X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2Fxdb%2Fgenbank%2FGenBankReference.java;fp=src%2Fjalview%2Fio%2Fxdb%2Fgenbank%2FGenBankReference.java;h=17ad8b4422194338d86af2f71ac6f859014dcc7a;hb=96f10f96255b4e9bb88601ce01adbf5faf16544c;hp=74f008074027068c34921f3f7e7ca4c37372fcde;hpb=2d63cfb4d8f84de5f40670bb301ee8a22db321ff;p=jalview.git

diff --git a/src/jalview/io/xdb/genbank/GenBankReference.java b/src/jalview/io/xdb/genbank/GenBankReference.java
index 74f0080..17ad8b4 100644
--- a/src/jalview/io/xdb/genbank/GenBankReference.java
+++ b/src/jalview/io/xdb/genbank/GenBankReference.java
@@ -1,135 +1,176 @@
 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();
-	}
-	
+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();
+  }
+
 }