Merge branch 'features/JAL-2360colourSchemeApplicability' into features/JAL-2371colle...

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

diff --git a/src/jalview/schemes/ColourSchemeI.java b/src/jalview/schemes/ColourSchemeI.java
index be8793b..f16ca21 100755 (executable)
--- a/src/jalview/schemes/ColourSchemeI.java
+++ b/src/jalview/schemes/ColourSchemeI.java
@@ -20,9 +20,7 @@
  */
 package jalview.schemes;
 
-import jalview.analysis.Conservation;
 import jalview.datamodel.AnnotatedCollectionI;
-import jalview.datamodel.ProfilesI;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
 
@@ -32,23 +30,6 @@ import java.util.Map;
 public interface ColourSchemeI
 {
   /**
-   * Returns the fixed colour for the colour scheme. For use when the colour
-   * does not vary.
-   * 
-   * @return
-   */
-  Color findColour();
-
-  /**
-   * Returns the colour for the given character. For use when the colour depends
-   * only on the symbol.
-   * 
-   * @param c
-   * @return
-   */
-  Color findColour(char c);
-
-  /**
    * Returns the possibly context dependent colour for the given symbol at the
    * aligned position in the given sequence. For example, the colour may depend
    * on the symbol's relationship to the consensus residue for the column.
@@ -56,67 +37,14 @@ public interface ColourSchemeI
    * @param symbol
    * @param position
    * @param seq
+   * @param consensusResidue
+   *          the modal symbol (e.g. K) or symbols (e.g. KF) for the column
+   * @param pid
+   *          the percentage identity of the column's consensus (if known)
    * @return
    */
-  Color findColour(char symbol, int position, SequenceI seq);
-
-  /**
-   * Assigns the given consensus profile for the colourscheme
-   */
-  void setConsensus(ProfilesI hconsensus);
-
-  /**
-   * Assigns the given conservation to the colourscheme
-   * 
-   * @param c
-   */
-  void setConservation(Conservation c);
-
-  /**
-   * Enable or disable conservation shading for this colourscheme
-   * 
-   * @param conservationApplied
-   */
-  void setConservationApplied(boolean conservationApplied);
-
-  /**
-   * Answers true if conservation shading is enabled for this colourscheme
-   * 
-   * @return
-   */
-  boolean conservationApplied();
-
-  /**
-   * Sets the scale factor for bleaching of colour in unconserved regions
-   * 
-   * @param i
-   */
-  void setConservationInc(int i);
-
-  /**
-   * Returns the scale factor for bleaching colour in unconserved regions
-   * 
-   * @return
-   */
-  int getConservationInc();
-
-  /**
-   * Returns the percentage identity threshold for applying colourscheme
-   * 
-   * @return
-   */
-  int getThreshold();
-
-  /**
-   * Sets the percentage identity threshold and type of %age identity
-   * calculation for shading
-   * 
-   * @param pct
-   *          0..100 percentage identity for applying this colourscheme
-   * @param ignoreGaps
-   *          when true, calculate PID without including gapped positions
-   */
-  void setThreshold(int pct, boolean ignoreGaps);
+  Color findColour(char symbol, int position, SequenceI seq,
+          String consensusResidue, float pid);
 
   /**
    * Recalculate dependent data using the given sequence collection, taking
@@ -159,4 +87,15 @@ public interface ColourSchemeI
    * @return
    */
   String getSchemeName();
+
+  /**
+   * Answers true if the colour scheme depends only on the sequence symbol, and
+   * not on other information such as alignment consensus or annotation. (Note
+   * that simple colour schemes may have a fading by percentage identity or
+   * conservation overlaid.) Simple colour schemes can be propagated to
+   * structure viewers.
+   * 
+   * @return
+   */
+  boolean isSimple();
 }