X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FColourSchemeI.java;h=dd1c5be08b9832bfc2dd11c458ec19b4936b89bd;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=65c24c1ef6a8907624dea93705f3d89595bb8052;hpb=9492f5b351797792472226ca975bb593653e8d94;p=jalview.git

diff --git a/src/jalview/schemes/ColourSchemeI.java b/src/jalview/schemes/ColourSchemeI.java
index 65c24c1..dd1c5be 100755
--- a/src/jalview/schemes/ColourSchemeI.java
+++ b/src/jalview/schemes/ColourSchemeI.java
@@ -1,19 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
  * Copyright (C) 2014 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.
+ * 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/>.
+ * 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.schemes;
@@ -38,10 +40,14 @@ public interface ColourSchemeI
 
   /**
    * 
-   * @param c - sequence symbol or gap
-   * @param j - position in seq
-   * @param seq - sequence being coloured
-   * @return context dependent colour for the given symbol at the position in the given sequence
+   * @param c
+   *          - sequence symbol or gap
+   * @param j
+   *          - position in seq
+   * @param seq
+   *          - sequence being coloured
+   * @return context dependent colour for the given symbol at the position in
+   *         the given sequence
    */
   public Color findColour(char c, int j, SequenceI seq);
 
@@ -52,11 +58,19 @@ public interface ColourSchemeI
 
   /**
    * assign the given conservation to the colourscheme
+   * 
    * @param c
    */
   public void setConservation(jalview.analysis.Conservation c);
 
   /**
+   * enable or disable conservation shading for this colourscheme
+   * 
+   * @param conservationApplied
+   */
+  public void setConservationApplied(boolean conservationApplied);
+
+  /**
    * 
    * @return true if conservation shading is enabled for this colourscheme
    */
@@ -64,13 +78,14 @@ public interface ColourSchemeI
 
   /**
    * set scale factor for bleaching of colour in unconserved regions
+   * 
    * @param i
    */
   public void setConservationInc(int i);
 
   /**
    * 
-   * @return scale factor for bleaching colour in unconserved regions 
+   * @return scale factor for bleaching colour in unconserved regions
    */
   public int getConservationInc();
 
@@ -81,18 +96,35 @@ public interface ColourSchemeI
   public int getThreshold();
 
   /**
-   * set percentage identity threshold and type of %age identity calculation for shading
-   * @param ct 0..100 percentage identity for applying this colourscheme
-   * @param ignoreGaps when true, calculate PID without including gapped positions
+   * set percentage identity threshold and type of %age identity calculation for
+   * shading
+   * 
+   * @param ct
+   *          0..100 percentage identity for applying this colourscheme
+   * @param ignoreGaps
+   *          when true, calculate PID without including gapped positions
    */
   public void setThreshold(int ct, boolean ignoreGaps);
 
   /**
-   * recalculate dependent data using the given sequence collection, taking account of hidden rows
+   * recalculate dependent data using the given sequence collection, taking
+   * account of hidden rows
+   * 
    * @param alignment
    * @param hiddenReps
    */
   public void alignmentChanged(AnnotatedCollectionI alignment,
           Map<SequenceI, SequenceCollectionI> hiddenReps);
 
+  /**
+   * create a new instance of the colourscheme configured to colour the given
+   * connection
+   * 
+   * @param sg
+   * @param hiddenRepSequences
+   * @return copy of current scheme with any inherited settings transfered
+   */
+  public ColourSchemeI applyTo(AnnotatedCollectionI sg,
+          Map<SequenceI, SequenceCollectionI> hiddenRepSequences);
+
 }