X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2FContactMatrixI.java;h=ce4b0d7dfe45e52d2af83b552fb46bd423ff497a;hb=f1b00517fe5f888f3213d70270e27a83dffe1695;hp=3510ed135f9809b4dd8c5f2d060fffb2c6926f3a;hpb=b7e9e2edf0c1557089eff0e4b5c17c0b31e698c2;p=jalview.git

diff --git a/src/jalview/datamodel/ContactMatrixI.java b/src/jalview/datamodel/ContactMatrixI.java
index 3510ed1..ce4b0d7 100644
--- 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
 {
 
@@ -14,10 +37,6 @@ public interface ContactMatrixI
 
   float getMax();
 
-  boolean hasReferenceSeq();
-
-  SequenceI getReferenceSeq();
-
   String getAnnotDescr();
 
   String getAnnotLabel();
@@ -33,47 +52,188 @@ public interface ContactMatrixI
   int getWidth();
 
   int getHeight();
-  
-  default boolean hasGroups() {
-    return false;
+
+  public GroupSetI getGroupSet();
+
+  /// proxy methods to simplify use of the interface
+  /// Mappable contact matrices can override these to perform mapping
+
+  default public boolean hasGroupSet()
+  {
+    return getGroupSet() != null;
   }
-  default BitSet getGroupsFor(int column) {
-    BitSet colbitset  = new BitSet();
-    colbitset.set(column);
-    return colbitset;
+
+  default boolean hasGroups()
+  {
+    return hasGroupSet() && getGroupSet().hasGroups();
   }
 
-  default List<BitSet> getGroups() {
-    return Arrays.asList();
+  default BitSet getGroupsFor(int column)
+  {
+    if (!hasGroupSet())
+    {
+      BitSet colbitset = new BitSet();
+      colbitset.set(column);
+      return colbitset;
+    }
+    return getGroupSet().getGroupsFor(column);
   }
 
-  default boolean hasTree() {
-    return false;
+  default List<BitSet> getGroups()
+  {
+    if (!hasGroupSet())
+    {
+      return Arrays.asList();
+    }
+    return getGroupSet().getGroups();
+  }
+
+  default boolean hasTree()
+  {
+    return hasGroupSet() ? getGroupSet().hasTree() : false;
   }
 
   /**
    * Newick representation of clustered matrix
+   * 
    * @return null unless hasTree is true
    */
-  default String getNewick() {
-    return null;
+  default String getNewick()
+  {
+    return hasGroupSet() ? getGroupSet().getNewick() : null;
+  }
+
+  default String getTreeMethod()
+  {
+    return hasGroupSet() ? getGroupSet().getTreeMethod() : null;
   }
 
-  default String getTreeMethod() {
-    return null;
+  default boolean hasCutHeight()
+  {
+    return hasGroupSet() ? getGroupSet().hasCutHeight() : false;
   }
 
-  default boolean hasCutHeight() {
-    return false;
+  default double getCutHeight()
+  {
+    return hasGroupSet() ? getGroupSet().getCutHeight() : 0;
   }
 
-  default double getCutHeight() {
-    return 0;
+  default void updateGroups(List<BitSet> colGroups)
+  {
+    if (hasGroupSet())
+    {
+      getGroupSet().updateGroups(colGroups);
+    }
   }
 
-  void updateGroups(List<BitSet> colGroups);
+  default void setColorForGroup(BitSet bs, Color color)
+  {
+    if (hasGroupSet())
+    {
+      getGroupSet().setColorForGroup(bs, color);
+    }
+  }
+
+  default Color getColourForGroup(BitSet bs)
+  {
+    if (hasGroupSet())
+    {
+      return getGroupSet().getColourForGroup(bs);
+    }
+    else
+    {
+      return Color.white;
+    }
+  }
 
-  void setColorForGroup(BitSet bs, Color color);
+  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);
 
-  default Color getColourForGroup(BitSet bs) { return Color.white;};
 }