JAL-1260 v2 patch from David Roldán-Martínez

[jalview.git] / src / jalview / io / xdb / genbank / GenBankReference.java

diff --git a/src/jalview/io/xdb/genbank/GenBankReference.java b/src/jalview/io/xdb/genbank/GenBankReference.java
new file mode 100644 (file)
index 0000000..74f0080
--- /dev/null
+++ b/src/jalview/io/xdb/genbank/GenBankReference.java
@@ -0,0 +1,135 @@
+package jalview.io.xdb.genbank;
+
+public class GenBankReference {
+       private int order;
+       private int begin;
+       private int end;
+       private String descriptor;
+       private String authors;
+       private String title;
+       private String journal;
+       private String pubmed;
+       private String medline;
+       private String consortia;
+       private String remark;
+
+       public GenBankReference() {
+               super();
+       }
+
+       public String getDescriptor() {
+               return descriptor;
+       }
+
+       public void setDescriptor(String descriptor) {
+               this.descriptor = descriptor;
+       }
+
+       public String getAuthors() {
+               return authors;
+       }
+
+       public void setAuthors(String authors) {
+               this.authors = authors;
+       }
+
+       public String getTitle() {
+               return title;
+       }
+
+       public void setTitle(String title) {
+               this.title = title;
+       }
+
+       public String getJournal() {
+               return journal;
+       }
+
+       public void setJournal(String journal) {
+               this.journal = journal;
+       }
+
+       public String getPubmed() {
+               return pubmed;
+       }
+
+       public void setPubmed(String pubmed) {
+               this.pubmed = pubmed;
+       }
+
+       public int getOrder() {
+               return order;
+       }
+
+       public void setOrder(int order) {
+               this.order = order;
+       }
+       public int getBegin() {
+               return begin;
+       }
+
+       public void setBegin(int begin) {
+               this.begin = begin;
+       }
+
+       public int getEnd() {
+               return end;
+       }
+
+       public void setEnd(int end) {
+               this.end = end;
+       }
+       
+       
+       public String getMedline() {
+               return medline;
+       }
+
+       public void setMedline(String medline) {
+               this.medline = medline;
+       }
+
+       public String getConsortia() {
+               return consortia;
+       }
+
+       public void setConsortia(String consortia) {
+               this.consortia = consortia;
+       }
+
+       public String getRemark() {
+               return remark;
+       }
+
+       public void setRemark(String remark) {
+               this.remark = remark;
+       }
+
+       public String toString(){
+//             References has the following format
+//             REFERENCE   1  (bases 1 to 1976)
+//               AUTHORS   Spritz,R.A., DeRiel,J.K., Forget,B.G. and Weissman,S.M.
+//               TITLE     Complete nucleotide sequence of the human delta-globin gene
+//               JOURNAL   Cell 21 (3), 639-646 (1980)
+//                PUBMED   7438204
+               
+               StringBuffer buf = new StringBuffer();
+               buf.append("REFERENCE   ").append(this.getOrder()).append("  (bases ").append(this.getBegin()).append(" to ").append(this.getEnd()).append(")\n");
+               if (this.getAuthors()!=null)
+                       buf.append("  AUTHORS   ").append(this.getAuthors()).append("\n");
+               if (this.getTitle()!=null)
+                       buf.append("  TITLE     ").append(this.getTitle()).append("\n");
+               if (this.getJournal()!=null)
+                       buf.append("  JOURNAL   ").append(this.getJournal()).append("\n");
+               if (this.getPubmed()!=null)
+                       buf.append("  PUBMED   ").append(this.getPubmed()).append("\n");;
+               if (this.getMedline()!=null)
+                       buf.append("  MEDLINE   ").append(this.getMedline()).append("\n");;
+               if (this.getRemark()!=null)
+                       buf.append("  REMARK   ").append(this.getRemark()).append("\n");;
+               if (this.getConsortia()!=null)
+                       buf.append("  CONSRTM   ").append(this.getConsortia()).append("\n");;
+               return buf.toString();
+       }
+       
+}