X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FColourSchemeI.java;h=64248c54aa07c66148028d3334811e66a85479fc;hb=7d6bf4ac01167499c0f4e07de63edcdd72a6d595;hp=7fc6981a3c5f716895087b46ad9c767fc21c5cb5;hpb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;p=jalview.git

diff --git a/src/jalview/schemes/ColourSchemeI.java b/src/jalview/schemes/ColourSchemeI.java
index 7fc6981..64248c5 100755
--- a/src/jalview/schemes/ColourSchemeI.java
+++ b/src/jalview/schemes/ColourSchemeI.java
@@ -1,53 +1,165 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * 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.
  * 
  * 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.
+ * 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/>.
+ * 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 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
 {
-  public Color findColour(char c);
+  /**
+   * 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);
 
-  public Color findColour(char c, int j, SequenceI seq);
+  /**
+   * Assigns the given consensus profile for the colourscheme
+   */
+  void setConsensus(ProfilesI hconsensus);
 
-  public void setConsensus(java.util.Hashtable[] h);
+  /**
+   * Assigns the given conservation to the colourscheme
+   * 
+   * @param c
+   */
+  void setConservation(Conservation c);
 
-  public void setConservation(jalview.analysis.Conservation c);
+  /**
+   * Enable or disable conservation shading for this colourscheme
+   * 
+   * @param conservationApplied
+   */
+  void setConservationApplied(boolean conservationApplied);
 
-  public boolean conservationApplied();
+  /**
+   * Answers true if conservation shading is enabled for this colourscheme
+   * 
+   * @return
+   */
+  boolean conservationApplied();
 
-  public void setConservationInc(int i);
+  /**
+   * Sets the scale factor for bleaching of colour in unconserved regions
+   * 
+   * @param i
+   */
+  void setConservationInc(int i);
 
-  public int getConservationInc();
+  /**
+   * Returns the scale factor for bleaching colour in unconserved regions
+   * 
+   * @return
+   */
+  int getConservationInc();
 
-  public int getThreshold();
+  /**
+   * Returns the percentage identity threshold for applying colourscheme
+   * 
+   * @return
+   */
+  int getThreshold();
 
-  public void setThreshold(int ct, boolean ignoreGaps);
+  /**
+   * 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);
 
-  public void alignmentChanged(AnnotatedCollectionI alignment,
+  /**
+   * 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();
+
+  /**
+   * 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();
 }