datadb/compbio/cassandra/readers/SequenceReader.java

   1 package compbio.cassandra.readers;
   2
   3 import java.util.ArrayList;
   4 import java.util.List;
   5
   6 import com.datastax.driver.core.ResultSet;
   7 import com.datastax.driver.core.Row;
   8
   9 import compbio.beans.ProteinBean;
  10
  11 /**
  12  * Reader class for making requests on protein sequences to cassandra.
  13  *
  14  * @author Alexander Sherstnev
  15  * @author Natasha Sherstneva
  16  *
  17  * @since 0.5
  18  * @version 1.0
  19  * @since December 2013
  20  */
  21 public class SequenceReader extends CassandraReader {
  22
  23         public SequenceReader() {
  24                 super();
  25         }
  26
  27         /**
  28          * query: protein sequence
  29          *
  30          * @param sequence
  31          *            protein sequence or partial of protein sequence
  32          * @param searchtype
  33          *            "whole" or "partial" of protein sequence
  34          *
  35          * @return List<ProteinBean> to the controller SequenceController
  36          *
  37          **/
  38         public List<ProteinBean> readProteins(String sequence, String searchtype) {
  39                 List<ProteinBean> query = new ArrayList<ProteinBean>();
  40                 if (searchtype.equals("whole")) {
  41                         ResultSet results = CassandraQuery("SELECT JobID, Predictions FROM ProteinRow WHERE Protein = '" + sequence + "';");
  42                         if (results.isExhausted())
  43                                 return null;
  44                         List<Row> rows = results.all();
  45                         ProteinBean structure = new ProteinBean(sequence, rows.get(0).getMap("Predictions", String.class, String.class));
  46                         for (Row r : rows) {
  47                                 structure.setJobid(r.getString("JobID"));
  48                         }
  49                         query.add(structure);
  50                 } else {
  51                         ResultSet results = CassandraQuery("SELECT * FROM ProteinRow;");
  52                         if (results.isExhausted())
  53                                 return null;
  54                         List<Row> rows = results.all();
  55                         for (Row r : rows) {
  56                                 String protein = r.getString("Protein");
  57                                 if (protein.matches("(.*)" + sequence + "(.*)")) {
  58                                         ProteinBean foundsequence = new ProteinBean(protein, r.getMap("Predictions", String.class, String.class));
  59                                         foundsequence.setJobid(r.getString("JobID"));
  60                                         query.add(foundsequence);
  61                                 }
  62                         }
  63                         for (ProteinBean entry : query) {
  64                                 entry.setSubProt(CreateSubprotein(entry.getSequence(), sequence));
  65                         }
  66                 }
  67                 return query;
  68         }
  69
  70         /**
  71          * create a list of parts of protein sequence for highlighting current value
  72          * in report;
  73          *
  74          * @param protein
  75          *            protein sequence
  76          * @param subprot
  77          *            partial of protein sequence
  78          *
  79          * @return List<String>
  80          *
  81          **/
  82         private static List<String> CreateSubprotein(String protein, String subprot) {
  83                 List<String> sub = new ArrayList<String>();
  84                 String subStr = protein;
  85                 while (subStr.length() > 0 && subStr.contains(subprot)) {
  86                         String first = subStr.substring(0, subStr.indexOf(subprot));
  87                         if (first.length() > 0)
  88                                 sub.add(first);
  89                         sub.add(subprot);
  90                         subStr = subStr.substring(subStr.indexOf(subprot) + subprot.length(), subStr.length());
  91                 }
  92                 if (subStr.length() > 0)
  93                         sub.add(subStr);
  94                 return sub;
  95         }
  96 }