2 * BioJava development code
4 * This code may be freely distributed and modified under the
5 * terms of the GNU Lesser General Public Licence. This should
6 * be distributed with the code. If you do not have a copy,
9 * http://www.gnu.org/copyleft/lesser.html
11 * Copyright for this code is held jointly by the individual
12 * authors. These should be listed in @author doc comments.
14 * For more information on the BioJava project and its aims,
15 * or to join the biojava-l mailing list, visit the home page
18 * http://www.biojava.org/
20 * Created on Feb 9, 2005
23 package org.biojava.dasobert.feature;
25 import java.util.List;
28 * A feature corresponds to a track in Ensembl
30 * @author Andreas Prlic
33 public interface FeatureTrack
36 public Object clone();
39 * returns true if the specified sequence position is within the range of this
43 * the position to check
44 * @return true if the position is within the ranges of the segments of this
47 public boolean overlaps(int seqPosition);
49 public String toString();
51 public void setSource(String s);
53 public String getSource();
55 public void setName(String nam);
57 public String getName();
59 public void setMethod(String methd);
61 public String getMethod();
63 public void setType(String typ);
65 public String getType();
67 public void setNote(String nte);
69 public String getNote();
71 public void setLink(String lnk);
73 public String getLink();
75 public void setScore(String score);
77 public String getScore();
79 public void setOrientation(String orientation);
81 public String getOrientation();
84 * test if two features are equivalent
87 * feature to compare with
88 * @return true if equivalend
90 public abstract boolean equals(FeatureTrack feat);
93 * add a segment to this feature
102 public abstract void addSegment(int start, int end, String name);
104 public abstract void addSegment(Segment s);
106 public abstract List getSegments();
109 * set the data from the DAS - type - id field (used for Ontology support)
113 public void setTypeID(String typeID);
116 * set the data from the DAS - type - category field (used for Ontology
119 * @param typeCategory
121 public void setTypeCategory(String typeCategory);
123 public String getTypeID();
125 public String getTypeCategory();