X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FColourSchemeI.java;h=1589356aecbe8c101dd6a3e977f1e426c82af9c9;hb=bdbd32582db88724697211a25b08f9cb8958bcb1;hp=c1550ccdf1650b45efce2fe2981335033579dace;hpb=47168f025aefdaa044802bd5f8f510ffe43a4808;p=jalview.git

diff --git a/src/jalview/schemes/ColourSchemeI.java b/src/jalview/schemes/ColourSchemeI.java
index c1550cc..1589356 100755
--- a/src/jalview/schemes/ColourSchemeI.java
+++ b/src/jalview/schemes/ColourSchemeI.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * 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.
  * 
@@ -20,15 +20,14 @@
  */
 package jalview.schemes;
 
-import java.awt.Color;
-import java.util.Map;
-
-import jalview.datamodel.AlignmentI;
+import jalview.analysis.Conservation;
 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
 {
   /**
@@ -40,10 +39,14 @@ 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);
 
@@ -54,15 +57,18 @@ public interface ColourSchemeI
 
   /**
    * assign the given conservation to the colourscheme
+   * 
    * @param c
    */
-  public void setConservation(jalview.analysis.Conservation c);
+  public void setConservation(Conservation c);
 
   /**
    * enable or disable conservation shading for this colourscheme
-   * @param conservationApplied 
+   * 
+   * @param conservationApplied
    */
   public void setConservationApplied(boolean conservationApplied);
+
   /**
    * 
    * @return true if conservation shading is enabled for this colourscheme
@@ -71,13 +77,14 @@ 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();
 
@@ -88,14 +95,20 @@ 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
    */
@@ -103,7 +116,9 @@ public interface ColourSchemeI
           Map<SequenceI, SequenceCollectionI> hiddenReps);
 
   /**
-   * create a new instance of the colourscheme configured to colour the given connection
+   * 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