From: Sasha Sherstnev <a.sherstnev@dundee.ac.uk>
Date: Mon, 25 Nov 2013 11:04:31 +0000 (+0000)
Subject: Merge branch 'servlets'
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=92420f700bca908529b5dc0e0e998dd2a7f98bc2;p=proteocache.git

Merge branch 'servlets'

Conflicts:
	datadb/compbio/cassandra/StructureProteinPrediction.java
	server/compbio/statistic/CassandraRequester.java
---

92420f700bca908529b5dc0e0e998dd2a7f98bc2
diff --cc datadb/compbio/cassandra/CassandraReader.java
index 28641db,b527738..6e3587b
--- a/datadb/compbio/cassandra/CassandraReader.java
+++ b/datadb/compbio/cassandra/CassandraReader.java
@@@ -84,11 -108,15 +108,15 @@@ public class CassandraReader 
  		List<Row> rows = results.all();
  		System.out.println("Query time is " + (queryTime - startTime) + " msec");
  		System.out.println(" rows analysed,  " + rows.size());
 -		List<StructureProteinPrediction> res = new ArrayList<StructureProteinPrediction>();
 +		List<AnnotatedProteinSequenceBean> res = new ArrayList<AnnotatedProteinSequenceBean>();
  		int c = 0;
  		for (Row r : rows) {
 -			StructureProteinPrediction structure = new StructureProteinPrediction(queryProtein, r.getString("JobID"), r.getMap(
 +			AnnotatedProteinSequenceBean structure = new AnnotatedProteinSequenceBean(queryProtein, r.getString("JobID"), r.getMap(
  					"Predictions", String.class, String.class));
+ 			if (structure.getPrediction().containsKey("jnetpred"))
+ 				structure.setJnetpred(structure.getPrediction().get("jnetpred"));
+ 			else
+ 				structure.setJnetpred("");
  			res.add(structure);
  			++c;
  		}
diff --cc server/compbio/statistic/CassandraRequester.java
index 214bf6f,afba67b..410a722
--- a/server/compbio/statistic/CassandraRequester.java
+++ b/server/compbio/statistic/CassandraRequester.java
@@@ -161,23 -194,26 +163,26 @@@ public class CassandraRequester 
  	 * query: protein sequence
  	 * */
  	public List<DataBase> readProteins(String protIn, String flag) {
+ 		if (protIn == null)
+ 			return null;
+ 		System.out.println(protIn.length());
  		query = new ArrayList<DataBase>();
 -		List<StructureProteinPrediction> res;
 +		List<AnnotatedProteinSequenceBean> res;
  		if (flag.equals("whole")) 
  			res = db.ReadWholeSequence(protIn);
  		 else 
- 			res = db.ReadPartOfSequence(protIn);
+ 			 res = (protIn.length() > 0) ? db.ReadPartOfSequence(protIn) : null;
  		if (res == null)
  			return null;
 -		for (StructureProteinPrediction entry : res) {
 -				DataBase bean = new DataBase();
 -				bean.setProt(entry.getSequence());
 -				bean.setId(entry.getJobid());
 -				bean.setJpred(entry.getJnetpred());
 -				if (flag.equals("part"))
 -					bean.setSubProt(CreateSubprot (entry.getSequence(), protIn));				
 -				query.add(bean);
 -			
 +		for (AnnotatedProteinSequenceBean entry : res) {
 +			DataBase db = new DataBase();
 +			db.setProt(entry.getSequence());
 +			db.setPredictions(entry);
 +			db.setId(entry.getJobid());
 +			if (flag.equals("part")) {
 +				db.setSubProt(CreateSubprot (entry.getSequence(), protIn));
 +			}
 +			query.add(db);
  		}
  		return query;
  	}