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 public class SequenceReader extends CassandraReader {
  12
  13         public SequenceReader() {
  14                 super();
  15         }
  16
  17         /**
  18          * query: protein sequence
  19          *
  20          * @param protIn
  21          *            protein sequence or partial of protein sequence
  22          * @param searchtype
  23          *            "whole" or "partial" of protein sequence
  24          *
  25          * @return List<ProteinBean> to the controller SequenceController
  26          *
  27          **/
  28         public List<ProteinBean> readProteins(String protIn, String searchtype) {
  29                 List<ProteinBean> query = new ArrayList<ProteinBean>();
  30                 if (searchtype.equals("whole")) {
  31                         ResultSet results = CassandraQuery("SELECT  JobID, Predictions FROM ProteinRow WHERE Protein = '" + protIn + "';");
  32                         if (results.isExhausted())
  33                                 return null;
  34                         List<Row> rows = results.all();
  35                         ProteinBean structure = new ProteinBean(protIn, rows.get(0).getMap("Predictions", String.class, String.class));
  36                         for (Row r : rows) {
  37                                 structure.setJobid(r.getString("JobID"));
  38                         }
  39                         query.add(structure);
  40                 } else {
  41                         ResultSet results = CassandraQuery("SELECT  * FROM ProteinRow;");
  42                         if (results.isExhausted())
  43                                 return null;
  44                         List<Row> rows = results.all();
  45                         for (Row r : rows) {
  46                                 String prot = r.getString("Protein");
  47                                 if (prot.matches("(.*)" + protIn + "(.*)")) {
  48                                         ProteinBean structure = new ProteinBean(prot, r.getMap("Predictions", String.class, String.class));
  49                                         structure.setJobid(r.getString("JobID"));
  50                                         query.add(structure);
  51                                 }
  52                         }
  53                 }
  54                 if (searchtype.equals("partial")) {
  55                         for (ProteinBean entry : query) {
  56                                 entry.setSubProt(CreateSubprotein(entry.getSequence(), protIn));
  57                         }
  58                 }
  59                 return query;
  60         }
  61
  62         /**
  63          * create a list of parts of protein sequence for highlighting current value
  64          * in report;
  65          *
  66          * @param protein
  67          *            protein sequence
  68          * @param subprot
  69          *            partial of protein sequence
  70          *
  71          * @return List<String>
  72          *
  73          **/
  74         private static List<String> CreateSubprotein(String protein, String subprot) {
  75                 List<String> sub = new ArrayList<String>();
  76                 String subStr = protein;
  77                 while (subStr.length() > 0 && subStr.contains(subprot)) {
  78                         String first = subStr.substring(0, subStr.indexOf(subprot));
  79                         if (first.length() > 0)
  80                                 sub.add(first);
  81                         sub.add(subprot);
  82                         subStr = subStr.substring(subStr.indexOf(subprot) + subprot.length(), subStr.length());
  83                 }
  84                 if (subStr.length() > 0)
  85                         sub.add(subStr);
  86                 return sub;
  87         }
  88 }