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

   1 package jalview.io.xdb.genbank;
   2
   3 public class GenBankReference {
   4         private int order;
   5         private int begin;
   6         private int end;
   7         private String descriptor;
   8         private String authors;
   9         private String title;
  10         private String journal;
  11         private String pubmed;
  12         private String medline;
  13         private String consortia;
  14         private String remark;
  15
  16         public GenBankReference() {
  17                 super();
  18         }
  19
  20         public String getDescriptor() {
  21                 return descriptor;
  22         }
  23
  24         public void setDescriptor(String descriptor) {
  25                 this.descriptor = descriptor;
  26         }
  27
  28         public String getAuthors() {
  29                 return authors;
  30         }
  31
  32         public void setAuthors(String authors) {
  33                 this.authors = authors;
  34         }
  35
  36         public String getTitle() {
  37                 return title;
  38         }
  39
  40         public void setTitle(String title) {
  41                 this.title = title;
  42         }
  43
  44         public String getJournal() {
  45                 return journal;
  46         }
  47
  48         public void setJournal(String journal) {
  49                 this.journal = journal;
  50         }
  51
  52         public String getPubmed() {
  53                 return pubmed;
  54         }
  55
  56         public void setPubmed(String pubmed) {
  57                 this.pubmed = pubmed;
  58         }
  59
  60         public int getOrder() {
  61                 return order;
  62         }
  63
  64         public void setOrder(int order) {
  65                 this.order = order;
  66         }
  67         public int getBegin() {
  68                 return begin;
  69         }
  70
  71         public void setBegin(int begin) {
  72                 this.begin = begin;
  73         }
  74
  75         public int getEnd() {
  76                 return end;
  77         }
  78
  79         public void setEnd(int end) {
  80                 this.end = end;
  81         }
  82
  83
  84         public String getMedline() {
  85                 return medline;
  86         }
  87
  88         public void setMedline(String medline) {
  89                 this.medline = medline;
  90         }
  91
  92         public String getConsortia() {
  93                 return consortia;
  94         }
  95
  96         public void setConsortia(String consortia) {
  97                 this.consortia = consortia;
  98         }
  99
 100         public String getRemark() {
 101                 return remark;
 102         }
 103
 104         public void setRemark(String remark) {
 105                 this.remark = remark;
 106         }
 107
 108         public String toString(){
 109 //              References has the following format
 110 //              REFERENCE   1  (bases 1 to 1976)
 111 //                AUTHORS   Spritz,R.A., DeRiel,J.K., Forget,B.G. and Weissman,S.M.
 112 //                TITLE     Complete nucleotide sequence of the human delta-globin gene
 113 //                JOURNAL   Cell 21 (3), 639-646 (1980)
 114 //                 PUBMED   7438204
 115
 116                 StringBuffer buf = new StringBuffer();
 117                 buf.append("REFERENCE   ").append(this.getOrder()).append("  (bases ").append(this.getBegin()).append(" to ").append(this.getEnd()).append(")\n");
 118                 if (this.getAuthors()!=null)
 119                         buf.append("  AUTHORS   ").append(this.getAuthors()).append("\n");
 120                 if (this.getTitle()!=null)
 121                         buf.append("  TITLE     ").append(this.getTitle()).append("\n");
 122                 if (this.getJournal()!=null)
 123                         buf.append("  JOURNAL   ").append(this.getJournal()).append("\n");
 124                 if (this.getPubmed()!=null)
 125                         buf.append("  PUBMED   ").append(this.getPubmed()).append("\n");;
 126                 if (this.getMedline()!=null)
 127                         buf.append("  MEDLINE   ").append(this.getMedline()).append("\n");;
 128                 if (this.getRemark()!=null)
 129                         buf.append("  REMARK   ").append(this.getRemark()).append("\n");;
 130                 if (this.getConsortia()!=null)
 131                         buf.append("  CONSRTM   ").append(this.getConsortia()).append("\n");;
 132                 return buf.toString();
 133         }
 134
 135 }