src/org/biojava/dasobert/feature/AbstractSegment.java

   1 /*
   2  *                  BioJava development code
   3  *
   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,
   7  * see:
   8  *
   9  *      http://www.gnu.org/copyleft/lesser.html
  10  *
  11  * Copyright for this code is held jointly by the individual
  12  * authors.  These should be listed in @author doc comments.
  13  *
  14  * For more information on the BioJava project and its aims,
  15  * or to join the biojava-l mailing list, visit the home page
  16  * at:
  17  *
  18  *      http://www.biojava.org/
  19  *
  20  * Created on May 22, 2007
  21  *
  22  */
  23
  24 package org.biojava.dasobert.feature;
  25
  26 import java.awt.Color;
  27
  28 public abstract class AbstractSegment implements Segment,Cloneable {
  29         int start   ;
  30         int end     ;
  31         String name ;
  32         Color color ;
  33         FeatureTrack parent ;
  34         String txtColor ;
  35         String note;
  36
  37         public abstract Object clone();
  38
  39         /* (non-Javadoc)
  40          * @see org.biojava.spice.feature.SegmentIF#toString()
  41          */
  42         public String toString() {
  43                 String str = "Segment: " +name + " " +start + " " + end ;
  44                 if ( ( note != null ) && ( ! note.equals("null")))
  45                         if ( note.length() >40)
  46                                 str += note.substring(0,39)+"...";
  47                         else
  48                                 str += note;
  49                 return str ;
  50         }
  51
  52         /* (non-Javadoc)
  53          * @see org.biojava.spice.feature.SegmentIF#getNote()
  54          */
  55         public String getNote() {
  56                 return note;
  57         }
  58
  59         /* (non-Javadoc)
  60          * @see org.biojava.spice.feature.SegmentIF#setNote(java.lang.String)
  61          */
  62         public void setNote(String note) {
  63                 this.note = note;
  64         }
  65
  66         /* (non-Javadoc)
  67          * @see org.biojava.spice.feature.SegmentIF#setStart(int)
  68          */
  69         public void setStart(int strt) {start = strt ; }
  70         /* (non-Javadoc)
  71          * @see org.biojava.spice.feature.SegmentIF#getStart()
  72          */
  73         public int  getStart() {return start ;}
  74
  75         /* (non-Javadoc)
  76          * @see org.biojava.spice.feature.SegmentIF#setEnd(int)
  77          */
  78         public void setEnd(int ed) { end = ed;}
  79         /* (non-Javadoc)
  80          * @see org.biojava.spice.feature.SegmentIF#getEnd()
  81          */
  82         public int getEnd() { return end;}
  83
  84         /* (non-Javadoc)
  85          * @see org.biojava.spice.feature.SegmentIF#setName(java.lang.String)
  86          */
  87         public void setName(String nam) { name = nam;}
  88         /* (non-Javadoc)
  89          * @see org.biojava.spice.feature.SegmentIF#getName()
  90          */
  91         public String getName() { return name ; }
  92
  93         /* (non-Javadoc)
  94          * @see org.biojava.spice.feature.SegmentIF#setColor(java.awt.Color)
  95          */
  96         public void setColor(Color col) { color = col; }
  97         /* (non-Javadoc)
  98          * @see org.biojava.spice.feature.SegmentIF#getColor()
  99          */
 100         public Color getColor() { return color ; }
 101
 102         /* (non-Javadoc)
 103          * @see org.biojava.spice.feature.SegmentIF#setParent(org.biojava.spice.feature.Feature)
 104          */
 105         public void setParent(FeatureTrack f) { parent = f;}
 106         /* (non-Javadoc)
 107          * @see org.biojava.spice.feature.SegmentIF#getParent()
 108          */
 109         public FeatureTrack getParent(){ return parent;}
 110
 111         /* (non-Javadoc)
 112          * @see org.biojava.spice.feature.SegmentIF#setTxtColor(java.lang.String)
 113          */
 114         public void setTxtColor(String str) { txtColor = str; }
 115         /* (non-Javadoc)
 116          * @see org.biojava.spice.feature.SegmentIF#getTxtColor()
 117          */
 118         public String getTxtColor() { return txtColor;}
 119
 120
 121         /* (non-Javadoc)
 122          * @see org.biojava.spice.feature.SegmentIF#overlaps(int)
 123          */
 124         public boolean overlaps(int seqPosition){
 125                 if ( ( getStart() <= seqPosition) && ( getEnd() >= seqPosition)){
 126                         return true;
 127                 }
 128                 return false;
 129         }
 130
 131
 132
 133         /* (non-Javadoc)
 134          * @see org.biojava.spice.feature.SegmentIF#overlaps(org.biojava.spice.feature.Segment)
 135          */
 136         public boolean overlaps(Segment segment){
 137                 if (! (this.start <= this.end ))
 138                         throw new IndexOutOfBoundsException("start > end for segment" + this);
 139
 140                 if ( ! (segment.getStart() <= segment.getEnd() ))
 141                         throw new IndexOutOfBoundsException("start > end for segment" + segment);
 142
 143                 // start must be in region of other
 144                 if ( this.start >= segment.getStart()){
 145                         if ( this.start <= segment.getEnd()){
 146                                 return true;
 147                         }
 148                 }
 149                 // or end must be in region of other..
 150                 if ( this.end >= segment.getStart() ) {
 151                         if ( this.end <= segment.getEnd()){
 152                                 return true;
 153                         }
 154                 }
 155
 156                 if ( this.start <= segment.getStart() ) {
 157                         if ( this.end >= segment.getEnd() ) {
 158                                 return true;
 159                         }
 160                 }
 161                 return false;
 162         }
 163 }