X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FColourSchemeI.java;h=64248c54aa07c66148028d3334811e66a85479fc;hb=7d6bf4ac01167499c0f4e07de63edcdd72a6d595;hp=dd1c5be08b9832bfc2dd11c458ec19b4936b89bd;hpb=ab43013b7e357b84b4abade0dba949668dfb2a0e;p=jalview.git

diff --git a/src/jalview/schemes/ColourSchemeI.java b/src/jalview/schemes/ColourSchemeI.java
index dd1c5be..64248c5 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 2.8.2b1)
- * 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.
  * 
@@ -20,111 +20,146 @@
  */
 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.ProfilesI;
 import jalview.datamodel.SequenceCollectionI;
-import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 
+import java.awt.Color;
+import java.util.Map;
+
 public interface ColourSchemeI
 {
   /**
+   * Returns the colour for the given character. For use when the colour depends
+   * only on the symbol.
    * 
    * @param c
-   * @return the colour for the given character
+   * @return
    */
-  public Color findColour(char c);
+  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 c
-   *          - sequence symbol or gap
-   * @param j
-   *          - position in seq
+   * @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 collection. Note that even simple colour schemes should return a
+   * new instance for each call to this method, as different instances may have
+   * differing shading by consensus or percentage identity applied.
    * 
    * @param sg
    * @param hiddenRepSequences
-   * @return copy of current scheme with any inherited settings transfered
+   * @return copy of current scheme with any inherited settings transferred
    */
-  public ColourSchemeI applyTo(AnnotatedCollectionI sg,
+  ColourSchemeI getInstance(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();
+
+  /**
+   * 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();
 }