JAL-2089 patch broken merge to master for Release 2.10.0b1

[jalview.git] / src / jalview / schemes / ColourSchemeI.java

diff --git a/src/jalview/schemes/ColourSchemeI.java b/src/jalview/schemes/ColourSchemeI.java
index 65c24c1..effdf59 100755 (executable)
--- a/src/jalview/schemes/ColourSchemeI.java
+++ b/src/jalview/schemes/ColourSchemeI.java
@@ -1,32 +1,32 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
+ * 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.
+ * 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;
 
-import java.awt.Color;
-import java.util.Map;
-
-import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.SequenceCollectionI;
-import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 
+import java.awt.Color;
+import java.util.Map;
+
 public interface ColourSchemeI
 {
   /**
@@ -38,10 +38,14 @@ 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 +56,19 @@ 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 +76,14 @@ 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 +94,35 @@ 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);
+
 }