add place for version and GenBank GI number in AccessionID class

jgrzebyta · jgrzebyta · commit 6b3343ffbbc8 · 2015-03-24T15:31:51.000Z
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/AccessionID.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/AccessionID.java
@@ -32,11 +32,14 @@
  * to identify the type of ID
  *
  * @author Scooter Willis
+ * @author Jacek Grzebyta
  */
 public class AccessionID {
 
     private String id = null;
     private DataSource source = DataSource.LOCAL;
+    private Integer version;
+    private String identifier = null;
 
     /**
      *
@@ -55,6 +58,7 @@ public AccessionID(String id) {
         this.id = id.trim();
         this.source = DataSource.LOCAL;
     }
+    
 
     /**
      *
@@ -65,6 +69,13 @@ public AccessionID(String id, DataSource source) {
         this.id = id.trim();
         this.source = source;
     }
+    
+    public AccessionID(String id, DataSource source, Integer version, String identifier) {
+        this.id = id;
+        this.source = source;
+        this.version = version;
+        this.identifier = identifier;
+    }
 
     /**
      * @return the id
@@ -86,8 +97,10 @@ public boolean equals(Object o) {
         if (Equals.classEqual(this, o)) {
             AccessionID l = (AccessionID) o;
             equals = (Equals.equal(getID(), l.getID())
-                    && Equals.equal(getDataSource(), l.getDataSource()));
-        }
+                    && Equals.equal(getDataSource(), l.getDataSource())
+                    && Equals.equal(getIdentifier(), l.getIdentifier())
+                    && Equals.equal(getVersion(), l.getVersion()));
+    }
         return equals;
     }
 
@@ -96,13 +109,42 @@ public int hashCode() {
         int r = Hashcoder.SEED;
         r = Hashcoder.hash(r, getID());
         r = Hashcoder.hash(r, getDataSource());
+        r = Hashcoder.hash(r, getIdentifier());
+        r = Hashcoder.hash(r, getVersion());
         return r;
-    }
+        }
 
  //   public void setDataSource(DataSource dataSource){
  //       source = dataSource;
  //   }
 
+
+    /**
+     * In case if the {@link #getID() } is not unique keeps the id version.
+     * @return the version
+     */
+    public Integer getVersion() {
+        return version;
+    }
+
+    public void setVersion(Integer version) {
+        this.version = version;
+    }
+
+    /**
+     * In case if {@link #getID() } in not unique keeps the alternative id, eg. NCBI GI number.
+     * 
+     * @return 
+     */
+    public String getIdentifier() {
+        return identifier;
+    }
+
+    public void setIdentifier(String identifier) {
+        this.identifier = identifier;
+    }
+    
+    
     @Override
     public String toString() {
         return id;
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderParser.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderParser.java
@@ -30,6 +30,7 @@
 import org.biojava.nbio.core.sequence.template.Compound;
 
 import java.util.ArrayList;
+import org.biojava.nbio.core.sequence.DataSource;
 
 public class GenericGenbankHeaderParser<S extends AbstractSequence<C>, C extends Compound> implements SequenceHeaderParserInterface<S,C> {
 
@@ -49,7 +50,7 @@ public class GenericGenbankHeaderParser<S extends AbstractSequence<C>, C extends
     @Override
 	public void parseHeader(String header, S sequence) {
     	sequence.setOriginalHeader(header);
-    	sequence.setAccession(new AccessionID(accession));
+        sequence.setAccession(new AccessionID(accession, DataSource.GENBANK, version, identifier));
     	sequence.setDescription(description);
     }
     
