Merge branch 'develop' into feature/JAL-1713_overviewInProject

[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)
index 0000000..7dd9778
--- /dev/null
+++ b/src/jalview/datamodel/SeqDistanceContactMatrix.java
@@ -0,0 +1,102 @@
+package jalview.datamodel;
+
+/**
+ * Dummy contact matrix based on sequence distance
+ * 
+ * @author jprocter
+ *
+ */
+public class SeqDistanceContactMatrix implements ContactMatrixI
+{
+  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 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";
+  }
+
+  @Override
+  public String getAnnotLabel()
+  {
+    return "Sequence Distance";
+  }
+}