merge from 2_4_Release branch

[jalview.git] / src / org / biojava / dasobert / feature / FeatureTrack.java

diff --git a/src/org/biojava/dasobert/feature/FeatureTrack.java b/src/org/biojava/dasobert/feature/FeatureTrack.java
index 42136ee..e7b6bbd 100644 (file)
--- a/src/org/biojava/dasobert/feature/FeatureTrack.java
+++ b/src/org/biojava/dasobert/feature/FeatureTrack.java
@@ -28,86 +28,100 @@ import java.util.List;
  * A feature corresponds to a track in Ensembl
  * 
  * @author Andreas Prlic
- *
+ * 
  */
-public interface FeatureTrack {
-    
-       
-       public Object clone();
-       
-    /** returns true if the specified sequence position is within the range of this Feature
-     * 
-     * @param seqPosition the position to check
-     * @return true if the position is within the ranges of the segments of this feature
-     */
-    public boolean overlaps(int seqPosition);
-    
-    public  String toString();
-
-    public  void setSource(String s);
-
-    public  String getSource();
-
-    public  void setName(String nam);
-
-    public  String getName();
-
-    public  void setMethod(String methd);
-
-    public  String getMethod();
-
-    public  void setType(String typ);
-
-    public  String getType();
-
-    public  void setNote(String nte);
-
-    public  String getNote();
-
-    public  void setLink(String lnk);
-
-    public  String getLink();
-    
-    public  void setScore(String score);
-    
-    public  String getScore();
-    
-    public void setOrientation(String orientation);
-    
-    public String getOrientation();
-    
-    /** test if two features are equivalent
-     * 
-     * @param feat feature to compare with 
-     * @return true if equivalend
-     */
-    public abstract boolean equals(FeatureTrack feat);
-
-    /** add a segment to this feature
-     * 
-     * @param start position
-     * @param end position 
-     * @param name of feature
-     */
-    public abstract void addSegment(int start, int end, String name);
-
-    public abstract void addSegment(Segment s);
-
-    public abstract List getSegments();
-    
-    /** set the data from the DAS - type - id field
-     * (used for Ontology support)
-     * @param typeID
-     */
-    public void setTypeID(String typeID);
-    
-    /** set the data from the DAS - type - category field
-     * (used for Ontology support)
-     * @param typeCategory
-     */
-    public void setTypeCategory(String typeCategory);
-    
-    public String getTypeID();
-    public String getTypeCategory();
-   
+public interface FeatureTrack
+{
+
+  public Object clone();
+
+  /**
+   * returns true if the specified sequence position is within the range of this
+   * Feature
+   * 
+   * @param seqPosition
+   *                the position to check
+   * @return true if the position is within the ranges of the segments of this
+   *         feature
+   */
+  public boolean overlaps(int seqPosition);
+
+  public String toString();
+
+  public void setSource(String s);
+
+  public String getSource();
+
+  public void setName(String nam);
+
+  public String getName();
+
+  public void setMethod(String methd);
+
+  public String getMethod();
+
+  public void setType(String typ);
+
+  public String getType();
+
+  public void setNote(String nte);
+
+  public String getNote();
+
+  public void setLink(String lnk);
+
+  public String getLink();
+
+  public void setScore(String score);
+
+  public String getScore();
+
+  public void setOrientation(String orientation);
+
+  public String getOrientation();
+
+  /**
+   * test if two features are equivalent
+   * 
+   * @param feat
+   *                feature to compare with
+   * @return true if equivalend
+   */
+  public abstract boolean equals(FeatureTrack feat);
+
+  /**
+   * add a segment to this feature
+   * 
+   * @param start
+   *                position
+   * @param end
+   *                position
+   * @param name
+   *                of feature
+   */
+  public abstract void addSegment(int start, int end, String name);
+
+  public abstract void addSegment(Segment s);
+
+  public abstract List getSegments();
+
+  /**
+   * set the data from the DAS - type - id field (used for Ontology support)
+   * 
+   * @param typeID
+   */
+  public void setTypeID(String typeID);
+
+  /**
+   * set the data from the DAS - type - category field (used for Ontology
+   * support)
+   * 
+   * @param typeCategory
+   */
+  public void setTypeCategory(String typeCategory);
+
+  public String getTypeID();
+
+  public String getTypeCategory();
+
 }
\ No newline at end of file