X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FContactListProviderI.java;h=9356026de1f21c9d3890bea4104cff3e5b130c6d;hb=bb82beaac6ab97bcb2d38244dafdff7adee173a7;hp=37c4e076b27f79c07049eb8af58ecce97d922c78;hpb=4a560601f94b229cca59f64561bf87f146cc896b;p=jalview.git

diff --git a/src/jalview/datamodel/ContactListProviderI.java b/src/jalview/datamodel/ContactListProviderI.java
index 37c4e07..9356026 100644
--- a/src/jalview/datamodel/ContactListProviderI.java
+++ b/src/jalview/datamodel/ContactListProviderI.java
@@ -1,9 +1,38 @@
+/*
+ * 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;
+
 public interface ContactListProviderI
 {
 
   /**
+   * 
+   * @return position index for this contact List (usually sequence position or
+   *         alignment column)
+   */
+  int getPosition();
+
+  /**
    * dimension of list where getContactAt(column<getContactHeight()) may return
    * a value
    * 
@@ -19,4 +48,23 @@ public interface ContactListProviderI
    */
   double getContactAt(int column);
 
+  /**
+   * Return positions in local reference corresponding to cStart and cEnd in
+   * matrix data. Positions are base 1 column indices for sequence associated
+   * matrices.
+   * 
+   * @param cStart
+   * @param cEnd
+   * @return int[] { start, end (inclusive) for each contiguous segment}
+   */
+  default int[] getMappedPositionsFor(int cStart, int cEnd)
+  {
+    return new int[] { cStart, cEnd };
+  }
+
+  default Color getColourForGroup()
+  {
+    return null;
+  }
+
 }