import java.util.Iterator;
import java.util.List;
-/** An Abstract class representing a Feature as being diplayed in the SeqFeaturePanel
- * A feature corresponds to everything that is visible in a "line" and can contain one or multiple Segments.
+/**
+ * An Abstract class representing a Feature as being diplayed in the
+ * SeqFeaturePanel A feature corresponds to everything that is visible in a
+ * "line" and can contain one or multiple Segments.
*
*
* @author Andreas Prlic
- *
+ *
*/
-public abstract class AbstractFeatureTrack implements FeatureTrack,Cloneable {
-
- String name;
- String method;
- String type;
- List segments ;
- String note;
- String link;
- String source;
- String score;
- String orientation;
- String typeID;
- String typeCategory;
-
- public AbstractFeatureTrack() {
- source = "Unknown";
- method = "Unknown";
- type = "Unknown";
- note = "";
- link = "";
- score = "";
- orientation = null;
- segments = new ArrayList();
-
- }
-
- public abstract Object clone();
-
-
- public String toString() {
- String str = "Feature: method: " + method +" type: " + type ;
- if ( name != null)
- str += " name: " + name;
-
- if (( note != null) && (! note.equals("null")))
- {
- if (note.length() > 40)
- str += "note: " +note.substring(0,39) + "...";
- else
- str += " note: "+note;
- }
- str += " # segments: " + segments.size() ;
- return str ;
- }
-
-
- /** 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){
- List segments = getSegments();
- Iterator iter =segments.iterator();
-
- while (iter.hasNext()){
-
- Segment seg = (Segment) iter.next();
- if ( seg.overlaps(seqPosition) )
- return true;
- }
-
- return false;
- }
-
- public void setSource(String s) { source = s;}
- public String getSource() { return source; };
-
-
- public void setName(String nam) { name = nam; }
- public String getName() { return name; }
-
- public void setMethod(String methd) { method = methd ; }
- public String getMethod() { return method ; }
-
- public void setType(String typ) { type = typ ; }
- public String getType() { return type ; }
-
- public void setNote(String nte) {
- if (nte != null)
- note = nte;
- }
- public String getNote() { return note ; }
-
- public void setLink(String lnk) { link = lnk;}
- public String getLink() { return link;}
-
- public void setScore(String s){ score = s;}
- public String getScore() { return score;}
-
- /** add a segment to this feature */
- public void addSegment(int start, int end, String name) {
- Segment s = new SegmentImpl() ;
- s.setStart(start);
- s.setEnd(end) ;
- s.setName(name);
- s.setParent(this);
- segments.add(s);
- }
-
- public void addSegment( Segment s ){
- s.setParent(this);
- segments.add(s);
- }
-
- public List getSegments() {
- return segments ;
- }
-
-
- public String getOrientation() {
- return orientation;
- }
-
- public void setOrientation(String orientation) {
- this.orientation = orientation;
- }
-
- /** test if two features are equivalent
- * important: only comares type,method and source.
- * The individual segments are not compared!
- *
- * */
- public boolean equals(FeatureTrack feat) {
-// if ( note == null) {
- // if (( feat.getNote() == null ) ||
- // ( feat.getNote().equals(""))) {
- //} else if ( this.note.equals(feat.getNote())){
- // return true;
- //}
- if ( this.type.equals(feat.getType())){
- if ( this.method.equals(feat.getMethod())){
- if ( this.source.equals(feat.getSource())){
- if (this.note.equals(feat.getNote())){
- return true;
- }
- }
- }
- }
- return false;
-
- }
- public String getTypeCategory() {
- // TODO Auto-generated method stub
- return typeCategory;
- }
-
- public String getTypeID() {
- // TODO Auto-generated method stub
- return typeID;
- }
-
- public void setTypeCategory(String typeCategory) {
- this.typeCategory = typeCategory;
-
- }
-
- public void setTypeID(String typeID) {
- this.typeID = typeID;
-
- }
-
-
+public abstract class AbstractFeatureTrack implements FeatureTrack,
+ Cloneable
+{
+
+ String name;
+
+ String method;
+
+ String type;
+
+ List segments;
+
+ String note;
+
+ String link;
+
+ String source;
+
+ String score;
+
+ String orientation;
+
+ String typeID;
+
+ String typeCategory;
+
+ public AbstractFeatureTrack()
+ {
+ source = "Unknown";
+ method = "Unknown";
+ type = "Unknown";
+ note = "";
+ link = "";
+ score = "";
+ orientation = null;
+ segments = new ArrayList();
+
+ }
+
+ public abstract Object clone();
+
+ public String toString()
+ {
+ String str = "Feature: method: " + method + " type: " + type;
+ if (name != null)
+ str += " name: " + name;
+
+ if ((note != null) && (!note.equals("null")))
+ {
+ if (note.length() > 40)
+ str += "note: " + note.substring(0, 39) + "...";
+ else
+ str += " note: " + note;
+ }
+ str += " # segments: " + segments.size();
+ return str;
+ }
+
+ /**
+ * 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)
+ {
+ List segments = getSegments();
+ Iterator iter = segments.iterator();
+
+ while (iter.hasNext())
+ {
+
+ Segment seg = (Segment) iter.next();
+ if (seg.overlaps(seqPosition))
+ return true;
+ }
+
+ return false;
+ }
+
+ public void setSource(String s)
+ {
+ source = s;
+ }
+
+ public String getSource()
+ {
+ return source;
+ };
+
+ public void setName(String nam)
+ {
+ name = nam;
+ }
+
+ public String getName()
+ {
+ return name;
+ }
+
+ public void setMethod(String methd)
+ {
+ method = methd;
+ }
+
+ public String getMethod()
+ {
+ return method;
+ }
+
+ public void setType(String typ)
+ {
+ type = typ;
+ }
+
+ public String getType()
+ {
+ return type;
+ }
+
+ public void setNote(String nte)
+ {
+ if (nte != null)
+ note = nte;
+ }
+
+ public String getNote()
+ {
+ return note;
+ }
+
+ public void setLink(String lnk)
+ {
+ link = lnk;
+ }
+
+ public String getLink()
+ {
+ return link;
+ }
+
+ public void setScore(String s)
+ {
+ score = s;
+ }
+
+ public String getScore()
+ {
+ return score;
+ }
+
+ /** add a segment to this feature */
+ public void addSegment(int start, int end, String name)
+ {
+ Segment s = new SegmentImpl();
+ s.setStart(start);
+ s.setEnd(end);
+ s.setName(name);
+ s.setParent(this);
+ segments.add(s);
+ }
+
+ public void addSegment(Segment s)
+ {
+ s.setParent(this);
+ segments.add(s);
+ }
+
+ public List getSegments()
+ {
+ return segments;
+ }
+
+ public String getOrientation()
+ {
+ return orientation;
+ }
+
+ public void setOrientation(String orientation)
+ {
+ this.orientation = orientation;
+ }
+
+ /**
+ * test if two features are equivalent important: only comares type,method and
+ * source. The individual segments are not compared!
+ *
+ */
+ public boolean equals(FeatureTrack feat)
+ {
+ // if ( note == null) {
+ // if (( feat.getNote() == null ) ||
+ // ( feat.getNote().equals(""))) {
+ // } else if ( this.note.equals(feat.getNote())){
+ // return true;
+ // }
+ if (this.type.equals(feat.getType()))
+ {
+ if (this.method.equals(feat.getMethod()))
+ {
+ if (this.source.equals(feat.getSource()))
+ {
+ if (this.note.equals(feat.getNote()))
+ {
+ return true;
+ }
+ }
+ }
+ }
+ return false;
+
+ }
+
+ public String getTypeCategory()
+ {
+ // TODO Auto-generated method stub
+ return typeCategory;
+ }
+
+ public String getTypeID()
+ {
+ // TODO Auto-generated method stub
+ return typeID;
+ }
+
+ public void setTypeCategory(String typeCategory)
+ {
+ this.typeCategory = typeCategory;
+
+ }
+
+ public void setTypeID(String typeID)
+ {
+ this.typeID = typeID;
+
+ }
}
git://source.jalview.org / jalview.git / blobdiff