+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.datamodel;
import java.awt.Color;
import java.util.HashMap;
import java.util.List;
+import jalview.util.MapList;
+import jalview.ws.datamodel.alphafold.MappableContactMatrix;
+
/**
* Dummy contact matrix based on sequence distance
*
* @author jprocter
*
*/
-public class SeqDistanceContactMatrix implements ContactMatrixI
+public class SeqDistanceContactMatrix
+ extends MappableContactMatrix<SeqDistanceContactMatrix>
+ implements ContactMatrixI
{
private static final String SEQUENCE_DISTANCE = "SEQUENCE_DISTANCE";
+
private int width = 0;
public SeqDistanceContactMatrix(int width)
}
@Override
- public boolean hasReferenceSeq()
- {
- // TODO Auto-generated method stub
- return false;
- }
-
- @Override
- public SequenceI getReferenceSeq()
- {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
public String getAnnotDescr()
{
return "Sequence distance matrix";
{
return width;
}
- private List<BitSet> groups=null;
- @Override
- public void updateGroups(List<BitSet> colGroups)
- {
- groups = colGroups;
- }
+
@Override
- public boolean hasGroups()
+ public double getElementAt(int _column, int i)
{
- return groups!=null;
+ return Math.abs(_column - i);
}
+
@Override
- public List<BitSet> getGroups()
+ protected SeqDistanceContactMatrix newMappableContactMatrix(
+ SequenceI newRefSeq, MapList newFromMapList)
{
- return groups;
- }
- HashMap<BitSet,Color> colorMap = new HashMap<>();
- @Override
- public Color getColourForGroup(BitSet bs)
- {
- if (bs==null) {
- return Color.white;
- }
- Color groupCol=colorMap.get(bs);
- if (groupCol==null)
- {
- return Color.white;
- }
- return groupCol;
- }
- @Override
- public void setColorForGroup(BitSet bs,Color color)
- {
- colorMap.put(bs,color);
+ return new SeqDistanceContactMatrix(width);
}
}