X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=datadb%2Fcompbio%2Fcassandra%2Freaders%2FSequenceReader.java;h=e64d215e90314e2a72ee04295b1aeffc54e2b662;hb=5aec34fb583587602104757aaadc13e7a32ca75c;hp=0aedbb24b4df110d2d149a75b6035bdb1be18d27;hpb=006363dc999cef4e9c49dd6a38ea0d78cbb62472;p=proteocache.git

diff --git a/datadb/compbio/cassandra/readers/SequenceReader.java b/datadb/compbio/cassandra/readers/SequenceReader.java
index 0aedbb2..e64d215 100644
--- a/datadb/compbio/cassandra/readers/SequenceReader.java
+++ b/datadb/compbio/cassandra/readers/SequenceReader.java
@@ -8,6 +8,16 @@ import com.datastax.driver.core.Row;
 
 import compbio.beans.ProteinBean;
 
+/**
+ * Reader class for making requests on protein sequences to cassandra.
+ * 
+ * @author Alexander Sherstnev
+ * @author Natasha Sherstneva
+ * 
+ * @since 0.5
+ * @version 1.0 
+ * @since December 2013
+ */
 public class SequenceReader extends CassandraReader {
 
 	public SequenceReader() {
@@ -17,7 +27,7 @@ public class SequenceReader extends CassandraReader {
 	/**
 	 * query: protein sequence
 	 * 
-	 * @param protIn
+	 * @param sequence
 	 *            protein sequence or partial of protein sequence
 	 * @param searchtype
 	 *            "whole" or "partial" of protein sequence
@@ -25,35 +35,33 @@ public class SequenceReader extends CassandraReader {
 	 * @return List<ProteinBean> to the controller SequenceController
 	 * 
 	 **/
-	public List<ProteinBean> readProteins(String protIn, String searchtype) {
+	public List<ProteinBean> readProteins(String sequence, String searchtype) {
 		List<ProteinBean> query = new ArrayList<ProteinBean>();
 		if (searchtype.equals("whole")) {
-			ResultSet results = CassandraQuery("SELECT  JobID, Predictions FROM ProteinRow WHERE Protein = '" + protIn + "';");
+			ResultSet results = CassandraQuery("SELECT JobID, Predictions FROM ProteinRow WHERE Protein = '" + sequence + "';");
 			if (results.isExhausted())
 				return null;
 			List<Row> rows = results.all();
-			ProteinBean structure = new ProteinBean(protIn, rows.get(0).getMap("Predictions", String.class, String.class));
+			ProteinBean structure = new ProteinBean(sequence, rows.get(0).getMap("Predictions", String.class, String.class));
 			for (Row r : rows) {
 				structure.setJobid(r.getString("JobID"));
 			}
 			query.add(structure);
 		} else {
-			ResultSet results = CassandraQuery("SELECT  * FROM ProteinRow;");
+			ResultSet results = CassandraQuery("SELECT * FROM ProteinRow;");
 			if (results.isExhausted())
 				return null;
 			List<Row> rows = results.all();
 			for (Row r : rows) {
-				String prot = r.getString("Protein");
-				if (prot.matches("(.*)" + protIn + "(.*)")) {
-					ProteinBean structure = new ProteinBean(prot, r.getMap("Predictions", String.class, String.class));
-					structure.setJobid(r.getString("JobID"));
-					query.add(structure);
+				String protein = r.getString("Protein");
+				if (protein.matches("(.*)" + sequence + "(.*)")) {
+					ProteinBean foundsequence = new ProteinBean(protein, r.getMap("Predictions", String.class, String.class));
+					foundsequence.setJobid(r.getString("JobID"));
+					query.add(foundsequence);
 				}
 			}
-		}
-		if (searchtype.equals("partial")) {
 			for (ProteinBean entry : query) {
-				entry.setSubProt(CreateSubprotein(entry.getSequence(), protIn));
+				entry.setSubProt(CreateSubprotein(entry.getSequence(), sequence));
 			}
 		}
 		return query;