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