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;
12 * Dummy contact matrix based on sequence distance
17 public class SeqDistanceContactMatrix
18 extends MappableContactMatrix<SeqDistanceContactMatrix>
19 implements ContactMatrixI
21 private static final String SEQUENCE_DISTANCE = "SEQUENCE_DISTANCE";
23 private int width = 0;
25 public SeqDistanceContactMatrix(int width)
43 public ContactListI getContactList(final int column)
45 if (column < 0 || column >= width)
49 return new ContactListImpl(new ContactListProviderI()
55 // public Color getColorForScore(int column)
57 // return jalview.util.ColorUtils.getGraduatedColour(Math.abs(column-p),
58 // 0, Color.white, width, Color.magenta);
61 // public Color getColorForRange(int from_column, int to_column)
63 // return jalview.util.ColorUtils.getGraduatedColour(
64 // Math.abs(to_column + from_column - 2 * p) / 2, 0, Color.white, width,
69 public int getContactHeight()
76 public int getPosition()
82 public double getContactAt(int column)
84 return Math.abs(column - p);
90 public String getAnnotDescr()
92 return "Sequence distance matrix";
96 public String getAnnotLabel()
98 return "Sequence Distance";
102 public String getType()
104 return SEQUENCE_DISTANCE;
108 public int getWidth()
114 public int getHeight()
120 protected double getElementAt(int _column, int i)
122 return Math.abs(_column - i);
126 protected SeqDistanceContactMatrix newMappableContactMatrix(
127 SequenceI newRefSeq, MapList newFromMapList)
130 return new SeqDistanceContactMatrix(width);