X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2Fxdb%2Fgenbank%2FGenBankSource.java;h=dbdba9f14ae603ce55a2d0745352d513f84f44cd;hb=96f10f96255b4e9bb88601ce01adbf5faf16544c;hp=c5ef3c2000e3a029e12ad1c1711177809a01a415;hpb=2d63cfb4d8f84de5f40670bb301ee8a22db321ff;p=jalview.git

diff --git a/src/jalview/io/xdb/genbank/GenBankSource.java b/src/jalview/io/xdb/genbank/GenBankSource.java
index c5ef3c2..dbdba9f 100644
--- a/src/jalview/io/xdb/genbank/GenBankSource.java
+++ b/src/jalview/io/xdb/genbank/GenBankSource.java
@@ -1,85 +1,112 @@
 package jalview.io.xdb.genbank;
 
 /**
- * <p>Free-format information including an abbreviated form of the organism
- * name, sometimes followed by a molecule type. (See section 3.4.10 of the
- * GenBank release notes for more info.)</p>
- * <p>Entrez Search Field: Organism [ORGN] </p>
- * <p>Search Tip: For some organisms that have well-established common names,
- * such as baker's yeast, mouse, and human, a search for the common name will
- * yield the same results as a search for the scientific name, e.g., a search
- * for "baker's yeast" in the organism field retrieves the same number of
- * documents as "Saccharomyces cerevisiae". This is true because the Organism
- * field is connected to the NCBI Taxonomy Database, which contains
- * cross-references between common names, scientific names, and synonyms for
- * organisms represented in the Sequence databases.</p>
+ * <p>
+ * Free-format information including an abbreviated form of the organism name,
+ * sometimes followed by a molecule type. (See section 3.4.10 of the GenBank
+ * release notes for more info.)
+ * </p>
+ * <p>
+ * Entrez Search Field: Organism [ORGN]
+ * </p>
+ * <p>
+ * Search Tip: For some organisms that have well-established common names, such
+ * as baker's yeast, mouse, and human, a search for the common name will yield
+ * the same results as a search for the scientific name, e.g., a search for
+ * "baker's yeast" in the organism field retrieves the same number of documents
+ * as "Saccharomyces cerevisiae". This is true because the Organism field is
+ * connected to the NCBI Taxonomy Database, which contains cross-references
+ * between common names, scientific names, and synonyms for organisms
+ * represented in the Sequence databases.
+ * </p>
  * <h1>Organism</h1>
- * <p>The formal scientific name for the source organism (genus and species,
- * where appropriate) and its lineage, based on the phylogenetic classification
- * scheme used in the NCBI Taxonomy Database. If the complete lineage of an
- * organism is very long, an abbreviated lineage will be shown in the GenBank
- * record and the complete lineage will be available in the Taxonomy Database.
- * (See also the /db_xref=taxon:nnnn Feature qualifer, below.)</p>
- * <p>Entrez Search Field: Organism [ORGN] </p>
- * <p>Search Tip: You can search the Organism field by any node in the taxonomic
+ * <p>
+ * The formal scientific name for the source organism (genus and species, where
+ * appropriate) and its lineage, based on the phylogenetic classification scheme
+ * used in the NCBI Taxonomy Database. If the complete lineage of an organism is
+ * very long, an abbreviated lineage will be shown in the GenBank record and the
+ * complete lineage will be available in the Taxonomy Database. (See also the
+ * /db_xref=taxon:nnnn Feature qualifer, below.)
+ * </p>
+ * <p>
+ * Entrez Search Field: Organism [ORGN]
+ * </p>
+ * <p>
+ * Search Tip: You can search the Organism field by any node in the taxonomic
  * hierarchy, e.g., you can search for the term "Saccharomyces cerevisiae",
  * "Saccharomycetales", "Ascomycota", etc. to retrieve all the sequences from
- * organisms in a particular taxon. </p>
+ * organisms in a particular taxon.
+ * </p>
  * 
  */
-public class GenBankSource {
-    private String source="";
-    private String organism="";
-    private String taxonomic="";
+public class GenBankSource
+{
+  private String source = "";
 
-    public GenBankSource() {
-    }
+  private String organism = "";
 
-    @Override
-    public String toString() {
-        return String.format("%s\n\t%s\n\t%s", getSource(), getOrganism(), getTaxonomic());
-    }
+  private String taxonomic = "";
 
-    /**
-     * @return the source
-     */
-    public String getSource() {
-        return source;
-    }
+  public GenBankSource()
+  {
+  }
 
-    /**
-     * @param source the source to set
-     */
-    public void setSource(String source) {
-        this.source = source;
-    }
+  @Override
+  public String toString()
+  {
+    return String.format("%s\n\t%s\n\t%s", getSource(), getOrganism(),
+            getTaxonomic());
+  }
 
-    /**
-     * @return the organism
-     */
-    public String getOrganism() {
-        return organism;
-    }
+  /**
+   * @return the source
+   */
+  public String getSource()
+  {
+    return source;
+  }
 
-    /**
-     * @param organism the organism to set
-     */
-    public void setOrganism(String organism) {
-        this.organism = organism;
-    }
+  /**
+   * @param source
+   *          the source to set
+   */
+  public void setSource(String source)
+  {
+    this.source = source;
+  }
 
-    /**
-     * @return the taxonomic
-     */
-    public String getTaxonomic() {
-        return taxonomic;
-    }
+  /**
+   * @return the organism
+   */
+  public String getOrganism()
+  {
+    return organism;
+  }
 
-    /**
-     * @param taxonomic the taxonomic to set
-     */
-    public void setTaxonomic(String taxonomic) {
-        this.taxonomic = taxonomic;
-    }
+  /**
+   * @param organism
+   *          the organism to set
+   */
+  public void setOrganism(String organism)
+  {
+    this.organism = organism;
+  }
+
+  /**
+   * @return the taxonomic
+   */
+  public String getTaxonomic()
+  {
+    return taxonomic;
+  }
+
+  /**
+   * @param taxonomic
+   *          the taxonomic to set
+   */
+  public void setTaxonomic(String taxonomic)
+  {
+    this.taxonomic = taxonomic;
+  }
 
 }