Merge branch 'develop' into features/JAL-518_justify_seqs_in_region

[jalview.git] / src / jalview / datamodel / SeqDistanceContactMatrix.java

diff --git a/src/jalview/datamodel/SeqDistanceContactMatrix.java b/src/jalview/datamodel/SeqDistanceContactMatrix.java
new file mode 100644 (file)
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+++ b/src/jalview/datamodel/SeqDistanceContactMatrix.java
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+/*
+ * 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.BitSet;
+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
+        extends MappableContactMatrix<SeqDistanceContactMatrix>
+        implements ContactMatrixI
+{
+  private static final String SEQUENCE_DISTANCE = "SEQUENCE_DISTANCE";
+
+  private int width = 0;
+
+  public SeqDistanceContactMatrix(int width)
+  {
+    this.width = width;
+  }
+
+  @Override
+  public float getMin()
+  {
+    return 0f;
+  }
+
+  @Override
+  public float getMax()
+  {
+    return width;
+  }
+
+  @Override
+  public ContactListI getContactList(final int column)
+  {
+    if (column < 0 || column >= width)
+    {
+      return null;
+    }
+    return new ContactListImpl(new ContactListProviderI()
+    {
+
+      int p = column;
+
+      // @Override
+      // public Color getColorForScore(int column)
+      // {
+      // return jalview.util.ColorUtils.getGraduatedColour(Math.abs(column-p),
+      // 0, Color.white, width, Color.magenta);
+      // }
+      // @Override
+      // public Color getColorForRange(int from_column, int to_column)
+      // {
+      // return jalview.util.ColorUtils.getGraduatedColour(
+      // Math.abs(to_column + from_column - 2 * p) / 2, 0, Color.white, width,
+      // Color.magenta);
+      // }
+
+      @Override
+      public int getContactHeight()
+      {
+        return width;
+
+      }
+
+      @Override
+      public int getPosition()
+      {
+        return p;
+      }
+
+      @Override
+      public double getContactAt(int column)
+      {
+        return Math.abs(column - p);
+      }
+    });
+  }
+
+  @Override
+  public String getAnnotDescr()
+  {
+    return "Sequence distance matrix";
+  }
+
+  @Override
+  public String getAnnotLabel()
+  {
+    return "Sequence Distance";
+  }
+
+  @Override
+  public String getType()
+  {
+    return SEQUENCE_DISTANCE;
+  }
+
+  @Override
+  public int getWidth()
+  {
+    return width;
+  }
+
+  @Override
+  public int getHeight()
+  {
+    return width;
+  }
+
+  @Override
+  public double getElementAt(int _column, int i)
+  {
+    return Math.abs(_column - i);
+  }
+
+  @Override
+  protected SeqDistanceContactMatrix newMappableContactMatrix(
+          SequenceI newRefSeq, MapList newFromMapList)
+  {
+
+    return new SeqDistanceContactMatrix(width);
+  }
+}