1 package jalview.datamodel;
4 * Dummy contact matrix based on sequence distance
9 public class SeqDistanceContactMatrix implements ContactMatrixI
11 private static final String SEQUENCE_DISTANCE = "SEQUENCE_DISTANCE";
13 private int width = 0;
15 public SeqDistanceContactMatrix(int width)
33 public ContactListI getContactList(final int column)
35 if (column < 0 || column >= width)
39 return new ContactListImpl(new ContactListProviderI()
45 // public Color getColorForScore(int column)
47 // return jalview.util.ColorUtils.getGraduatedColour(Math.abs(column-p),
48 // 0, Color.white, width, Color.magenta);
51 // public Color getColorForRange(int from_column, int to_column)
53 // return jalview.util.ColorUtils.getGraduatedColour(
54 // Math.abs(to_column + from_column - 2 * p) / 2, 0, Color.white, width,
59 public int getContactHeight()
66 public int getPosition()
72 public double getContactAt(int column)
74 return Math.abs(column - p);
80 public boolean hasReferenceSeq()
82 // TODO Auto-generated method stub
87 public SequenceI getReferenceSeq()
89 // TODO Auto-generated method stub
94 public String getAnnotDescr()
96 return "Sequence distance matrix";
100 public String getAnnotLabel()
102 return "Sequence Distance";
106 public String getType()
108 return SEQUENCE_DISTANCE;
112 public int getWidth()
118 public int getHeight()