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[jalview.git] / src / org / biojava / dasobert / feature / AbstractSegment.java
diff --git a/src/org/biojava/dasobert/feature/AbstractSegment.java b/src/org/biojava/dasobert/feature/AbstractSegment.java
index daa7f75..12c5e1d 100644 (file)
--- a/src/org/biojava/dasobert/feature/AbstractSegment.java
+++ b/src/org/biojava/dasobert/feature/AbstractSegment.java
@@ -25,139 +25,232 @@ package org.biojava.dasobert.feature;
 
 import java.awt.Color;
 
-public abstract class AbstractSegment implements Segment,Cloneable {
-       int start   ;
-       int end     ;
-       String name ;
-       Color color ;
-       FeatureTrack parent ;
-       String txtColor ;
-       String note;
-
-       public abstract Object clone();
-       
-       /* (non-Javadoc)
-        * @see org.biojava.spice.feature.SegmentIF#toString()
-        */
-       public String toString() {
-               String str = "Segment: " +name + " " +start + " " + end ;
-               if ( ( note != null ) && ( ! note.equals("null")))
-                       if ( note.length() >40)
-                               str += note.substring(0,39)+"...";
-                       else
-                               str += note;
-               return str ;
-       }
-
-       /* (non-Javadoc)
-        * @see org.biojava.spice.feature.SegmentIF#getNote()
-        */
-       public String getNote() {
-               return note;
-       }
-
-       /* (non-Javadoc)
-        * @see org.biojava.spice.feature.SegmentIF#setNote(java.lang.String)
-        */
-       public void setNote(String note) {
-               this.note = note;
-       }
-
-       /* (non-Javadoc)
-        * @see org.biojava.spice.feature.SegmentIF#setStart(int)
-        */
-       public void setStart(int strt) {start = strt ; }
-       /* (non-Javadoc)
-        * @see org.biojava.spice.feature.SegmentIF#getStart()
-        */
-       public int  getStart() {return start ;}
-
-       /* (non-Javadoc)
-        * @see org.biojava.spice.feature.SegmentIF#setEnd(int)
-        */
-       public void setEnd(int ed) { end = ed;}
-       /* (non-Javadoc)
-        * @see org.biojava.spice.feature.SegmentIF#getEnd()
-        */
-       public int getEnd() { return end;}
-
-       /* (non-Javadoc)
-        * @see org.biojava.spice.feature.SegmentIF#setName(java.lang.String)
-        */
-       public void setName(String nam) { name = nam;}
-       /* (non-Javadoc)
-        * @see org.biojava.spice.feature.SegmentIF#getName()
-        */
-       public String getName() { return name ; }
-
-       /* (non-Javadoc)
-        * @see org.biojava.spice.feature.SegmentIF#setColor(java.awt.Color)
-        */
-       public void setColor(Color col) { color = col; }
-       /* (non-Javadoc)
-        * @see org.biojava.spice.feature.SegmentIF#getColor()
-        */
-       public Color getColor() { return color ; }
-
-       /* (non-Javadoc)
-        * @see org.biojava.spice.feature.SegmentIF#setParent(org.biojava.spice.feature.Feature)
-        */
-       public void setParent(FeatureTrack f) { parent = f;}
-       /* (non-Javadoc)
-        * @see org.biojava.spice.feature.SegmentIF#getParent()
-        */
-       public FeatureTrack getParent(){ return parent;}
-
-       /* (non-Javadoc)
-        * @see org.biojava.spice.feature.SegmentIF#setTxtColor(java.lang.String)
-        */
-       public void setTxtColor(String str) { txtColor = str; }
-       /* (non-Javadoc)
-        * @see org.biojava.spice.feature.SegmentIF#getTxtColor()
-        */
-       public String getTxtColor() { return txtColor;}
-
-
-       /* (non-Javadoc)
-        * @see org.biojava.spice.feature.SegmentIF#overlaps(int)
-        */
-       public boolean overlaps(int seqPosition){
-               if ( ( getStart() <= seqPosition) && ( getEnd() >= seqPosition)){
-                       return true;             
-               }   
-               return false;
-       }
-
-
-
-       /* (non-Javadoc)
-        * @see org.biojava.spice.feature.SegmentIF#overlaps(org.biojava.spice.feature.Segment)
-        */
-       public boolean overlaps(Segment segment){
-               if (! (this.start <= this.end )) 
-                       throw new IndexOutOfBoundsException("start > end for segment" + this);
-
-               if ( ! (segment.getStart() <= segment.getEnd() ))
-                       throw new IndexOutOfBoundsException("start > end for segment" + segment);
-
-               // start must be in region of other
-               if ( this.start >= segment.getStart()){
-                       if ( this.start <= segment.getEnd()){
-                               return true;
-                       }
-               }
-               // or end must be in region of other..
-               if ( this.end >= segment.getStart() ) {
-                       if ( this.end <= segment.getEnd()){
-                               return true;
-                       }
-               }
-
-               if ( this.start <= segment.getStart() ) {
-                       if ( this.end >= segment.getEnd() ) {
-                               return true;
-                       }
-               }
-               return false;
-       }
+public abstract class AbstractSegment implements Segment, Cloneable
+{
+  int start;
+
+  int end;
+
+  String name;
+
+  Color color;
+
+  FeatureTrack parent;
+
+  String txtColor;
+
+  String note;
+
+  public abstract Object clone();
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see org.biojava.spice.feature.SegmentIF#toString()
+   */
+  public String toString()
+  {
+    String str = "Segment: " + name + " " + start + " " + end;
+    if ((note != null) && (!note.equals("null")))
+      if (note.length() > 40)
+        str += note.substring(0, 39) + "...";
+      else
+        str += note;
+    return str;
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see org.biojava.spice.feature.SegmentIF#getNote()
+   */
+  public String getNote()
+  {
+    return note;
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see org.biojava.spice.feature.SegmentIF#setNote(java.lang.String)
+   */
+  public void setNote(String note)
+  {
+    this.note = note;
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see org.biojava.spice.feature.SegmentIF#setStart(int)
+   */
+  public void setStart(int strt)
+  {
+    start = strt;
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see org.biojava.spice.feature.SegmentIF#getStart()
+   */
+  public int getStart()
+  {
+    return start;
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see org.biojava.spice.feature.SegmentIF#setEnd(int)
+   */
+  public void setEnd(int ed)
+  {
+    end = ed;
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see org.biojava.spice.feature.SegmentIF#getEnd()
+   */
+  public int getEnd()
+  {
+    return end;
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see org.biojava.spice.feature.SegmentIF#setName(java.lang.String)
+   */
+  public void setName(String nam)
+  {
+    name = nam;
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see org.biojava.spice.feature.SegmentIF#getName()
+   */
+  public String getName()
+  {
+    return name;
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see org.biojava.spice.feature.SegmentIF#setColor(java.awt.Color)
+   */
+  public void setColor(Color col)
+  {
+    color = col;
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see org.biojava.spice.feature.SegmentIF#getColor()
+   */
+  public Color getColor()
+  {
+    return color;
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see org.biojava.spice.feature.SegmentIF#setParent(org.biojava.spice.feature.Feature)
+   */
+  public void setParent(FeatureTrack f)
+  {
+    parent = f;
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see org.biojava.spice.feature.SegmentIF#getParent()
+   */
+  public FeatureTrack getParent()
+  {
+    return parent;
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see org.biojava.spice.feature.SegmentIF#setTxtColor(java.lang.String)
+   */
+  public void setTxtColor(String str)
+  {
+    txtColor = str;
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see org.biojava.spice.feature.SegmentIF#getTxtColor()
+   */
+  public String getTxtColor()
+  {
+    return txtColor;
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see org.biojava.spice.feature.SegmentIF#overlaps(int)
+   */
+  public boolean overlaps(int seqPosition)
+  {
+    if ((getStart() <= seqPosition) && (getEnd() >= seqPosition))
+    {
+      return true;
+    }
+    return false;
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see org.biojava.spice.feature.SegmentIF#overlaps(org.biojava.spice.feature.Segment)
+   */
+  public boolean overlaps(Segment segment)
+  {
+    if (!(this.start <= this.end))
+      throw new IndexOutOfBoundsException("start > end for segment" + this);
+
+    if (!(segment.getStart() <= segment.getEnd()))
+      throw new IndexOutOfBoundsException("start > end for segment"
+              + segment);
+
+    // start must be in region of other
+    if (this.start >= segment.getStart())
+    {
+      if (this.start <= segment.getEnd())
+      {
+        return true;
+      }
+    }
+    // or end must be in region of other..
+    if (this.end >= segment.getStart())
+    {
+      if (this.end <= segment.getEnd())
+      {
+        return true;
+      }
+    }
+
+    if (this.start <= segment.getStart())
+    {
+      if (this.end >= segment.getEnd())
+      {
+        return true;
+      }
+    }
+    return false;
+  }
 }