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";
17 private int width = 0;
19 public SeqDistanceContactMatrix(int width)
37 public ContactListI getContactList(final int column)
39 if (column < 0 || column >= width)
43 return new ContactListImpl(new ContactListProviderI()
49 // public Color getColorForScore(int column)
51 // return jalview.util.ColorUtils.getGraduatedColour(Math.abs(column-p),
52 // 0, Color.white, width, Color.magenta);
55 // public Color getColorForRange(int from_column, int to_column)
57 // return jalview.util.ColorUtils.getGraduatedColour(
58 // Math.abs(to_column + from_column - 2 * p) / 2, 0, Color.white, width,
63 public int getContactHeight()
70 public int getPosition()
76 public double getContactAt(int column)
78 return Math.abs(column - p);
84 public boolean hasReferenceSeq()
86 // TODO Auto-generated method stub
91 public SequenceI getReferenceSeq()
93 // TODO Auto-generated method stub
98 public String getAnnotDescr()
100 return "Sequence distance matrix";
104 public String getAnnotLabel()
106 return "Sequence Distance";
110 public String getType()
112 return SEQUENCE_DISTANCE;
116 public int getWidth()
122 public int getHeight()
126 private List<BitSet> groups=null;
128 public void updateGroups(List<BitSet> colGroups)
133 public boolean hasGroups()
138 public List<BitSet> getGroups()
143 HashMap<BitSet,Color> colorMap = new HashMap<>();
145 public Color getColourForGroup(BitSet bs)
150 Color groupCol=colorMap.get(bs);
158 public void setColorForGroup(BitSet bs,Color color)
160 colorMap.put(bs,color);