Merge branch 'feature/JAL-3127_seqidChainshading' into merge/JAL-3127

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

diff --git a/src/jalview/schemes/ColourSchemeI.java b/src/jalview/schemes/ColourSchemeI.java
index 372b569..7b79d88 100755 (executable)
--- a/src/jalview/schemes/ColourSchemeI.java
+++ b/src/jalview/schemes/ColourSchemeI.java
@@ -20,9 +20,8 @@
  */
 package jalview.schemes;
 
-import jalview.analysis.Conservation;
+import jalview.api.AlignViewportI;
 import jalview.datamodel.AnnotatedCollectionI;
-import jalview.datamodel.ProfilesI;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
 
@@ -32,23 +31,6 @@ 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 +38,14 @@ 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
@@ -134,12 +63,14 @@ public interface ColourSchemeI
    * new instance for each call to this method, as different instances may have
    * differing shading by consensus or percentage identity applied.
    * 
+   * @param viewport
+   *          - the parent viewport
    * @param sg
-   * @param hiddenRepSequences
+   *          - the collection of sequences to be coloured
    * @return copy of current scheme with any inherited settings transferred
    */
-  ColourSchemeI getInstance(AnnotatedCollectionI sg,
-          Map<SequenceI, SequenceCollectionI> hiddenRepSequences);
+  ColourSchemeI getInstance(AlignViewportI viewport,
+          AnnotatedCollectionI sg);
 
   /**
    * Answers true if the colour scheme is suitable for the given data, else
@@ -170,4 +101,11 @@ public interface ColourSchemeI
    * @return
    */
   boolean isSimple();
+
+  /**
+   * Answers true if the colour scheme has a colour specified for gaps.
+   * 
+   * @return
+   */
+  boolean hasGapColour();
 }