1 package jalview.datamodel;
4 import java.util.BitSet;
5 import java.util.HashMap;
8 import jalview.util.MapList;
9 import jalview.ws.datamodel.alphafold.MappableContactMatrix;
11 * Dummy contact matrix based on sequence distance
16 public class SeqDistanceContactMatrix
17 extends MappableContactMatrix<SeqDistanceContactMatrix>
18 implements ContactMatrixI
20 private static final String SEQUENCE_DISTANCE = "SEQUENCE_DISTANCE";
21 private int width = 0;
23 public SeqDistanceContactMatrix(int width)
41 public ContactListI getContactList(final int column)
43 if (column < 0 || column >= width)
47 return new ContactListImpl(new ContactListProviderI()
53 // public Color getColorForScore(int column)
55 // return jalview.util.ColorUtils.getGraduatedColour(Math.abs(column-p),
56 // 0, Color.white, width, Color.magenta);
59 // public Color getColorForRange(int from_column, int to_column)
61 // return jalview.util.ColorUtils.getGraduatedColour(
62 // Math.abs(to_column + from_column - 2 * p) / 2, 0, Color.white, width,
67 public int getContactHeight()
74 public int getPosition()
80 public double getContactAt(int column)
82 return Math.abs(column - p);
88 public String getAnnotDescr()
90 return "Sequence distance matrix";
94 public String getAnnotLabel()
96 return "Sequence Distance";
100 public String getType()
102 return SEQUENCE_DISTANCE;
106 public int getWidth()
112 public int getHeight()
117 public double getElementAt(int _column, int i)
119 return Math.abs(_column - i);
122 protected SeqDistanceContactMatrix newMappableContactMatrix(
123 SequenceI newRefSeq, MapList newFromMapList)
126 return new SeqDistanceContactMatrix(width);