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;
+ }
}