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 public class ProteinBean implements PredictionIndex{
  11         private String sequence;
  12         private String jnetpred;
  13         private List<String> jobid;
  14         private LinkedHashMap<String,String> predictions;
  15         private List<String> subProt;           // protein sequence divided by several parts for highlighting the particular part
  16         private int size;
  17
  18         public ProteinBean (String seq, Map<String,String> pred) {
  19                 this.sequence = seq;
  20                 this.predictions = new LinkedHashMap<String,String>();
  21                 this.jobid = new ArrayList<String>();
  22                 setPredictions(pred);
  23         }
  24
  25         public void setSequence (String seq) {
  26                 this.sequence = seq;
  27         }
  28
  29         public void setPredictions(Map<String,String> pred) {
  30                 if (predictions == null)
  31                         predictions = new LinkedHashMap<String,String>();
  32                 for (String index : predIndex) {
  33                         this.predictions.put(index, pred.get(index));
  34                 }
  35                 this.size = predictions.size();
  36         }
  37
  38         public String getSequence () {
  39                 return sequence;
  40         }
  41
  42         public String getJnetpred () {
  43                 return jnetpred;
  44         }
  45
  46         public void setJnetpred (Map<String,String> pred) {
  47                 if (pred != null) {
  48                         if (pred.containsKey("jnetpred"))
  49                                 jnetpred = pred.get("jnetpred");
  50                 }
  51         }
  52
  53         public List<String> getJobid () {
  54                 return jobid;
  55         }
  56
  57         public void setJobid (String id) {
  58                 this.jobid.add(id);
  59         }
  60
  61         public int getSize () {
  62                 return size;
  63         }
  64
  65         public LinkedHashMap<String,String> getPredictions () {
  66                 return predictions;
  67         }
  68
  69         public void setSubProt(List<String> subProt) {
  70                 this.subProt = subProt;
  71         }
  72
  73         public List<String> getSubProt() {
  74                 return subProt;
  75         }
  76
  77 }