datamodel/compbio/data/sequence/RNAstruct.java

   1 package compbio.data.sequence;
   2
   3 import java.util.List;
   4
   5 import javax.xml.bind.annotation.XmlAccessType;
   6 import javax.xml.bind.annotation.XmlAccessorType;
   7
   8 import compbio.util.annotation.Immutable;
   9
  10 /*
  11  * RNA secondary structure
  12  */
  13
  14 @XmlAccessorType(XmlAccessType.FIELD)
  15 public final class RNAstruct {
  16
  17         private String sequence;
  18         private String structure; // needs to be array to deal with all output
  19         private Float minEnergy;
  20         private Float energySum1; private Float energySum2;
  21
  22
  23         public RNAstruct() {
  24                 // default JaxB Constructor
  25         }
  26
  27         public RNAstruct(String sequence, String structure, Float minEnergy
  28                         , Float energySum1, Float energySum2) {
  29                 this.sequence = sequence;
  30                 this.structure = structure;
  31                 this.minEnergy = minEnergy;
  32                 this.energySum1 = energySum1;
  33                 this.energySum2 = energySum2;
  34         }
  35
  36         public String getSequence() {
  37                 return sequence;
  38         }
  39
  40         public String getStructure() {
  41                 return structure;
  42         }
  43
  44         public Float getEnergy() {
  45                 return minEnergy;
  46         }
  47
  48
  49         @Override
  50         public String toString() {
  51                 String newLine = System.getProperty("line.separator",".");
  52                 return sequence + newLine + structure + " (" + minEnergy.toString()
  53                                 + " = " + energySum1.toString() + " +  " + energySum2.toString()
  54                                 + ")";
  55         }
  56
  57         @Override
  58         public boolean equals(Object obj) {
  59                 if (obj == null) {
  60                         return false;
  61                 }
  62                 if (!(obj instanceof RNAstruct)) {
  63                         return false;
  64                 }
  65                 RNAstruct st = (RNAstruct) obj;
  66                 if (!(this.getSequence() == st.getSequence() &&
  67                                 this.getStructure() == st.getStructure() &&
  68                                 this.getEnergy() == st.getEnergy())) {
  69                         return false;
  70                 }
  71
  72                 return true;
  73         }
  74 }
  75
  76