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
  16                                                                         // for highlighting the particular part
  17         private int size;
  18
  19         public ProteinBean(String seq, Map<String, String> pred) {
  20                 this.sequence = seq;
  21                 this.predictions = new LinkedHashMap<String, String>();
  22                 this.jobid = new ArrayList<String>();
  23                 setPredictions(pred);
  24                 setJnetpred(pred);
  25         }
  26
  27         public void setSequence(String seq) {
  28                 this.sequence = seq;
  29         }
  30
  31         public void setPredictions(Map<String, String> pred) {
  32                 if (predictions == null)
  33                         predictions = new LinkedHashMap<String, String>();
  34                 for (String index : predIndex) {
  35                         this.predictions.put(index, pred.get(index));
  36                 }
  37                 this.size = predictions.size();
  38         }
  39
  40         public String getSequence() {
  41                 return sequence;
  42         }
  43
  44         public String getJnetpred() {
  45                 return jnetpred;
  46         }
  47
  48         public void setJnetpred(Map<String, String> pred) {
  49                 if (pred != null) {
  50                         if (pred.containsKey("jnetpred"))
  51                                 jnetpred = pred.get("jnetpred");
  52                 }
  53         }
  54
  55         public List<String> getJobid() {
  56                 return jobid;
  57         }
  58
  59         public void setJobid(String id) {
  60                 this.jobid.add(id);
  61         }
  62
  63         public int getSize() {
  64                 return size;
  65         }
  66
  67         public LinkedHashMap<String, String> getPredictions() {
  68                 return predictions;
  69         }
  70
  71         public void setSubProt(List<String> subProt) {
  72                 this.subProt = subProt;
  73         }
  74
  75         public List<String> getSubProt() {
  76                 return subProt;
  77         }
  78
  79 }