datamodel/compbio/data/sequence/AnnotatedSequence.java

   1 package compbio.data.sequence;\r
   2 \r
   3 import java.util.Arrays;\r
   4 \r
   5 public class AnnotatedSequence extends FastaSequence {\r
   6 \r
   7         private float[] annotation;\r
   8 \r
   9         private AnnotatedSequence() {\r
  10                 super();\r
  11                 // JAXB default constructor\r
  12         }\r
  13 \r
  14         public AnnotatedSequence(String id, String sequence, float[] annotation) {\r
  15                 super(id, sequence);\r
  16                 this.annotation = annotation;\r
  17                 if (annotation == null || annotation.length != sequence.length()) {\r
  18                         throw new IllegalArgumentException("The length of the annotation ("\r
  19                                         + ((annotation != null) ? annotation.length : "0")\r
  20                                         + ") does not match the length of the sequence ("\r
  21                                         + sequence.length() + ")!");\r
  22                 }\r
  23         }\r
  24 \r
  25         public AnnotatedSequence(FastaSequence fsequence, float[] annotation) {\r
  26                 this(fsequence.getId(), fsequence.getSequence(), annotation);\r
  27         }\r
  28 \r
  29         public float[] getAnnotation() {\r
  30                 return annotation;\r
  31         }\r
  32 \r
  33         @Override\r
  34         public int hashCode() {\r
  35                 final int prime = 7;\r
  36                 int result = super.hashCode();\r
  37                 result = prime * result + Arrays.hashCode(annotation);\r
  38                 return result;\r
  39         }\r
  40 \r
  41         @Override\r
  42         public boolean equals(Object obj) {\r
  43                 if (this == obj)\r
  44                         return true;\r
  45                 if (!super.equals(obj))\r
  46                         return false;\r
  47                 if (getClass() != obj.getClass())\r
  48                         return false;\r
  49                 AnnotatedSequence other = (AnnotatedSequence) obj;\r
  50                 if (!Arrays.equals(annotation, other.annotation))\r
  51                         return false;\r
  52                 return true;\r
  53         }\r
  54 \r
  55         @Override\r
  56         public String toString() {\r
  57                 return super.toString() + "Annotation:\n "\r
  58                                 + Arrays.toString(annotation) + "\n";\r
  59         }\r
  60 \r
  61 }\r