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() {
/**
* query: protein sequence
*
- * @param protIn
+ * @param sequence
* protein sequence or partial of protein sequence
* @param searchtype
* "whole" or "partial" of protein sequence
* @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));
+ 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;