X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSeqDistanceContactMatrix.java;h=987ea36ed6f1f32f34352f245ac3ca813eab734f;hb=HEAD;hp=f6377b1605828c9b667094d1f96fb4c7374c1d38;hpb=9e40070f757fc662aba39ba6314be4937276ead4;p=jalview.git
diff --git a/src/jalview/datamodel/SeqDistanceContactMatrix.java b/src/jalview/datamodel/SeqDistanceContactMatrix.java
index f6377b1..987ea36 100644
--- a/src/jalview/datamodel/SeqDistanceContactMatrix.java
+++ b/src/jalview/datamodel/SeqDistanceContactMatrix.java
@@ -1,3 +1,23 @@
+/*
+ * 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.datamodel;
import java.awt.Color;
@@ -14,9 +34,12 @@ import jalview.ws.datamodel.alphafold.MappableContactMatrix;
* @author jprocter
*
*/
-public class SeqDistanceContactMatrix extends MappableContactMatrix implements ContactMatrixI
+public class SeqDistanceContactMatrix
+ extends MappableContactMatrix
+ implements ContactMatrixI
{
private static final String SEQUENCE_DISTANCE = "SEQUENCE_DISTANCE";
+
private int width = 0;
public SeqDistanceContactMatrix(int width)
@@ -82,6 +105,7 @@ public class SeqDistanceContactMatrix extends MappableContactMatrix groups=null;
- @Override
- public void updateGroups(List colGroups)
- {
- groups = colGroups;
- }
- @Override
- public boolean hasGroups()
- {
- return groups!=null;
- }
- @Override
- public List getGroups()
- {
- return groups;
- }
- HashMap 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);
- }
@Override
- protected double getElementAt(int _column, int i)
+ public double getElementAt(int _column, int i)
{
- return Math.abs(_column-i);
+ return Math.abs(_column - i);
}
@Override
protected SeqDistanceContactMatrix newMappableContactMatrix(
SequenceI newRefSeq, MapList newFromMapList)
{
-
+
return new SeqDistanceContactMatrix(width);
}
}