removed all dasobert code and begun to replace with Jdas calls.

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

diff --git a/src/org/biojava/dasobert/feature/AbstractFeatureTrack.java b/src/org/biojava/dasobert/feature/AbstractFeatureTrack.java
deleted file mode 100644 (file)
index 0ad2df7..0000000
--- a/src/org/biojava/dasobert/feature/AbstractFeatureTrack.java
+++ /dev/null
@@ -1,278 +0,0 @@
-/*
- *                  BioJava development code
- *
- * This code may be freely distributed and modified under the
- * terms of the GNU Lesser General Public Licence.  This should
- * be distributed with the code.  If you do not have a copy,
- * see:
- *
- *      http://www.gnu.org/copyleft/lesser.html
- *
- * Copyright for this code is held jointly by the individual
- * authors.  These should be listed in @author doc comments.
- *
- * For more information on the BioJava project and its aims,
- * or to join the biojava-l mailing list, visit the home page
- * at:
- *
- *      http://www.biojava.org/
- * 
- * Created on Feb 9, 2005
- *
- */
-package org.biojava.dasobert.feature;
-
-import java.util.ArrayList;
-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.
- * 
- * 
- * @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;
-
-  }
-
-}