datadb/compbio/beans/ProteinBean.java

   1 package compbio.beans;
   2
   3 import java.util.ArrayList;
   4 import java.util.LinkedHashMap;
   5 import java.util.List;
   6 import java.util.Map;
   7
   8 import compbio.cassandra.PredictionIndex;
   9
  10 /**
  11  * POJO bean with information on a protein
  12  *
  13  * @author Natasha Sherstneva
  14  *
  15  * @version 1.0
  16  * @since Jan 2014
  17  */
  18 public class ProteinBean implements PredictionIndex {
  19         private String sequence; // protein sequence
  20         private String jnetpred; // the main Jpred prediction sequence
  21         private List<String> jobid;  // job IDd: all jobs with the protein
  22         private LinkedHashMap<String, String> predictions; // predictions: Key - prediction ID, Value - prediction sequence
  23         private List<String> subProt; // protein sequence divided in several parts
  24                                                                         // for highlighting a particular part
  25         private int size; // a number of predictions for the protein
  26
  27         public ProteinBean(String seq, Map<String, String> pred) {
  28                 this.sequence = seq;
  29                 this.predictions = new LinkedHashMap<String, String>();
  30                 this.jobid = new ArrayList<String>();
  31                 setPredictions(pred);
  32                 setJnetpred(pred);
  33         }
  34
  35         public void setSequence(String seq) {
  36                 this.sequence = seq;
  37         }
  38
  39         public void setPredictions(Map<String, String> pred) {
  40                 if (predictions == null)
  41                         predictions = new LinkedHashMap<String, String>();
  42                 for (String index : predIndex) {
  43                         this.predictions.put(index, pred.get(index));
  44                 }
  45                 this.size = predictions.size();
  46         }
  47
  48         public String getSequence() {
  49                 return sequence;
  50         }
  51
  52         public String getJnetpred() {
  53                 return jnetpred;
  54         }
  55
  56         public void setJnetpred(Map<String, String> pred) {
  57                 if (pred != null) {
  58                         if (pred.containsKey("jnetpred"))
  59                                 jnetpred = pred.get("jnetpred");
  60                 }
  61         }
  62
  63         public List<String> getJobid() {
  64                 return jobid;
  65         }
  66
  67         public void setJobid(String id) {
  68                 this.jobid.add(id);
  69         }
  70
  71         public int getSize() {
  72                 return size;
  73         }
  74
  75         public LinkedHashMap<String, String> getPredictions() {
  76                 return predictions;
  77         }
  78
  79         public void setSubProt(List<String> subProt) {
  80                 this.subProt = subProt;
  81         }
  82
  83         public List<String> getSubProt() {
  84                 return subProt;
  85         }
  86
  87 }