src/jalview/io/xdb/genbank/GenBankSequence.java

   1 package jalview.io.xdb.genbank;
   2
   3 import java.util.Vector;
   4 /**
   5  * A line like the following:
   6  *   1 aatgaaggtt catttttcat tctcacaaac taatgaaacc ctgcttatct taaaccaacc
   7  * will be mapped as:
   8  *      id: 1
   9  *  sequences: {"aatgaaggtt", "catttttcat", "tctcacaaac", "taatgaaacc", "ctgcttatct", "taaaccaacc"}
  10  *  Each sequence has 8 nucleotides long
  11  * @author darolmar
  12  *
  13  */
  14 public class GenBankSequence {
  15         //Initial position
  16         private int id;
  17         //Sequences in that line
  18         private Vector<String> sequences;
  19
  20         public GenBankSequence() {
  21                 super();
  22                 sequences = new Vector<String>();
  23         }
  24
  25         public int getId() {
  26                 return id;
  27         }
  28
  29         public void setId(int id) {
  30                 this.id = id;
  31         }
  32
  33         public Vector<String> getSequences() {
  34                 return sequences;
  35         }
  36
  37         public void setSequences(Vector<String> sequences) {
  38                 this.sequences = sequences;
  39         }
  40
  41         public String getSequencesAsString(){
  42                 StringBuffer sb = new StringBuffer();
  43                 for (String seq:sequences)
  44                         sb.append(seq).append(" ");
  45                 return sb.toString();
  46         }
  47
  48         public String toString(){
  49                 StringBuffer sb = new StringBuffer()
  50                         .append("        ").append(this.id);
  51                 for (String seq:sequences)
  52                         sb.append(" ").append(seq);
  53                 sb.append("\n");
  54                 return sb.toString();
  55         }
  56
  57 }