Source code: jalview/annotation/SeqFeature.java

   package jalview.annotation;
   
   import jalview.seq.SequenceI;
   
   public class SeqFeature implements SeqFeatureI {
   
       protected long        start;
       protected long        end;
       protected String      name;
      protected String      source_tag;
      protected String      primary_tag;
      protected int         strand;
      protected double      score = 0.0;
      protected SeqFeatureI refFeature;
      protected SequenceI   seq;
      protected String      type;
  
      public SeqFeature() {
      }
  
      public SeqFeature(long start, long end, String name) {
    this.start = start;
    this.end   = end;
    this.name  = name;
      }
      
      public void setStart(long start) {
    this.start = start;
      }
      public long getStart() {
    return start;
      }
  
      public void setEnd(long end) {
    this.end = end;
      }
      public long getEnd() {
    return end;
      }
  
      public SequenceI getSequenceI() {
    return seq;
      }
      public void setSequenceI(SequenceI sequence) {
    this.seq = sequence;
      }
  
      public SeqFeatureI getRefFeature() {
    return refFeature;
      }
      public void setRefFeature(SeqFeatureI refFeature) {
    this.refFeature = refFeature;
      }
  
      public FeatureSetI getProducedFeatures() {
    return null;
      }
      public void setProducedFeatures(FeatureSetI producedFeatures) {
      }
  
      public String getType() {
    return this.type;
      }
      public void setType(String type) {
    this.type = type;
      }
  
      public void setStrand(int strand) {
    this.strand = strand;
      }
      public int getStrand() {
    return strand;
      }
  
      public void setName(String name) {
    this.name = name;
      }
      public String getName() {
    return name;
      }
  
      public double getScore() {
    return score;
      }
      public void setScore(double score) {
    this.score = score;
      }
  
      public boolean overlaps(SeqFeatureI se) {
    if (getStart() <= se.getEnd() && getEnd() >= se.getStart()) {
        return true;
    }
    return false;
      }
      public OverlapI findOverlap(SeqFeatureI feature) {
    return null;
      }
  
      public String toString() {
   return getName() + " " + getStart() + " " + getEnd();
     }
 }