Merge branch 'releases/Release_2_11_3_Branch'

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

diff --git a/src/jalview/datamodel/ContactMatrixI.java b/src/jalview/datamodel/ContactMatrixI.java
index 1d20987..ce4b0d7 100644 (file)
--- a/src/jalview/datamodel/ContactMatrixI.java
+++ b/src/jalview/datamodel/ContactMatrixI.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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.datamodel;
 
 import java.awt.Color;
@@ -5,6 +25,9 @@ import java.util.Arrays;
 import java.util.BitSet;
 import java.util.List;
 
+import jalview.util.ColorUtils;
+import jalview.ws.datamodel.MappableContactMatrixI;
+
 public interface ContactMatrixI
 {
 
@@ -27,7 +50,9 @@ public interface ContactMatrixI
   String getType();
 
   int getWidth();
+
   int getHeight();
+
   public GroupSetI getGroupSet();
 
   /// proxy methods to simplify use of the interface
@@ -122,4 +147,93 @@ public interface ContactMatrixI
   }
 
   void setGroupSet(GroupSet makeGroups);
+
+  default void randomlyReColourGroups()
+  {
+    if (hasGroupSet())
+    {
+      GroupSetI groups = getGroupSet();
+      for (BitSet group : groups.getGroups())
+      {
+        groups.setColorForGroup(group, ColorUtils.getARandomColor());
+      }
+    }
+  }
+
+  default void transferGroupColorsTo(AlignmentAnnotation aa)
+  {
+    if (hasGroupSet())
+    {
+      GroupSetI groups = getGroupSet();
+      // stash colors in linked annotation row.
+      // doesn't work yet. TESTS!
+      int sstart = aa.sequenceRef != null ? aa.sequenceRef.getStart() - 1
+              : 0;
+      Annotation ae;
+      Color gpcol = null;
+      int[] seqpos = null;
+      for (BitSet gp : groups.getGroups())
+      {
+        gpcol = groups.getColourForGroup(gp);
+        for (int p = gp.nextSetBit(0); p >= 0
+                && p < Integer.MAX_VALUE; p = gp.nextSetBit(p + 1))
+        {
+          if (this instanceof MappableContactMatrixI)
+          {
+            MappableContactMatrixI mcm = (MappableContactMatrixI) this;
+            seqpos = mcm.getMappedPositionsFor(aa.sequenceRef, p);
+            if (seqpos == null)
+            {
+              // no mapping for this column.
+              continue;
+            }
+            // TODO: handle ranges...
+            ae = aa.getAnnotationForPosition(seqpos[0]);
+          }
+          else
+          {
+            ae = aa.getAnnotationForPosition(p + sstart);
+          }
+          if (ae != null)
+          {
+            ae.colour = gpcol.brighter().darker();
+          }
+        }
+      }
+    }
+  }
+
+  /**
+   * look up the colour for a column in the associated contact matrix
+   * 
+   * @return Color.white or assigned colour
+   */
+  default Color getGroupColorForPosition(int column)
+  {
+    if (hasGroupSet())
+    {
+      GroupSetI groups = getGroupSet();
+      for (BitSet gp : groups.getGroups())
+      {
+        if (gp.get(column))
+        {
+          return groups.getColourForGroup(gp);
+        }
+      }
+    }
+    return Color.white;
+  }
+
+  /**
+   * direct access to column and row position of matrix
+   * 
+   * Implementations are allowed to throw RunTimeExceptions if _column/i are out
+   * of bounds
+   * 
+   * @param column
+   * @param row
+   * @return
+   */
+  double getElementAt(int column, int row);
+
 }