X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FColourSchemeI.java;h=f2e888efd06023b99620e9c80d145f56c5008c12;hb=b0cee3aaf7d8873910939f97b6acb217d518968d;hp=effdf595f4cdbd91884e6f77fb25e8704192ca74;hpb=4d7f98a6dd54d9863ba449ec79dcd95d25ed863d;p=jalview.git

diff --git a/src/jalview/schemes/ColourSchemeI.java b/src/jalview/schemes/ColourSchemeI.java
index effdf59..f2e888e 100755
--- a/src/jalview/schemes/ColourSchemeI.java
+++ b/src/jalview/schemes/ColourSchemeI.java
@@ -20,7 +20,9 @@
  */
 package jalview.schemes;
 
+import jalview.analysis.Conservation;
 import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.ProfilesI;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
 
@@ -30,99 +32,129 @@ import java.util.Map;
 public interface ColourSchemeI
 {
   /**
+   * Returns the fixed colour for the colour scheme. For use when the colour
+   * does not vary.
    * 
-   * @param c
-   * @return the colour for the given character
+   * @return
    */
-  public Color findColour(char c);
+  Color findColour();
 
   /**
+   * Returns the colour for the given character. For use when the colour depends
+   * only on the symbol.
    * 
    * @param c
-   *          - sequence symbol or gap
-   * @param j
-   *          - position in seq
+   * @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.
+   * 
+   * @param symbol
+   * @param position
    * @param seq
-   *          - sequence being coloured
-   * @return context dependent colour for the given symbol at the position in
-   *         the given sequence
+   * @return
    */
-  public Color findColour(char c, int j, SequenceI seq);
+  Color findColour(char symbol, int position, SequenceI seq);
 
   /**
-   * assign the given consensus profile for the colourscheme
+   * Assigns the given consensus profile for the colourscheme
    */
-  public void setConsensus(java.util.Hashtable[] h);
+  void setConsensus(ProfilesI hconsensus);
 
   /**
-   * assign the given conservation to the colourscheme
+   * Assigns the given conservation to the colourscheme
    * 
    * @param c
    */
-  public void setConservation(jalview.analysis.Conservation c);
+  void setConservation(Conservation c);
 
   /**
-   * enable or disable conservation shading for this colourscheme
+   * Enable or disable conservation shading for this colourscheme
    * 
    * @param conservationApplied
    */
-  public void setConservationApplied(boolean conservationApplied);
+  void setConservationApplied(boolean conservationApplied);
 
   /**
+   * Answers true if conservation shading is enabled for this colourscheme
    * 
-   * @return true if conservation shading is enabled for this colourscheme
+   * @return
    */
-  public boolean conservationApplied();
+  boolean conservationApplied();
 
   /**
-   * set scale factor for bleaching of colour in unconserved regions
+   * Sets the scale factor for bleaching of colour in unconserved regions
    * 
    * @param i
    */
-  public void setConservationInc(int i);
+  void setConservationInc(int i);
 
   /**
+   * Returns the scale factor for bleaching colour in unconserved regions
    * 
-   * @return scale factor for bleaching colour in unconserved regions
+   * @return
    */
-  public int getConservationInc();
+  int getConservationInc();
 
   /**
+   * Returns the percentage identity threshold for applying colourscheme
    * 
-   * @return percentage identity threshold for applying colourscheme
+   * @return
    */
-  public int getThreshold();
+  int getThreshold();
 
   /**
-   * set percentage identity threshold and type of %age identity calculation for
-   * shading
+   * Sets the percentage identity threshold and type of %age identity
+   * calculation for shading
    * 
-   * @param ct
+   * @param pct
    *          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);
+  void setThreshold(int pct, boolean ignoreGaps);
 
   /**
-   * recalculate dependent data using the given sequence collection, taking
+   * Recalculate dependent data using the given sequence collection, taking
    * account of hidden rows
    * 
    * @param alignment
    * @param hiddenReps
    */
-  public void alignmentChanged(AnnotatedCollectionI alignment,
+  void alignmentChanged(AnnotatedCollectionI alignment,
           Map<SequenceI, SequenceCollectionI> hiddenReps);
 
   /**
-   * create a new instance of the colourscheme configured to colour the given
-   * connection
+   * Creates and returns 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,
+  ColourSchemeI applyTo(AnnotatedCollectionI sg,
           Map<SequenceI, SequenceCollectionI> hiddenRepSequences);
 
+  /**
+   * Answers true if the colour scheme is suitable for the given data, else
+   * false. For example, some colour schemes are specific to either peptide or
+   * nucleotide, or only apply if certain kinds of annotation are present.
+   * 
+   * @param ac
+   * @return
+   */
+  // TODO can make this method static in Java 8
+  boolean isApplicableTo(AnnotatedCollectionI ac);
+
+  /**
+   * Answers the 'official' name of the colour scheme (as used, for example, as
+   * a Jalview startup parameter)
+   * 
+   * @return
+   */
+  String getSchemeName();
 }