X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fschemes%2FColourSchemeI.java;h=be8793bae816bdec82ce8ba61ff0895f58f4065f;hb=94751f42fae76e075240eeac0c708abbc8cf9253;hp=d82e5f516dd1996054479a100bdee08e2a15a7da;hpb=8a1f881bef0980cbd70d5d280b97feb50bd39536;p=jalview.git

diff --git a/src/jalview/schemes/ColourSchemeI.java b/src/jalview/schemes/ColourSchemeI.java
index d82e5f5..be8793b 100755
--- a/src/jalview/schemes/ColourSchemeI.java
+++ b/src/jalview/schemes/ColourSchemeI.java
@@ -1,13 +1,162 @@
-package jalview.schemes;
-
-import jalview.datamodel.*;
-import java.awt.*;
-import java.util.*;
-
-public interface ColourSchemeI
-{
-  public Color   findColour(String aa);
-  public Color   findColour(String s,int j, Vector aa);
-  public boolean canThreshold();
-  public boolean isUserDefinable();
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.schemes;
+
+import jalview.analysis.Conservation;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.ProfilesI;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceI;
+
+import java.awt.Color;
+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.
+   * 
+   * @param symbol
+   * @param position
+   * @param seq
+   * @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);
+
+  /**
+   * Recalculate dependent data using the given sequence collection, taking
+   * account of hidden rows
+   * 
+   * @param alignment
+   * @param hiddenReps
+   */
+  void alignmentChanged(AnnotatedCollectionI alignment,
+          Map<SequenceI, SequenceCollectionI> hiddenReps);
+
+  /**
+   * 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 transferred
+   */
+  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();
+}