1 package jalview.datamodel;
4 import java.util.BitSet;
5 import java.util.HashMap;
9 * Dummy contact matrix based on sequence distance
14 public class SeqDistanceContactMatrix implements ContactMatrixI
16 private static final String SEQUENCE_DISTANCE = "SEQUENCE_DISTANCE";
18 private int width = 0;
20 public SeqDistanceContactMatrix(int width)
38 public ContactListI getContactList(final int column)
40 if (column < 0 || column >= width)
44 return new ContactListImpl(new ContactListProviderI()
50 // public Color getColorForScore(int column)
52 // return jalview.util.ColorUtils.getGraduatedColour(Math.abs(column-p),
53 // 0, Color.white, width, Color.magenta);
56 // public Color getColorForRange(int from_column, int to_column)
58 // return jalview.util.ColorUtils.getGraduatedColour(
59 // Math.abs(to_column + from_column - 2 * p) / 2, 0, Color.white, width,
64 public int getContactHeight()
71 public int getPosition()
77 public double getContactAt(int column)
79 return Math.abs(column - p);
85 public boolean hasReferenceSeq()
87 // TODO Auto-generated method stub
92 public SequenceI getReferenceSeq()
94 // TODO Auto-generated method stub
99 public String getAnnotDescr()
101 return "Sequence distance matrix";
105 public String getAnnotLabel()
107 return "Sequence Distance";
111 public String getType()
113 return SEQUENCE_DISTANCE;
117 public int getWidth()
123 public int getHeight()
128 private List<BitSet> groups = null;
131 public void updateGroups(List<BitSet> colGroups)
137 public boolean hasGroups()
139 return groups != null;
143 public List<BitSet> getGroups()
148 HashMap<BitSet, Color> colorMap = new HashMap<>();
151 public Color getColourForGroup(BitSet bs)
157 Color groupCol = colorMap.get(bs);
158 if (groupCol == null)
166 public void setColorForGroup(BitSet bs, Color color)
168 colorMap.put(bs, color);