / SequenceController.java

diff --git a/server/compbio/controllers/SequenceController.java b/server/compbio/controllers/SequenceController.java
index 105ef2f..76903f8 100644 (file)
--- 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;
@@ -13,7 +14,6 @@ import compbio.beans.ProteinBean;
 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
@@ -97,7 +97,7 @@ public class SequenceController extends BasicController {
                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);
@@ -107,8 +107,23 @@ public class SequenceController extends BasicController {
                                        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";
@@ -149,14 +164,31 @@ public class SequenceController extends BasicController {
                        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);